5ZU9

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

PDB DOI: https://doi.org/10.2210/pdb5ZU9/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: 1.50 Å
R-Value Free: 0.177
R-Value Work: 0.150
R-Value Observed: 0.153

Starting Model: experimental
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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 ADP

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

To be published.

Macromolecule Content

Total Structure Weight: 18.2 kDa
Atom Count: 1,446
Modelled Residue Count: 165
Deposited Residue Count: 168
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	T2B9G2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-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: 1.50 Å
R-Value Free: 0.177
R-Value Work: 0.150
R-Value Observed: 0.153
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.421	α = 90
b = 39.423	β = 102.3
c = 45.514	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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 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 R01GM133198.