Research workbench
Crystal structure of the SARS-cov-2 plpro with GRL0617
Analyse Crystal structure of the SARS-cov-2 plpro with GRL0617 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CMD
- Type
- protein
- Length
- 1,229 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- TTT, ZN
- Pockets
- 15 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 306 | 27% helix, 35% strand | P0DTD1 |
| B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 308 | 25% helix, 36% strand | P0DTD1 |
| C | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 308 | 25% helix, 34% strand | P0DTD1 |
| D | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 307 | 25% helix, 34% strand | P0DTD1 |
Ligands and binding sites
- TTT · 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 9 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.64 | 0.80 | 52 | empty |
| 2 | 407 | 0.63 | 0.78 | 45 | empty |
| 3 | 384 | 0.63 | 0.78 | 41 | empty |
| 4 | 324 | 0.59 | 0.77 | 38 | ZN |
| 5 | 149 | 0.48 | 0.77 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–C · 672 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 664 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 278 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 209 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 199 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7CMD · Crystal structure of the SARS-CoV-2 PLpro with GRL0617 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTD1
- Elsewhere: RCSB PDB 7CMD · PDBe 7CMD · UniProt P0DTD1
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