MolNFT v1 · #109758 · protein
Isobutyryl-CoA mutase fused with bound butyryl-CoA, GDP, and mg and without cobalamin (apo-ICMF/GDP)
4XC8: “Isobutyryl-CoA mutase fused with bound butyryl-CoA, GDP, and mg and without cobalamin (apo-ICMF/GDP)”. X-ray diffraction, 3 ligands (BCO, GDP, MG), 18 pockets (best druggability 0.82). MolNFT v1 #109758 on GenesisL1: 3D structure…
- PDB
- 4XC8
- Type
- protein
- Length
- 2,118 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isobutyryl-CoA mutase fused
- EC
- 5.4.99.13
- UniProt
- Q1LRY0
- Ligands
- BCO, GDP, MG
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isobutyryl-CoA mutase fused (EC 5.4.99.13) | protein | 1058 | 50% helix, 11% strand | Q1LRY0 |
| B | Isobutyryl-CoA mutase fused (EC 5.4.99.13) | protein | 1060 | 50% helix, 11% strand | Q1LRY0 |
Ligands and binding sites
- BCO · Butyryl Coenzyme A · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.82 | 0.83 | 115 | GDP, MG |
| 2 | 927 | 0.82 | 0.84 | 107 | BCO |
| 3 | 122 | 0.81 | 0.98 | 24 | empty |
| 4 | 669 | 0.76 | 0.82 | 84 | GDP, MG |
| 5 | 183 | 0.76 | 0.92 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 4060 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- Q1LRY0 · AlphaFold monomer V2.0 prediction for fused isobutyryl-CoA mutase (Q1LRY0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q1LRY0
- Elsewhere: RCSB PDB 4XC8 · PDBe 4XC8 · UniProt Q1LRY0
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