Research workbench
Structure of the periplasmic domain of yejm from salmonella typhimurium (twinned)
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
- 6VDF
- Type
- protein
- Length
- 1,372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic domain of the cardiolipin transporter protein YEJM/PBGA
- UniProt
- A0A5K1U4E1
- Ligands
- PSE, MN, PO4
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Periplasmic domain of the cardiolipin transporter protein YEJM/PBGA | protein | 343 | 34% helix, 18% strand | A0A5K1U4E1 |
Ligands and binding sites
- PSE · O-phosphoethanolamine · ligand · 2 copies · chains C, D
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D
- PGE · Triethylene glycol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.69 | 0.77 | 62 | empty |
| 2 | 440 | 0.62 | 0.77 | 29 | empty |
| 3 | 106 | 0.56 | 0.84 | 18 | empty |
| 4 | 57 | 0.52 | 0.87 | 19 | empty |
| 5 | 198 | 0.48 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- C–D · 621 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 271 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VDF · Structure of the periplasmic domain of YejM from Salmonella typhimurium (twinned) · 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 A0A5K1U4E1
- Elsewhere: RCSB PDB 6VDF · PDBe 6VDF · UniProt A0A5K1U4E1
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