Research workbench
Main protease of hcov-HKU1
Analyse Main protease of hcov-HKU1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D23
- Type
- protein
- Length
- 1,209 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
- Q5MQD2
- Ligands
- 02J, PJE, 010
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 3C-like proteinase (EC 3.4.22.-) | protein | 301 | 24% helix, 29% strand | Q5MQD2 |
| A | 3C-like proteinase (EC 3.4.22.-) | protein | 299 | 24% helix, 29% strand | Q5MQD2 |
| C | 3C-like proteinase (EC 3.4.22.-) | protein | 298 | 23% helix, 29% strand | Q5MQD2 |
| D | 3C-like proteinase (EC 3.4.22.-) | protein | 299 | 24% helix, 28% strand | Q5MQD2 |
| H, F, E, G | 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, 33% strand | — |
Ligands and binding sites
- 02J · 5-methyl-1,2-oxazole-3-carboxylic acid · ligand · 4 copies · chains B, H, A, F, C, E, D, G
- PJE · (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid · ligand · 4 copies · chains B, H, A, F, C, E, D, G
- 010 · phenylmethanol · ligand · 4 copies · chains B, H, A, F, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.77 | 0.80 | 82 | empty |
| 2 | 783 | 0.72 | 0.78 | 79 | PJE, 010 |
| 3 | 59 | 0.68 | 0.95 | 14 | empty |
| 4 | 412 | 0.61 | 0.76 | 62 | empty |
| 5 | 250 | 0.53 | 0.76 | 38 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1333 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 476 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 469 Ų buried · 5 hydrogen bonds · protein-protein
- D–G · 335 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 334 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 3D23 · Main protease of HCoV-HKU1 · the same entry in another collection · chain B against B, 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 Q5MQD2
- Elsewhere: RCSB PDB 3D23 · PDBe 3D23 · UniProt Q5MQD2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.