Research workbench
Vibrio parahaemolyticus VTRA/VTRC complex bound to the bile salt taurodeoxycholate
Analyse Vibrio parahaemolyticus VTRA/VTRC complex bound to the bile salt… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KEW
- Type
- protein
- Length
- 651 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vtra protein; Vtrc protein
- UniProt
- Q87GI4, Q87GI3
- Ligands
- 6SB, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vtra protein | protein | 89 | 34% helix, 33% strand | Q87GI4 |
| B | Vtrc protein | protein | 132 | 5% helix, 69% strand | Q87GI3 |
| C | Vtra protein | protein | 90 | 33% helix, 34% strand | Q87GI4 |
| D | Vtrc protein | protein | 125 | 6% helix, 67% strand | Q87GI3 |
| E | Vtra protein | protein | 88 | 33% helix, 34% strand | Q87GI4 |
| F | Vtrc protein | protein | 127 | 11% helix, 65% strand | Q87GI3 |
Ligands and binding sites
- 6SB · Taurodeoxycholate · ligand · 4 copies · chains A, B, D, F
- SO4 · Sulfate ion · ion · 5 copies · chains B, C, D, E, F
- ACT · Acetate ion · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.78 | 0.81 | 75 | 6SB |
| 2 | 698 | 0.76 | 0.81 | 75 | 6SB |
| 3 | 433 | 0.73 | 0.82 | 43 | 6SB |
| 4 | 67 | 0.31 | 0.75 | 15 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1230 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1168 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1111 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 442 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 203 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5KEW · Vibrio parahaemolyticus VtrA/VtrC complex bound to the bile salt taurodeoxycholate · 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 Q87GI4
- Every structure of UniProt Q87GI3
- Elsewhere: RCSB PDB 5KEW · PDBe 5KEW · UniProt Q87GI4 · UniProt Q87GI3
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