The crystal structure of COVID-19 main protease in complex with GC376
Zhang, S.Y., Luan, X.D., Wang, F.To be published.
7C8U
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
- 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
- R-Value Work: 0.211
Starting Model: experimental
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This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| 3C-like proteinase | 306 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69 | ||
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1 | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DTD1 | ||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| K36 Query on K36 | 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 | |||
Biologically Interesting Molecules (External Reference) 1 Unique
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
|---|---|---|---|---|---|
| PRD_002495 (K36) Query on PRD_002495 | B [auth A] | GC376 | Peptide-like / Inhibitor | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.273
- R-Value Work: 0.211
- 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 Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 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 | 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