MolNFT v1 · #151114 · protein
Crystal structure of 2-hydroxyisobutyryl-CoA ligase (hcl) in the postadenylation state in complex with S3-hb-AMP
6HDY · 2-hydroxyisobutyryl-CoA synthetase: “Crystal structure of 2-hydroxyisobutyryl-CoA ligase (hcl) in the postadenylation state in complex with…”. X-ray diffraction, 3 ligands (3HL, 8LQ, SO4), 3 pockets (best druggability 0.76). MolNFT…
- PDB
- 6HDY
- Type
- protein
- Length
- 474 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-hydroxyisobutyryl-CoA synthetase
- EC
- 6.2.1.-
- UniProt
- I3VE75
- Ligands
- 3HL, 8LQ, SO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-hydroxyisobutyryl-CoA synthetase (EC 6.2.1.-) | protein | 474 | 38% helix, 20% strand | I3VE75 |
Ligands and binding sites
- 3HL · (3S)-3-hydroxybutanoic acid · ligand · chains A
- 8LQ · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (3~{S})-3-oxidanylbutanoate · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.76 | 0.84 | 71 | 3HL, 8LQ |
| 2 | 94 | 0.40 | 0.77 | 21 | empty |
| 3 | 72 | 0.37 | 0.77 | 16 | empty |
Compared structures
- 6HDY · Crystal structure of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in the postadenylation state in… · 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 I3VE75
- Elsewhere: RCSB PDB 6HDY · PDBe 6HDY · UniProt I3VE75
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