Research workbench
Structure of the periplasmic domain of yejm from salmonella typhimurium
Analyse Structure of the periplasmic domain of yejm from salmonella typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VAT
- Type
- protein
- Length
- 2,066 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic domain of the cardiolipin transporter protein YEJM/PBGA
- UniProt
- A0A4V1IDU5
- Ligands
- ETA, MG, CA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic domain of the cardiolipin transporter protein YEJM/PBGA | protein | 344 | 35% helix, 21% strand | A0A4V1IDU5 |
| B | Periplasmic domain of the cardiolipin transporter protein YEJM/PBGA | protein | 343 | 36% helix, 19% strand | A0A4V1IDU5 |
| C | Periplasmic domain of the cardiolipin transporter protein YEJM/PBGA | protein | 345 | 35% helix, 19% strand | A0A4V1IDU5 |
| D | Periplasmic domain of the cardiolipin transporter protein YEJM/PBGA | protein | 343 | 37% helix, 18% strand | A0A4V1IDU5 |
| E | Periplasmic domain of the cardiolipin transporter protein YEJM/PBGA | protein | 346 | 32% helix, 20% strand | A0A4V1IDU5 |
| F | Periplasmic domain of the cardiolipin transporter protein YEJM/PBGA | protein | 345 | 34% helix, 21% strand | A0A4V1IDU5 |
Ligands and binding sites
- ETA · Ethanolamine · ligand · 3 copies · chains A, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- CA · Calcium ion · metal · 3 copies · chains B, C, E
- PG4 · Tetraethylene glycol · additive · 7 copies · chains A, B, C, E, D
- 1PE · Pentaethylene glycol · additive · 4 copies · chains A, C, E, F
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C, D
- PGE · Triethylene glycol · additive · 3 copies · chains B, C, F
- P6G · Hexaethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.69 | 0.77 | 70 | ETA |
| 2 | 340 | 0.66 | 0.81 | 29 | empty |
| 3 | 83 | 0.64 | 0.91 | 26 | empty |
| 4 | 106 | 0.63 | 0.89 | 27 | empty |
| 5 | 305 | 0.61 | 0.79 | 27 | PG4 |
Interfaces
11 interfaces between chains.
- C–E · 428 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 419 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 356 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 269 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 255 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6VAT · Structure of the periplasmic domain of YejM from Salmonella typhimurium · 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 A0A4V1IDU5
- Elsewhere: RCSB PDB 6VAT · PDBe 6VAT · UniProt A0A4V1IDU5
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