MolNFT v1 · #108643 · protein
Crystal structure of a bacterial bestrophin homolog from klebsiella pneumoniae by zn-sad phasing
4WD7 · Bestrophin domain protein: “Crystal structure of a bacterial bestrophin homolog from klebsiella pneumoniae by zn-sad phasing”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability 0.81). MolNFT v1 #108643 on GenesisL1: 3D…
- PDB
- 4WD7
- Type
- protein
- Length
- 1,345 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bestrophin domain protein
- UniProt
- S7AS11
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Bestrophin domain protein | protein | 268 | 81% helix, 1% strand | S7AS11 |
| B | Bestrophin domain protein | protein | 270 | 80% helix, 1% strand | S7AS11 |
| C | Bestrophin domain protein | protein | 269 | 80% helix, 1% strand | S7AS11 |
| E | Bestrophin domain protein | protein | 270 | 80% helix, 1% strand | S7AS11 |
Ligands and binding sites
- ZN · Zinc ion · metal · 15 copies · chains A, E, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.81 | 0.85 | 96 | empty |
| 2 | 735 | 0.71 | 0.78 | 60 | empty |
| 3 | 307 | 0.63 | 0.80 | 30 | empty |
| 4 | 246 | 0.59 | 0.80 | 45 | empty |
| 5 | 51 | 0.53 | 0.89 | 15 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2679 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 2617 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 2557 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2549 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 2490 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4WD7 · Crystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae by Zn-SAD… · 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 S7AS11
- Elsewhere: RCSB PDB 4WD7 · PDBe 4WD7 · UniProt S7AS11
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