MolNFT v1 · #151118 · protein
Crystal structure of an open conformation of 2-hydroxyisobutyryl-CoA ligase (hcl) in complex with 2-hib-AMP and CoA
6HE2 · 2-hydroxyisobutyryl-CoA synthetase: “Crystal structure of an open conformation of 2-hydroxyisobutyryl-CoA ligase (hcl) in complex with 2-hib-AMP…”. X-ray diffraction, 3 ligands (AMP, 8LE, COA), 7 pockets (best druggability 0.66).…
- PDB
- 6HE2
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-hydroxyisobutyryl-CoA synthetase
- EC
- 6.2.1.-
- UniProt
- I3VE75
- Ligands
- AMP, 8LE, COA
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-hydroxyisobutyryl-CoA synthetase (EC 6.2.1.-) | protein | 460 | 36% helix, 21% strand | I3VE75 |
| B | 2-hydroxyisobutyryl-CoA synthetase (EC 6.2.1.-) | protein | 430 | 39% helix, 19% strand | I3VE75 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- 8LE · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 2-methyl-2-oxidanyl-propanoate · ligand · 2 copies · chains A, B
- COA · Coenzyme A · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.66 | 0.81 | 25 | empty |
| 2 | 507 | 0.63 | 0.76 | 61 | AMP, 8LE |
| 3 | 479 | 0.63 | 0.76 | 62 | AMP, 8LE |
| 4 | 64 | 0.41 | 0.81 | 19 | empty |
| 5 | 94 | 0.40 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1562 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6HE2 · Crystal structure of an open conformation of 2-Hydroxyisobutyryl-CoA Ligase (HCL) 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 6HE2 · PDBe 6HE2 · UniProt I3VE75
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