5ZUA | pdb_00005zua

Crystal structure of MERS-CoV macro domain in complex with ATP

PDB DOI: https://doi.org/10.2210/pdb5ZUA/pdb

Classification: VIRAL PROTEIN
Organism(s): Middle East respiratory syndrome-related coronavirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-05-07 Released: 2019-06-05
Deposition Author(s): Lin, M.-H., Cho, C.-C., Chien, C.-Y., Hsu, C.-H.
Funding Organization(s): National Science Council (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free:
0.235 (Depositor), 0.215 (DCC)
R-Value Work:
0.170 (Depositor)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5ZUA

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of MERS-CoV macro domain in complex with ATP

Lin, M.-H., Cho, C.-C., Chien, C.-Y., Hsu, C.-H.

To be published.

Macromolecule Content

Total Structure Weight: 18.28 kDa
Atom Count: 1,292
Modeled Residue Count: 166
Deposited Residue Count: 168
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1a	A	168	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0
UniProt
Find proteins for T2B9G2 (Middle East respiratory syndrome-related coronavirus) Explore T2B9G2 Go to UniProtKB: T2B9G2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T2B9G2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.235 (Depositor), 0.215 (DCC)
R-Value Work: 0.170 (Depositor)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.036	α = 90
b = 39.113	β = 101.61
c = 45.065	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Council (Taiwan)	Taiwan	103-2113-M-002-009-MY2

Revision History (Full details and data files)

Version 1.0: 2019-06-05
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.