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), 0.275 (DCC)
R-Value Work:
0.224 (Depositor), 0.231 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.275 (DCC)
R-Value Work: 0.224 (Depositor), 0.231 (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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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

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