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Archaeal oligopeptide permease a (oppa) from thermococcus kodakaraensis in complex with an endogenous pentapeptide
Analyse Archaeal oligopeptide permease a (oppa) from thermococcus kodakaraensis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FI3
- Type
- protein
- Length
- 2,916 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC-type DIPEPTIDE/OLIGOPEPTIDE transport system; Endogenous pentapeptide
- UniProt
- Q5JJ92
- Ligands
- NA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ABC-type DIPEPTIDE/OLIGOPEPTIDE transport system | protein | 724 | 36% helix, 23% strand | Q5JJ92 |
| E, F, G, H | Endogenous pentapeptide | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, C, B, D
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, C, B, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.87 | 0.88 | 103 | P6G |
| 2 | 1053 | 0.87 | 0.87 | 99 | P6G |
| 3 | 1120 | 0.85 | 0.85 | 70 | empty |
| 4 | 1101 | 0.84 | 0.85 | 67 | empty |
| 5 | 1095 | 0.84 | 0.85 | 67 | empty |
Interfaces
10 interfaces between chains.
- A–C · 1915 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1883 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1067 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1039 Ų buried · 18 hydrogen bonds · protein-protein
- D–H · 458 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 7FI3 · Archaeal oligopeptide permease A (OppA) from Thermococcus kodakaraensis in complex with… · 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 Q5JJ92
- Elsewhere: RCSB PDB 7FI3 · PDBe 7FI3 · UniProt Q5JJ92
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