Research workbench
Crystal structure of a membrane protein S19A
Analyse Crystal structure of a membrane protein S19A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IVQ
- Type
- protein
- Length
- 1,350 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ibestrophin
- UniProt
- W9BH30
- Ligands
- ZN, NA, CL
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ibestrophin | protein | 270 | 79% helix, 1% strand | W9BH30 |
| B | Ibestrophin | protein | 271 | 79% helix, 1% strand | W9BH30 |
| C | Ibestrophin | protein | 269 | 81% helix, 0% strand | W9BH30 |
| D | Ibestrophin | protein | 269 | 80% helix, 1% strand | W9BH30 |
| E | Ibestrophin | protein | 271 | 81% helix, 0% strand | W9BH30 |
Ligands and binding sites
- ZN · Zinc ion · metal · 17 copies · chains A, E, B, C, D
- NA · Sodium ion · metal · chains C, D
- CL · Chloride ion · ion · 12 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
- PG4 · Tetraethylene glycol · additive · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.81 | 0.82 | 138 | EDO, PG4 |
| 2 | 50 | 0.71 | 0.99 | 16 | empty |
| 3 | 579 | 0.70 | 0.79 | 39 | empty |
| 4 | 258 | 0.65 | 0.82 | 44 | empty |
| 5 | 306 | 0.62 | 0.79 | 31 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2776 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 2621 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2578 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 2524 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 2523 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6IVQ · Crystal structure of a membrane protein S19A · 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 6IVQ · PDBe 6IVQ · UniProt W9BH30
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