MolNFT v1 · #33819 · protein
Crystal structure of human hmg-CoA lyase: insights into catalysis and the molecular basis for hydroxymethylglutaric aciduria
2CW6 · Hydroxymethylglutaryl-CoA lyase, mitochondrial: “Crystal structure of human hmg-CoA lyase: insights into catalysis and the molecular basis for…”. X-ray diffraction, 2 ligands (3HG, MG), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 2CW6
- Type
- protein
- Length
- 1,752 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxymethylglutaryl-CoA lyase, mitochondrial
- EC
- 4.1.3.4
- UniProt
- P35914
- Ligands
- 3HG, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Hydroxymethylglutaryl-CoA lyase, mitochondrial (EC 4.1.3.4) | protein | 296 | 46% helix, 16% strand | P35914 |
| C | Hydroxymethylglutaryl-CoA lyase, mitochondrial (EC 4.1.3.4) | protein | 294 | 45% helix, 16% strand | P35914 |
| D | Hydroxymethylglutaryl-CoA lyase, mitochondrial (EC 4.1.3.4) | protein | 282 | 46% helix, 17% strand | P35914 |
| F | Hydroxymethylglutaryl-CoA lyase, mitochondrial (EC 4.1.3.4) | protein | 288 | 47% helix, 16% strand | P35914 |
Ligands and binding sites
- 3HG · 3-hydroxypentanedioic acid · ligand · chains A
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.84 | 0.86 | 71 | empty |
| 2 | 1070 | 0.74 | 0.77 | 95 | empty |
| 3 | 291 | 0.73 | 0.86 | 31 | empty |
| 4 | 346 | 0.73 | 0.84 | 37 | 3HG |
| 5 | 82 | 0.70 | 0.94 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1283 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1191 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1176 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 690 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 377 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2CW6 · Crystal Structure of Human HMG-CoA Lyase: Insights into Catalysis and the Molecular Basis… · the same entry in another collection · chain F against F, TM-score 1.00
- P35914 · AlphaFold monomer V2.0 prediction for hydroxymethylglutaryl-CoA lyase, mitochondrial… · a predicted model of the same protein · chain D 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 P35914
- Elsewhere: RCSB PDB 2CW6 · PDBe 2CW6 · UniProt P35914
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