Research workbench
Crystal structure of human lyase in complex with inhibitor hg-CoA
Analyse Crystal structure of human lyase in complex with inhibitor hg-CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MP3
- Type
- protein
- Length
- 1,769 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxymethylglutaryl-CoA lyase
- EC
- 4.1.3.4
- UniProt
- P35914
- Ligands
- 3HG, HGG, MG
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) | protein | 296 | 45% helix, 16% strand | P35914 |
| D | Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) | protein | 289 | 44% helix, 17% strand | P35914 |
Ligands and binding sites
- 3HG · 3-hydroxypentanedioic acid · ligand · chains A
- HGG · (3R,5S,9R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,21-tetrahydroxy-8,8-dimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide · ligand · chains B
- 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
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.82 | 0.85 | 65 | MG |
| 2 | 995 | 0.77 | 0.79 | 87 | MG |
| 3 | 109 | 0.74 | 0.95 | 31 | empty |
| 4 | 328 | 0.73 | 0.85 | 42 | 3HG, MG |
| 5 | 336 | 0.69 | 0.83 | 37 | MG |
Interfaces
6 interfaces between chains.
- A–B · 1302 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1271 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1208 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 694 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 432 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3MP3 · Crystal Structure of Human Lyase in complex with inhibitor HG-CoA · 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 3MP3 · PDBe 3MP3 · UniProt P35914
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