MolNFT v1 · #81854 · protein
The biochemical and structural basis for inhibition of enterococcus faecalis hmg-CoA synthase, mvas, by hymeglusin
3V4X: “The biochemical and structural basis for inhibition of enterococcus faecalis hmg-CoA synthase, mvas, by…”. X-ray diffraction, 1 ligand (F24), 14 pockets (best druggability 0.77). MolNFT v1 #81854 on GenesisL1: 3D structure, binding…
- PDB
- 3V4X
- Type
- protein
- Length
- 1,545 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hmg-CoA synthase
- EC
- 2.3.3.10
- UniProt
- Q9FD71
- Ligands
- F24
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hmg-CoA synthase (EC 2.3.3.10) | protein | 387 | 39% helix, 25% strand | Q9FD71 |
| B, C, D | Hmg-CoA synthase (EC 2.3.3.10) | protein | 386 | 40% helix, 25% strand | Q9FD71 |
Ligands and binding sites
- F24 · (7R,12R,13R)-13-formyl-12,14-dihydroxy-3,5,7-trimethyltetradeca-2,4-dienoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.77 | 0.84 | 56 | empty |
| 2 | 370 | 0.75 | 0.85 | 34 | empty |
| 3 | 396 | 0.74 | 0.84 | 39 | empty |
| 4 | 485 | 0.69 | 0.80 | 42 | empty |
| 5 | 443 | 0.69 | 0.80 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2956 Ų buried · 63 hydrogen bonds · protein-protein
- B–D · 446 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 225 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3V4X · The Biochemical and Structural Basis for Inhibition of Enterococcus faecalis HMG-CoA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9FD71 · AlphaFold monomer V2.0 prediction for hydroxymethylglutaryl-CoA synthase (Q9FD71) · a predicted model of the same protein · chain B 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 Q9FD71
- Elsewhere: RCSB PDB 3V4X · PDBe 3V4X · UniProt Q9FD71
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