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The biochemical and structural basis for inhibition of enterococcus faecalis hmg-CoA synthatse, mvas, by hymeglusin
Analyse The biochemical and structural basis for inhibition of enterococcus faecalis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V4N
- Type
- protein
- Length
- 1,537 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
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 39% 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 | Hmg-CoA synthase (EC 2.3.3.10) | protein | 384 | 39% helix, 25% strand | Q9FD71 |
| C, D | Hmg-CoA synthase (EC 2.3.3.10) | protein | 383 | 39% helix, 25% strand | Q9FD71 |
Ligands and binding sites
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.76 | 0.84 | 51 | empty |
| 2 | 431 | 0.73 | 0.83 | 36 | empty |
| 3 | 614 | 0.70 | 0.78 | 52 | empty |
| 4 | 484 | 0.69 | 0.79 | 45 | empty |
| 5 | 472 | 0.67 | 0.79 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2889 Ų buried · 67 hydrogen bonds · protein-protein
- B–D · 679 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 195 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 63 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 3V4N · 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 C 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 Q9FD71
- Elsewhere: RCSB PDB 3V4N · PDBe 3V4N · UniProt Q9FD71
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