Research workbench
Crystal structure of native translocator protein 18KDA (tspo) from rhodobacter sphaeroides (A139T mutant) in C2 space group
Analyse Crystal structure of native translocator protein 18KDA (tspo) from rhodobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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