7H7O | pdb_00007h7o

Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z952016136 (CHIKV_MacB-x0894)

PDB DOI: https://doi.org/10.2210/pdb7H7O/pdb
Deposition Group: G_1002294 (changed state) ExploreG_1002294

Classification: VIRAL PROTEIN
Organism(s): Chikungunya virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-26 Released: 2024-05-29
Deposition Author(s): Aschenbrenner, J.C., Fairhead, M., Godoy, A.S., Balcomb, B.H., Capkin, E., Chandran, A.V., Dolci, I., Golding, M., Koekemoer, L., Lithgo, R.M., Marples, P.G., Ni, X., Oliva, G., Thompson, W., Tomlinson, C.W.E., Wild, C., Winokan, M., Xavier, M.-A.E., Fearon, D., von Delft, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 ?
R-Value Free:
0.219 (Depositor), 0.240 (DCC)
R-Value Work:
0.184 (Depositor), 0.220 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain

Aschenbrenner, J.C., Fairhead, M., Godoy, A.S., Balcomb, B.H., Capkin, E., Chandran, A.V., Dolci, I., Golding, M., Koekemoer, L., Lithgo, R.M., Marples, P.G., Ni, X., Oliva, G., Thompson, W., Tomlinson, C.W.E., Wild, C., Winokan, M., Xavier, M.-A.E., Fearon, D., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 73.69 kDa
Atom Count: 5,865
Modeled Residue Count: 648
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B, C, D	163	Chikungunya virus	Mutation(s): 0 EC: 3.1.3.84
UniProt
Find proteins for Q8JUX6 (Chikungunya virus (strain S27-African prototype)) Explore Q8JUX6 Go to UniProtKB: Q8JUX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8JUX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KBU (Subject of Investigation/LOI) Query on KBU Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C]	AA [auth C] L [auth A] M [auth A] S [auth B] T [auth B] AA [auth C], L [auth A], M [auth A], S [auth B], T [auth B], Z [auth C]	4-chloro-1H-benzimidazole C₇ H₅ Cl N₂ RPYPMOKNVPZWKZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Y [auth C] SDF format, chain CA [auth D] SDF format, chain X [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain X [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain X [auth C]	BA [auth C] CA [auth D] DA [auth D] E [auth A] EA [auth D] BA [auth C], CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], G [auth A], I [auth A], J [auth A], N [auth A], O [auth B], P [auth B], X [auth C], Y [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C] Focus chain Y [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	FA [auth D] GA [auth D] K [auth A] Q [auth B] R [auth B] FA [auth D], GA [auth D], K [auth A], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]