Research workbench
High resolution crystal structure of translocator protein 18KDA (tspo) from rhodobacter sphaeroides (A139T mutant) in C2 space group
Analyse High resolution crystal structure of translocator protein 18KDA (tspo) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UC1
- Type
- protein
- Length
- 462 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translocator protein tspo
- UniProt
- Q9RFC8
- Ligands
- PP9, Z0P, MOE
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translocator protein tspo | protein | 157 | 73% helix, 0% strand | Q9RFC8 |
| B | Translocator protein tspo | protein | 156 | 77% helix, 0% strand | Q9RFC8 |
| C | Translocator protein tspo | protein | 149 | 80% helix, 0% strand | Q9RFC8 |
Ligands and binding sites
- PP9 · Protoporphyrin IX · ligand · chains A, C
- Z0P · (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate · ligand · chains A, B, C
- MOE · Methoxy-ethoxyl · ligand · chains C
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 17 copies · chains A, C, B
- P4C · O-acetaldehydyl-hexaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.79 | 0.82 | 63 | PP9 |
| 2 | 215 | 0.71 | 0.87 | 35 | empty |
| 3 | 174 | 0.64 | 0.84 | 28 | empty |
| 4 | 150 | 0.48 | 0.76 | 18 | OLC |
| 5 | 92 | 0.47 | 0.81 | 14 | OLC |
Interfaces
3 interfaces between chains.
- A–B · 1286 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 780 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4UC1 · High resolution crystal structure of 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 B 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 Q9RFC8
- Elsewhere: RCSB PDB 4UC1 · PDBe 4UC1 · UniProt Q9RFC8
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