8ZCC | pdb_00008zcc

Crystal structure of HCoV-NL63 main protease with X77

PDB DOI: https://doi.org/10.2210/pdb8ZCC/pdb

Classification: VIRAL PROTEIN
Organism(s): Human coronavirus NL63
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-04-29 Released: 2025-05-07
Deposition Author(s): Xu, J., Li, W.W., Yin, X.S., Li, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.214 (Depositor), 0.215 (DCC)
R-Value Work:
0.193 (Depositor), 0.193 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of HCoV-NL63 main protease with X77

Xu, J., Li, W.W., Yin, X.S., Li, J.

To be published.

Macromolecule Content

Total Structure Weight: 65.56 kDa
Atom Count: 4,899
Modeled Residue Count: 597
Deposited Residue Count: 598
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCoV-NL63 main protease	A, B	299	Human coronavirus NL63	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22
UniProt
Find proteins for P0C6X5 (Human coronavirus NL63) Explore P0C6X5 Go to UniProtKB: P0C6X5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C6X5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X77 (Subject of Investigation/LOI) Query on X77 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide C₂₇ H₃₃ N₅ O₂ MUNFBYOTGGMQOS-XMMPIXPASA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.214 (Depositor), 0.215 (DCC)
R-Value Work: 0.193 (Depositor), 0.193 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.852	α = 90
b = 82.235	β = 108.416
c = 64.136	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-07
Type: Initial release

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.