MolNFT v1 · #152856 · protein
Crystal structure of a membrane protein P208A
6IVO · Bestrophin: “Crystal structure of a membrane protein P208A”. X-ray diffraction, 3 ligands (ZN, NA, CL), 13 pockets (best druggability 0.87). MolNFT v1 #152856 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IVO
- Type
- protein
- Length
- 1,352 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bestrophin
- UniProt
- W9BH30
- Ligands
- ZN, NA, CL
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 79% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bestrophin | protein | 269 | 79% helix, 1% strand | W9BH30 |
| B | Bestrophin | protein | 270 | 80% helix, 1% strand | W9BH30 |
| C | Bestrophin | protein | 269 | 78% helix, 1% strand | W9BH30 |
| D | Bestrophin | protein | 273 | 78% helix, 1% strand | W9BH30 |
| E | Bestrophin | protein | 271 | 82% helix, 1% strand | W9BH30 |
Ligands and binding sites
- ZN · Zinc ion · metal · 18 copies · chains A, E, B, D, C
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 12 copies · chains A, E, B, D, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, C, D
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, C, D, E
- PG4 · Tetraethylene glycol · additive · chains A, E
- ACY · Acetic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.87 | 0.88 | 120 | PGE, EDO |
| 2 | 647 | 0.70 | 0.78 | 48 | empty |
| 3 | 105 | 0.68 | 0.91 | 23 | PG4 |
| 4 | 403 | 0.64 | 0.78 | 53 | empty |
| 5 | 367 | 0.62 | 0.77 | 54 | empty |
Interfaces
10 interfaces between chains.
- A–E · 2596 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2567 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2489 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 2475 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2474 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6IVO · Crystal structure of a membrane protein P208A · 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 W9BH30
- Elsewhere: RCSB PDB 6IVO · PDBe 6IVO · UniProt W9BH30
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