Research workbench
The octameric SARS-cov main protease
Analyse The octameric SARS-cov main protease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IWM
- Type
- protein
- Length
- 1,214 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; N-[(5-methylisoxazol-3-YL)CARBONYL]ALANYL-L-valyl-N~1~…
- EC
- 3.4.22.-
- UniProt
- P0C6U8
- Ligands
- 02J, PJE, 010
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.-) | protein | 301 | 22% helix, 23% strand | P0C6U8 |
| C, D | 3C-like proteinase (EC 3.4.22.-) | protein | 300 | 20% helix, 25% strand | P0C6U8 |
| H, F, G, E | N-[(5-methylisoxazol-3-YL)CARBONYL]ALANYL-L-valyl-N~1~- ((1R,2Z)-4-(benzyloxy)-4-oxo-1-{[(3R)-2-oxopyrrolidin-3- YL]METHYL}BUT-2-enyl)-L-leucinamide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 02J · 5-methyl-1,2-oxazole-3-carboxylic acid · ligand · 4 copies · chains A, H, B, F, C, G, D, E
- PJE · (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid · ligand · 4 copies · chains A, B, H, F, C, G, D, E
- 010 · phenylmethanol · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.76 | 0.79 | 74 | empty |
| 2 | 313 | 0.68 | 0.83 | 30 | empty |
| 3 | 163 | 0.50 | 0.78 | 27 | PJE, 010 |
| 4 | 171 | 0.50 | 0.77 | 27 | PJE, 010 |
| 5 | 212 | 0.49 | 0.75 | 42 | empty |
Interfaces
10 interfaces between chains.
- A–C · 4367 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 4318 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1047 Ų buried · 28 hydrogen bonds · protein-protein
- C–G · 327 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 323 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 3IWM · The octameric SARS-CoV main protease · the same entry in another collection · chain E against E, 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 P0C6U8
- Elsewhere: RCSB PDB 3IWM · PDBe 3IWM · UniProt P0C6U8
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