9GD9 | pdb_00009gd9

NME1 94-Oligophosphoserine

PDB DOI: https://doi.org/10.2210/pdb9GD9/pdb
EM Map EMD-51251: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-08-05 Released: 2025-06-11
Deposition Author(s): Roderer, D., Schoepf, F., Fiedler, D., Celik, A.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Nucleoside diphosphate kinase A (NME1) catalyzes its own oligophosphorylation

Celif, A., Schoepf, F., Stieger, C.E., Morgan, J.A.M., Lampe, S., Ruwolt, M., Liu, F., Hackenberger, C.P.R., Roderer, D., Fiedler, D.

To be published.

Macromolecule Content

Total Structure Weight: 103.57 kDa
Atom Count: 6,744
Modeled Residue Count: 846
Deposited Residue Count: 900
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase A	A [auth B] B [auth C] C [auth D] D [auth E] E [auth F] A [auth B], B [auth C], C [auth D], D [auth E], E [auth F], F [auth A]	150	Homo sapiens	Mutation(s): 1 Gene Names: NME1, NDPKA, NM23 EC: 2.7.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P15531 (Homo sapiens) Explore P15531 Go to UniProtKB: P15531
PHAROS: P15531 GTEx: ENSG00000239672
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15531
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1IKP Query on A1IKP	A [auth B] B [auth C] C [auth D] D [auth E] E [auth F] A [auth B], B [auth C], C [auth D], D [auth E], E [auth F], F [auth A]	L-PEPTIDE LINKING	C₃ H₁₀ N O₁₂ P₃		SER

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4.0
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	469186007

Revision History (Full details and data files)

Version 1.0: 2025-06-11
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.