MolNFT v1 · #115440 · protein
Isobutyryl-CoA mutase fused with bound adenosylcobalamin, GDP, mg (holo-ICMF/GDP), and substrate isovaleryl-coenzyme a
5CJV: “Isobutyryl-CoA mutase fused with bound adenosylcobalamin, GDP, mg (holo-ICMF/GDP), and substrate…”. X-ray diffraction, 5 ligands (B12, IVC, GDP), 18 pockets (best druggability 0.88). MolNFT v1 #115440 on GenesisL1: 3D structure…
- PDB
- 5CJV
- Type
- protein
- Length
- 2,120 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isobutyryl-CoA mutase fused
- EC
- 5.4.99.2
- UniProt
- Q1LRY0
- Ligands
- B12, IVC, GDP, 5AD, MG
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isobutyryl-CoA mutase fused (EC 5.4.99.2) | protein | 1061 | 50% helix, 12% strand | Q1LRY0 |
| B | Isobutyryl-CoA mutase fused (EC 5.4.99.2) | protein | 1059 | 50% helix, 12% strand | Q1LRY0 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 2 copies · chains A, B
- IVC · Isovaleryl-coenzyme A · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- 5AD · 5'-deoxyadenosine · ligand · chains A
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.88 | 0.89 | 115 | B12, 5AD, IVC |
| 2 | 967 | 0.80 | 0.82 | 94 | GDP, MG |
| 3 | 116 | 0.80 | 0.98 | 23 | empty |
| 4 | 252 | 0.77 | 0.90 | 36 | empty |
| 5 | 409 | 0.73 | 0.84 | 51 | GDP, MG |
Interfaces
1 interface between chains.
- A–B · 4041 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5CJV · Isobutyryl-CoA mutase fused with bound adenosylcobalamin, GDP, Mg (holo-IcmF/GDP), and… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.97
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 Q1LRY0
- Elsewhere: RCSB PDB 5CJV · PDBe 5CJV · UniProt Q1LRY0
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