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Crystal structure of a membrane protein W16A
Analyse Crystal structure of a membrane protein W16A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IVR
- Type
- protein
- Length
- 1,346 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Klebsiella pneumoniae
- Molecule
- Ibestrophin
- UniProt
- W9BH30
- Ligands
- ZN, CL
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.8 · 4 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ibestrophin | protein | 268 | 79% helix, 1% strand | W9BH30 |
| B | Ibestrophin | protein | 270 | 79% helix, 0% strand | W9BH30 |
| C | Ibestrophin | protein | 269 | 80% helix, 0% strand | W9BH30 |
| E | Ibestrophin | protein | 271 | 80% helix, 0% strand | W9BH30 |
Ligands and binding sites
- ZN · Zinc ion · metal · 15 copies · chains A, E, B, D, C
- CL · Chloride ion · ion · 11 copies · chains A, E, B, C, D
- ACY · Acetic acid · additive · 2 copies · chains B, C, E
- EDO · 1,2-ethanediol · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.82 | 0.83 | 126 | EDO |
| 2 | 576 | 0.69 | 0.79 | 39 | empty |
| 3 | 210 | 0.62 | 0.82 | 29 | empty |
| 4 | 283 | 0.61 | 0.79 | 27 | empty |
| 5 | 115 | 0.59 | 0.85 | 25 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2710 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 2658 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2589 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 2583 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 2451 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6IVR · Crystal structure of a membrane protein W16A · 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 6IVR · PDBe 6IVR · UniProt W9BH30
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