Research workbench
Hmg-CoA reductase from pseudomonas mevalonii complexed with dithio- hmg-CoA
Analyse Hmg-CoA reductase from pseudomonas mevalonii complexed with dithio- hmg-CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I56
- Type
- protein
- Length
- 749 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxy-3-methylglutaryl-coenzyme a reductase
- EC
- 1.1.1.88
- UniProt
- P13702
- Ligands
- 1CZ, SO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxy-3-methylglutaryl-coenzyme a reductase (EC 1.1.1.88) | protein | 373 | 47% helix, 22% strand | P13702 |
| B | 3-hydroxy-3-methylglutaryl-coenzyme a reductase (EC 1.1.1.88) | protein | 376 | 47% helix, 22% strand | P13702 |
Ligands and binding sites
- 1CZ · (3S,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-8,8,21-trimethyl-10,14-dioxo-19-thioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.68 | 0.81 | 50 | SO4, GOL |
| 2 | 498 | 0.68 | 0.79 | 54 | GOL, SO4 |
| 3 | 54 | 0.33 | 0.78 | 15 | empty |
| 4 | 66 | 0.30 | 0.74 | 18 | empty |
| 5 | 59 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 4816 Ų buried · 81 hydrogen bonds · protein-protein
Compared structures
- 4I56 · HMG-CoA reductase from pseudomonas mevalonii complexed with dithio-HMG-coa · the same entry in another collection · chain A against A, TM-score 1.00
- P13702 · AlphaFold monomer V2.0 prediction for 3-hydroxy-3-methylglutaryl- coenzyme a reductase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P13702
- Elsewhere: RCSB PDB 4I56 · PDBe 4I56 · UniProt P13702
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