Research workbench
Identification of a druggable VP1-VP3 interprotomer pocket in the capsid of enteroviruses
Analyse Identification of a druggable VP1-VP3 interprotomer pocket in the capsid of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GZV
- Type
- protein
- Length
- 818 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- P03313
- Ligands
- FHK
- Pockets
- 10 · best druggability 0.54
Structure
electron microscopy · 4 distinct chains · 6% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 269 | 7% helix, 29% strand | P03313 |
| B | Capsid protein VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 255 | 6% helix, 34% strand | P03313 |
| C | Capsid protein VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 238 | 6% helix, 30% strand | P03313 |
| D | Capsid protein VP4 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 56 | 0% helix, 13% strand | P03313 |
Ligands and binding sites
- FHK · 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.54 | 0.81 | 25 | empty |
| 2 | 84 | 0.47 | 0.82 | 22 | empty |
| 3 | 71 | 0.45 | 0.82 | 22 | empty |
| 4 | 77 | 0.44 | 0.81 | 20 | empty |
| 5 | 117 | 0.40 | 0.76 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4371 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2168 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1573 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1193 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 980 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6GZV · Identification of a druggable VP1-VP3 interprotomer pocket in the capsid of enteroviruses · 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 P03313
- Elsewhere: RCSB PDB 6GZV · PDBe 6GZV · UniProt P03313
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