3TLO | pdb_00003tlo

Crystal structure of HCoV-NL63 3C-like protease

PDB DOI: https://doi.org/10.2210/pdb3TLO/pdb

Classification: HYDROLASE
Organism(s): Human coronavirus NL63
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-08-30 Released: 2012-09-05
Deposition Author(s): Chuck, C.P., Wong, K.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.202 (Depositor), 0.190 (DCC)
R-Value Work:
0.175 (Depositor), 0.164 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3TLO

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

Literature

Crystal structure of human coronavirus NL63 3C-like protease

Chuck, C.P., Wong, K.B.

To be published.

Macromolecule Content

Total Structure Weight: 66.09 kDa
Atom Count: 5,308
Modeled Residue Count: 604
Deposited Residue Count: 606
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	303	Human coronavirus NL63	Mutation(s): 0 Gene Names: 1a EC: 3.4.22
UniProt
Find proteins for P0C6U6 (Human coronavirus NL63) Explore P0C6U6 Go to UniProtKB: P0C6U6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6U6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.202 (Depositor), 0.190 (DCC)
R-Value Work: 0.175 (Depositor), 0.164 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.144	α = 90
b = 83.497	β = 109.2
c = 64.852	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-05
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.