MolNFT v1 · #167152 · protein
Structure of the F349A mutant of the periplasmic domain of yejm from salmonella typhimurium
6VC7 · Periplasmic domain of the cardiolipin transporter protein…: “Structure of the F349A mutant of the periplasmic domain of yejm from salmonella typhimurium”. X-ray diffraction, 3 ligands (ETA, MG, K), 16 pockets (best druggability…
- PDB
- 6VC7
- Type
- protein
- Length
- 2,064 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
- A0A5A8TP41
- Ligands
- ETA, MG, K
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Periplasmic domain of the cardiolipin transporter protein YEJM/PBGA | protein | 344 | 36% helix, 22% strand | A0A5A8TP41 |
Ligands and binding sites
- ETA · Ethanolamine · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 3 copies · chains A, C, B, E, D, F
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B, C, D, E, F
- PG4 · Tetraethylene glycol · additive · 7 copies · chains A, C, B, D, E, F
- P6G · Hexaethylene glycol · additive · 3 copies · chains A, C, B
- 1PE · Pentaethylene glycol · additive · 3 copies · chains C, D, E
- PGE · Triethylene glycol · additive · 2 copies · chains A, B, E
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.76 | 0.79 | 96 | EDO |
| 2 | 56 | 0.69 | 0.97 | 24 | empty |
| 3 | 163 | 0.53 | 0.79 | 27 | P6G |
| 4 | 68 | 0.51 | 0.86 | 22 | empty |
| 5 | 159 | 0.50 | 0.78 | 26 | P6G |
Interfaces
7 interfaces between chains.
- D–F · 542 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 527 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 509 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 489 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 371 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6VC7 · Structure of the F349A mutant of the periplasmic domain of YejM from Salmonella… · 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 A0A5A8TP41
- Elsewhere: RCSB PDB 6VC7 · PDBe 6VC7 · UniProt A0A5A8TP41
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