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Crystal structure of human mitochondrial 3-hydroxy-3- methylglutaryl-coenzyme a synthase 2 (HMGCS2)
Analyse Crystal structure of human mitochondrial 3-hydroxy-3- methylglutaryl-coenzyme a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WYA
- Type
- protein
- Length
- 1,840 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxymethylglutaryl-CoA synthase, mitochondrial
- EC
- 2.3.3.10
- UniProt
- P54868
- Ligands
- HMG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hydroxymethylglutaryl-CoA synthase, mitochondrial (EC 2.3.3.10) | protein | 460 | 45% helix, 20% strand | P54868 |
Ligands and binding sites
- HMG · 3-hydroxy-3-methylglutaryl-coenzyme A · ligand · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.81 | 0.97 | 46 | empty |
| 2 | 149 | 0.81 | 0.97 | 45 | empty |
| 3 | 91 | 0.75 | 0.97 | 27 | empty |
| 4 | 86 | 0.75 | 0.97 | 27 | empty |
| 5 | 81 | 0.74 | 0.97 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–D · 2991 Ų buried · 76 hydrogen bonds · protein-protein
- B–C · 2966 Ų buried · 74 hydrogen bonds · protein-protein
- A–B · 659 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2WYA · Crystal structure of human mitochondrial 3-hydroxy-3-methylglutaryl- coenzyme a synthase… · the same entry in another collection · chain A against A, TM-score 1.00
- P54868 · AlphaFold monomer V2.0 prediction for hydroxymethylglutaryl-CoA synthase, mitochondrial… · a predicted model of the same protein · 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 P54868
- Elsewhere: RCSB PDB 2WYA · PDBe 2WYA · UniProt P54868
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