MolNFT v1 · #65006 · protein
Crystal structure of 4-hydroxybutyrate CoA-transferase from clostridium aminobutyricum
3GK7: “Crystal structure of 4-hydroxybutyrate CoA-transferase from clostridium aminobutyricum”. X-ray diffraction, 1 ligand (SPD), 10 pockets (best druggability 0.71). MolNFT v1 #65006 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3GK7
- Type
- protein
- Length
- 894 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxybutyrate CoA-transferase
- EC
- 2.8.3.-
- UniProt
- Q9RM86
- Ligands
- SPD
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-hydroxybutyrate CoA-transferase (EC 2.8.3.-) | protein | 447 | 31% helix, 23% strand | Q9RM86 |
Ligands and binding sites
- SPD · Spermidine · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.71 | 0.81 | 43 | SPD |
| 2 | 516 | 0.71 | 0.80 | 59 | SPD |
| 3 | 221 | 0.45 | 0.73 | 30 | empty |
| 4 | 104 | 0.42 | 0.77 | 19 | empty |
| 5 | 73 | 0.42 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2180 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3GK7 · Crystal structure of 4-hydroxybutyrate CoA-Transferase from Clostridium aminobutyricum · 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 Q9RM86
- Elsewhere: RCSB PDB 3GK7 · PDBe 3GK7 · UniProt Q9RM86
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.