7C8U | pdb_00007c8u

The crystal structure of COVID-19 main protease in complex with GC376

PDB DOI: https://doi.org/10.2210/pdb7C8U/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-03 Released: 2020-06-24
Deposition Author(s): Luan, X., Shang, W., Wang, Y., Yin, W., Jiang, Y., Feng, S., Wang, Y., Liu, M., Zhou, R., Zhang, Z., Wang, F., Cheng, W., Gao, M., Wang, H., Wu, W., Tian, R., Tian, Z., Jin, Y., Jiang, H.W., Zhang, L., Xu, H.E., Zhang, S.
Funding Organization(s): CAMS Innovation Fund for Medical Sciences (CIFMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.273 (Depositor), 0.280 (DCC)
R-Value Work:
0.211 (Depositor), 0.220 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of COVID-19 main protease in complex with GC376

Zhang, S.Y., Luan, X.D., Wang, F.

To be published.

Macromolecule Content

Total Structure Weight: 34.31 kDa
Atom Count: 2,417
Modeled Residue Count: 300
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K36 Query on K36 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]	(1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid C₂₁ H₃₁ N₃ O₈ S BSPZFJDYQHDZNR-HTCLRFROSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002495 (K36) Query on PRD_002495	B [auth A]	GC376	Peptide-like / Inhibitor		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.273 (Depositor), 0.280 (DCC)
R-Value Work: 0.211 (Depositor), 0.220 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.303	α = 90
b = 53.874	β = 101.576
c = 45.233	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-06-24

Deposition Author(s):

Funding Organization	Location	Grant Number
CAMS Innovation Fund for Medical Sciences (CIFMS)	China	2016-I2M-3-011
CAMS Innovation Fund for Medical Sciences (CIFMS)	China	2016-I2M-1-002

Revision History (Full details and data files)

Version 1.0: 2020-06-24
Type: Initial release
Version 1.1: 2021-03-10
Changes: Structure summary
Version 1.2: 2023-11-29
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary