MolNFT v1 · #105399 · protein
Crystal structure of 2-hydroxyisobutyryl-CoA mutase
4R3U · 2-hydroxyisobutyryl-CoA mutase large subunit: “Crystal structure of 2-hydroxyisobutyryl-CoA mutase”. X-ray diffraction, 4 ligands (3HC, 3KK, B12), 11 pockets (best druggability 0.88). MolNFT v1 #105399 on GenesisL1: 3D structure…
- PDB
- 4R3U
- Type
- protein
- Length
- 1,372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-hydroxyisobutyryl-CoA mutase large subunit; 2-hydroxyisobutyryl-CoA mutase small subunit
- EC
- 5.4.99.-
- UniProt
- I3VE77, I3VE74
- Ligands
- 3HC, 3KK, B12, 5AD
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-hydroxyisobutyryl-CoA mutase large subunit (EC 5.4.99.-) | protein | 557 | 53% helix, 7% strand | I3VE77 |
| B | 2-hydroxyisobutyryl-CoA mutase large subunit (EC 5.4.99.-) | protein | 555 | 54% helix, 8% strand | I3VE77 |
| C | 2-hydroxyisobutyryl-CoA mutase small subunit | protein | 131 | 44% helix, 21% strand | I3VE74 |
| D | 2-hydroxyisobutyryl-CoA mutase small subunit | protein | 129 | 46% helix, 21% strand | I3VE74 |
Ligands and binding sites
- 3HC · 3-hydroxybutanoyl-coenzyme A · ligand · 2 copies · chains A, B
- 3KK · S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3, 5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2, 4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2-hydroxy-2-methylpropanethioate · ligand · 2 copies · chains A, B
- B12 · Cobalamin · ligand · 2 copies · chains A, C, B, D
- 5AD · 5'-deoxyadenosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.88 | 0.89 | 132 | 3HC, 3KK, 5AD, B12 |
| 2 | 1135 | 0.87 | 0.89 | 128 | 3HC, 3KK, B12 |
| 3 | 894 | 0.80 | 0.82 | 100 | empty |
| 4 | 77 | 0.50 | 0.84 | 16 | empty |
| 5 | 72 | 0.44 | 0.81 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1374 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1353 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 274 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 258 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4R3U · Crystal structure of 2-Hydroxyisobutyryl-CoA Mutase · 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 I3VE77
- Every structure of UniProt I3VE74
- Elsewhere: RCSB PDB 4R3U · PDBe 4R3U · UniProt I3VE77 · UniProt I3VE74
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