MolNFT v1 · #189189 · protein
Structural insights into the substrate selectivity of acyl-CoA transferase
7V5I · 2-amino-3-ketobutyrate coenzyme a ligase: “Structural insights into the substrate selectivity of acyl-CoA transferase”. X-ray diffraction, 1 ligand (PLP), 13 pockets (best druggability 0.85). MolNFT v1 #189189 on GenesisL1: 3D…
- PDB
- 7V5I
- Type
- protein
- Length
- 1,600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-3-ketobutyrate coenzyme a ligase
- EC
- 2.3.1.29
- UniProt
- U3BPN5
- Ligands
- PLP
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2-amino-3-ketobutyrate coenzyme a ligase (EC 2.3.1.29) | protein | 400 | 45% helix, 18% strand | U3BPN5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.85 | 0.86 | 111 | PLP |
| 2 | 855 | 0.79 | 0.82 | 102 | PLP |
| 3 | 855 | 0.76 | 0.80 | 92 | empty |
| 4 | 746 | 0.76 | 0.80 | 85 | PLP |
| 5 | 82 | 0.74 | 0.96 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4882 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 4852 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 494 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 270 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 218 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7V5I · Structural insights into the substrate selectivity of acyl-CoA transferase · 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 U3BPN5
- Elsewhere: RCSB PDB 7V5I · PDBe 7V5I · UniProt U3BPN5
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