8X3V | pdb_00008x3v

Crystal structure of 2C from encephalomyocarditis virus bound with ATP

PDB DOI: https://doi.org/10.2210/pdb8X3V/pdb

Classification: HYDROLASE
Organism(s): Encephalomyocarditis virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-14 Released: 2024-09-04
Deposition Author(s): Zhang, H., Zhao, H., Dong, Y.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.273 (Depositor), 0.272 (DCC)
R-Value Work:
0.224 (Depositor), 0.226 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of 2C from encephalomyocarditis virus bound with ATP

Zhang, H., Zhao, H., Dong, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 48.69 kDa
Atom Count: 3,266
Modeled Residue Count: 417
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein 2C	A, B	218	Encephalomyocarditis virus	Mutation(s): 0 EC: 3.6.4.13
UniProt
Find proteins for P03304 (Encephalomyocarditis virus) Explore P03304 Go to UniProtKB: P03304
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03304
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.273 (Depositor), 0.272 (DCC)
R-Value Work: 0.224 (Depositor), 0.226 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171	α = 90
b = 171	β = 90
c = 77.01	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31970152

Revision History (Full details and data files)

Version 1.0: 2024-09-04
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.