Research workbench
Crystal structure of a bacterial bestrophin homolog from klebsiella pneumoniae with a mutation L177T
Analyse Crystal structure of a bacterial bestrophin homolog from klebsiella pneumoniae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X87
- Type
- protein
- Length
- 1,343 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bestrophin
- UniProt
- W1ELP7
- Ligands
- ZN
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Bestrophin | protein | 268 | 80% helix, 0% strand | W1ELP7 |
| C | Bestrophin | protein | 269 | 77% helix, 0% strand | W1ELP7 |
| E | Bestrophin | protein | 270 | 79% helix, 1% strand | W1ELP7 |
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
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.84 | 0.85 | 125 | empty |
| 2 | 664 | 0.71 | 0.78 | 51 | ZN |
| 3 | 325 | 0.65 | 0.80 | 30 | empty |
| 4 | 294 | 0.62 | 0.80 | 48 | empty |
| 5 | 136 | 0.59 | 0.84 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–E · 2639 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2626 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2593 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 2548 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 2534 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5X87 · Crystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae with a… · 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 W1ELP7
- Elsewhere: RCSB PDB 5X87 · PDBe 5X87 · UniProt W1ELP7
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