MolNFT v1 · #14994 · protein
Swine vesicular disease virus coat protein
1MQT · Polyprotein: “Swine vesicular disease virus coat protein”. X-ray diffraction, 1 ligand (SPL), 11 pockets (best druggability 0.79). MolNFT v1 #14994 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1MQT
- Type
- protein
- Length
- 818 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein; Polyprotein capsid protein
- UniProt
- Q8B8X4
- Ligands
- SPL
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprotein | protein | 271 | 9% helix, 31% strand | Q8B8X4 |
| B | Polyprotein capsid protein | protein | 254 | 10% helix, 36% strand | Q8B8X4 |
| C | Polyprotein capsid protein | protein | 238 | 10% helix, 32% strand | Q8B8X4 |
| D | Polyprotein capsid protein | protein | 55 | 5% helix, 16% strand | Q8B8X4 |
Ligands and binding sites
- SPL · Octanoic acid (2-hydroxy-1-hydroxymethyl-heptadec-3-enyl)-amide · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.79 | 0.85 | 64 | SPL |
| 2 | 161 | 0.49 | 0.78 | 28 | empty |
| 3 | 87 | 0.49 | 0.82 | 30 | empty |
| 4 | 84 | 0.45 | 0.81 | 23 | empty |
| 5 | 81 | 0.41 | 0.79 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4245 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 2223 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1540 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1084 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 902 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1MQT · Swine Vesicular Disease Virus coat protein · 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 Q8B8X4
- Elsewhere: RCSB PDB 1MQT · PDBe 1MQT · UniProt Q8B8X4
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