9QT5 | pdb_00009qt5

Structure of the 50S ribosomal subunit from the antibiotic-producing bacterium Streptomyces fradiae

PDB DOI: https://doi.org/10.2210/pdb9QT5/pdb
EM Map EMD-53347: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Streptomyces fradiae ATCC 10745 = DSM 40063
Mutation(s): No

Deposited: 2025-04-07 Released: 2025-05-14
Deposition Author(s): Ekemezie, C.L., Melnikov, S.V.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Royal Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Evolution of drug-binding sites in bacterial ribosomes

Ekemezie, C.L., Chan, L.I., Brown, C.R., Helena-Bueno, K., Williams, T.A., Melnikov, S.V.

To be published.

Macromolecule Content

Total Structure Weight: 1,431.85 kDa
Atom Count: 81,897
Modelled Residue Count: 5,829
Deposited Residue Count: 6,716
Unique protein chains: 28
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL16	A [auth M]	139	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NNE1 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NNE1 Go to UniProtKB: A0A1Y2NNE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NNE1
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL2	C [auth B]	278	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NM84 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NM84 Go to UniProtKB: A0A1Y2NM84
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NM84
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL3	D [auth C]	214	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NM83 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NM83 Go to UniProtKB: A0A1Y2NM83
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NM83
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	E [auth D]	216	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NM93 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NM93 Go to UniProtKB: A0A1Y2NM93
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NM93
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL5	F [auth E]	185	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NM88 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NM88 Go to UniProtKB: A0A1Y2NM88
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NM88
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL6	G [auth F]	179	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NNJ7 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NNJ7 Go to UniProtKB: A0A1Y2NNJ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NNJ7
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL9	H [auth G]	148	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2P0X7 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2P0X7 Go to UniProtKB: A0A1Y2P0X7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2P0X7
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13	I [auth J]	147	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NMA9 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NMA9 Go to UniProtKB: A0A1Y2NMA9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NMA9
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL14	J [auth K]	122	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NM92 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NM92 Go to UniProtKB: A0A1Y2NM92
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NM92
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL18	K [auth O]	127	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NNX4 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NNX4 Go to UniProtKB: A0A1Y2NNX4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NNX4
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL15	L	151	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NN24 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NN24 Go to UniProtKB: A0A1Y2NN24
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NN24
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL19	M [auth P]	116	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NTT8 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NTT8 Go to UniProtKB: A0A1Y2NTT8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NTT8
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL20	N [auth Q]	128	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NZD1 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NZD1 Go to UniProtKB: A0A1Y2NZD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NZD1
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL21	O [auth R]	106	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NZA8 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NZA8 Go to UniProtKB: A0A1Y2NZA8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NZA8
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL22	P [auth S]	115	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NNI7 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NNI7 Go to UniProtKB: A0A1Y2NNI7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NNI7
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	Q [auth T]	107	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NM78 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NM78 Go to UniProtKB: A0A1Y2NM78
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NM78
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL24	R [auth U]	107	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NM97 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NM97 Go to UniProtKB: A0A1Y2NM97
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NM97
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL25	S [auth V]	195	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2P3K7 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2P3K7 Go to UniProtKB: A0A1Y2P3K7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2P3K7
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL27	T [auth W]	84	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NZJ9 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NZJ9 Go to UniProtKB: A0A1Y2NZJ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NZJ9
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL28	U [auth X]	61	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NV37 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NV37 Go to UniProtKB: A0A1Y2NV37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NV37
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL29	V [auth Y]	74	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NMI9 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NMI9 Go to UniProtKB: A0A1Y2NMI9
Entity Groups
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UniProt Group	A0A1Y2NMI9
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Reference Sequence

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL30	W [auth Z]	60	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NMJ7 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NMJ7 Go to UniProtKB: A0A1Y2NMJ7
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NMJ7
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Reference Sequence

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL32	X [auth 3]	57	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NTQ5 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NTQ5 Go to UniProtKB: A0A1Y2NTQ5
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UniProt Group	A0A1Y2NTQ5
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL33	Y [auth 4]	54	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2P044 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2P044 Go to UniProtKB: A0A1Y2P044
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2P044
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL34	Z [auth 5]	45	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2P0X6 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2P0X6 Go to UniProtKB: A0A1Y2P0X6
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2P0X6
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL35	AA [auth 6]	64	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NZ92 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NZ92 Go to UniProtKB: A0A1Y2NZ92
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y2NZ92
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL36	BA [auth 7]	37	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NMD2 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NMD2 Go to UniProtKB: A0A1Y2NMD2
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UniProt Group	A0A1Y2NMD2
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL17	CA [auth N]	164	Streptomyces fradiae ATCC 10745 = DSM 40063	Mutation(s): 0
UniProt
Find proteins for A0A1Y2NMK7 (Streptomyces fradiae ATCC 10745 = DSM 40063) Explore A0A1Y2NMK7 Go to UniProtKB: A0A1Y2NMK7
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UniProt Group	A0A1Y2NMK7
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
5S rRNA	B [auth 2]	117	Streptomyces fradiae ATCC 10745 = DSM 40063
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Reference Sequence

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Entity ID: 30
Molecule	Chains	Length	Organism	Image
23S rRNA	DA [auth 1]	3,119	Streptomyces fradiae ATCC 10745 = DSM 40063
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4.6

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Ekemezie, C.L.

Melnikov, S.V.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N013840/1
Royal Society	United Kingdom	RGS/R2/202003

Revision History (Full details and data files)

Version 1.0: 2025-05-14
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9QT5 | pdb_00009qt5

Structure of the 50S ribosomal subunit from the antibiotic-producing bacterium Streptomyces fradiae

Evolution of drug-binding sites in bacterial ribosomes

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

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Sequence Annotations

Entity ID: 4

UniProt

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Sequence Annotations

Entity ID: 5

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Entity ID: 6

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Entity ID: 7

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Entity ID: 8

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Entity ID: 9

UniProt

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Entity ID: 10

UniProt

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Entity ID: 11

UniProt

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Entity ID: 12

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Entity ID: 13

UniProt

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Entity ID: 14

UniProt

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Entity ID: 15

UniProt

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Entity ID: 16

UniProt

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Entity ID: 17

UniProt

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Entity ID: 18

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Entity ID: 19

UniProt

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Entity ID: 20

9QT5 | pdb_00009qt5