5GRB | pdb_00005grb

Crystal structure of 2C helicase from enterovirus 71 (EV71) bound with ATPgammaS

PDB DOI: https://doi.org/10.2210/pdb5GRB/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Enterovirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-09 Released: 2017-05-17
Deposition Author(s): Guan, H.X., Tian, J., Qin, B., Wojdyla, J., Wang, M.T., Cui, S.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.296 (Depositor), 0.297 (DCC)
R-Value Work:
0.245 (Depositor), 0.245 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of 2C helicase from enterovirus 71

Guan, H.X., Tian, J., Qin, B., Wojdyla, J., Wang, B., Zhao, Z.D., Wang, M.T., Cui, S.

(2017) Sci Adv 3: e1602573-e1602573

DOI: https://doi.org/10.1126/sciadv.1602573

Macromolecule Content

Total Structure Weight: 144.78 kDa
Atom Count: 9,755
Modeled Residue Count: 1,241
Deposited Residue Count: 1,284
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EV71 2C ATPase	A, B, C, D, E A, B, C, D, E, F	214	Enterovirus	Mutation(s): 0
UniProt
Find proteins for B9VUU3 (Human enterovirus 71) Explore B9VUU3 Go to UniProtKB: B9VUU3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9VUU3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain L [auth C] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain L [auth C]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.296 (Depositor), 0.297 (DCC)
R-Value Work: 0.245 (Depositor), 0.245 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.668	α = 90
b = 54.912	β = 89.98
c = 163.097	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-05-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81572005

Revision History (Full details and data files)

Version 1.0: 2017-05-17
Type: Initial release
Version 1.1: 2017-09-27
Changes: Data collection
Version 1.2: 2018-07-18
Changes: Data collection, Structure summary
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

5GRB | pdb_00005grb

Crystal structure of 2C helicase from enterovirus 71 (EV71) bound with ATPgammaS

Literature

Crystal structure of 2C helicase from enterovirus 71

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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