7HID | pdb_00007hid

Group deposition for combi-soaks of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z1041785508 and Z50145861 (CHIKV_MacB-x1487)

PDB DOI: https://doi.org/10.2210/pdb7HID/pdb
Deposition Group: G_1002309 (changed state) ExploreG_1002309

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

Deposited: 2024-10-02 Released: 2024-10-16
Deposition Author(s): Aschenbrenner, J.C., Fairhead, M., Godoy, A.S., Balcomb, B.H., Capkin, E., Chandran, A.V., Golding, M., Koekemoer, L., Lithgo, R.M., Marples, P.G., Ni, X., 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: 1.50 Å
R-Value Free:
0.222 (Depositor), 0.254 (DCC)
R-Value Work:
0.190 (Depositor), 0.233 (DCC)
R-Value Observed:
0.191 (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 combi-soaks of Chikungunya virus nsP3 macrodomain

Aschenbrenner, J.C., Fairhead, M., Godoy, A.S., Balcomb, B.H., Capkin, E., Chandran, A.V., Golding, M., Koekemoer, L., Lithgo, R.M., Marples, P.G., Ni, X., 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: 73.67 kDa
Atom Count: 5,881
Modeled Residue Count: 648
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W1P (Subject of Investigation/LOI) Query on W1P Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C]	BA [auth D], K [auth A], Q [auth B], V [auth C]	5-methyl-2-phenyl-2,4-dihydro-3H-pyrazol-3-one C₁₀ H₁₀ N₂ O QELUYTUMUWHWMC-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain V [auth C]
K34 (Subject of Investigation/LOI) Query on K34 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain R [auth B] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C]	CA [auth D], R [auth B], W [auth C]	5-(1,3-thiazol-2-yl)-1H-1,2,4-triazole C₅ H₄ N₄ S WFEGFRJBAYCOHP-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain R [auth B] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain R [auth B] Focus chain W [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain X [auth D]	F [auth A], X [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain X [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain U [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	E [auth A] G [auth A] H [auth A] L [auth A] M [auth A] E [auth A], G [auth A], H [auth A], L [auth A], M [auth A], N [auth A], O [auth A], U [auth C], Y [auth D], Z [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C]	AA [auth D] I [auth A] J [auth A] P [auth B] S [auth C] AA [auth D], I [auth A], J [auth A], P [auth B], S [auth C], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C]