MolNFT v1 · #8712 · protein
Echovirus 11
1H8T · Echovirus 11 coat protein VP1: “Echovirus 11”. X-ray diffraction, 2 ligands (DOA, MYR), 9 pockets (best druggability 0.78). MolNFT v1 #8712 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1H8T
- Type
- protein
- Length
- 839 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Echovirus 11 coat protein VP1; Echovirus 11 coat protein VP2; Echovirus 11 coat protein…
- UniProt
- P29813
- Ligands
- DOA, MYR
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Echovirus 11 coat protein VP1 | protein | 289 | 11% helix, 30% strand | P29813 |
| B | Echovirus 11 coat protein VP2 | protein | 252 | 10% helix, 38% strand | P29813 |
| C | Echovirus 11 coat protein VP3 | protein | 238 | 10% helix, 33% strand | P29813 |
| D | Echovirus 11 coat protein VP4 | protein | 60 | 10% helix, 17% strand | P29813 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.78 | 0.85 | 74 | DOA |
| 2 | 74 | 0.61 | 0.90 | 15 | empty |
| 3 | 60 | 0.52 | 0.87 | 23 | empty |
| 4 | 262 | 0.51 | 0.75 | 35 | empty |
| 5 | 117 | 0.45 | 0.78 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4466 Ų buried · 79 hydrogen bonds · protein-protein
- A–B · 1987 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1616 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1472 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 942 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1H8T · Echovirus 11 · 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 P29813
- Elsewhere: RCSB PDB 1H8T · PDBe 1H8T · UniProt P29813
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