Research workbench
Structure of the F349A mutant of the periplasmic domain of yejm from salmonella typhimurium
Analyse Structure of the F349A mutant of the periplasmic domain of yejm from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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