4R3D | pdb_00004r3d

Crystal structure of MERS Coronavirus papain like protease

PDB DOI: https://doi.org/10.2210/pdb4R3D/pdb

Classification: HYDROLASE
Organism(s): Betacoronavirus England 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-15 Released: 2015-08-19
Deposition Author(s): Kong, L.Y., Wang, Q., Ming, Z.H., Shaw, N., Sun, Y.N., Yan, L.M., Lou, Z.Y., Rao, Z.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.224 (Depositor), 0.233 (DCC)
R-Value Work:
0.185 (Depositor), 0.192 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Crystal Structures of Middle East Respiratory Syndrome Coronavirus Papain-like Protease and Its Complex with an Inhibitor

Kong, L.Y., Wang, Q., Ming, Z.H., Sun, Y.N., Shaw, N., Yan, L.M., Lou, Z.Y., Rao, Z.H.

To be published.

Macromolecule Content

Total Structure Weight: 74.77 kDa
Atom Count: 5,103
Modeled Residue Count: 639
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A [auth B], B [auth A]	336	Betacoronavirus England 1	Mutation(s): 0 Gene Names: 1a EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for K9N638 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N638 Go to UniProtKB: K9N638
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K9N638
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth B]	C [auth B], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.224 (Depositor), 0.233 (DCC)
R-Value Work: 0.185 (Depositor), 0.192 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.624	α = 90
b = 136.624	β = 90
c = 239.518	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-08-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-08-19
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.