MolNFT v1 · #116988 · protein
Crystal structure of native translocator protein 18KDA (tspo) from rhodobacter sphaeroides (A139T mutant) in C2 space group
5DUO · Tryptophan-rich sensory protein: “Crystal structure of native translocator protein 18KDA (tspo) from rhodobacter sphaeroides (A139T mutant) in…”. X-ray diffraction, 1 ligand (PP9), 6 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 5DUO
- Type
- protein
- Length
- 463 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan-rich sensory protein
- UniProt
- Q9RFC8
- Ligands
- PP9
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tryptophan-rich sensory protein | protein | 157 | 75% helix, 0% strand | Q9RFC8 |
| C | Tryptophan-rich sensory protein | protein | 149 | 78% helix, 0% strand | Q9RFC8 |
Ligands and binding sites
- PP9 · Protoporphyrin IX · ligand · chains A, C
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 15 copies · chains A, C, B
- FMT · Formic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.79 | 0.82 | 64 | OLC, PP9 |
| 2 | 223 | 0.73 | 0.88 | 35 | empty |
| 3 | 121 | 0.58 | 0.84 | 21 | empty |
| 4 | 247 | 0.52 | 0.75 | 29 | OLC |
| 5 | 85 | 0.45 | 0.80 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1264 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 804 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5DUO · Crystal structure of native translocator protein 18kDa (TSPO) from Rhodobacter… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RFC8 · AlphaFold monomer V2.0 prediction for tryptophan-rich sensory protein (Q9RFC8) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9RFC8
- Elsewhere: RCSB PDB 5DUO · PDBe 5DUO · UniProt Q9RFC8
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