Research workbench
Pksg, a hmg-CoA synthase from bacillus subtilis
Analyse Pksg, a hmg-CoA synthase from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YXQ
- Type
- protein
- Length
- 1,618 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-acp synthase pksg
- EC
- 2.3.3.-
- UniProt
- P40830
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-acp synthase pksg (EC 2.3.3.-) | protein | 407 | 38% helix, 26% strand | P40830 |
| B | Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-acp synthase pksg (EC 2.3.3.-) | protein | 402 | 37% helix, 27% strand | P40830 |
| D | Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-acp synthase pksg (EC 2.3.3.-) | protein | 402 | 37% helix, 26% strand | P40830 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.79 | 0.85 | 55 | empty |
| 2 | 521 | 0.78 | 0.85 | 55 | empty |
| 3 | 423 | 0.76 | 0.85 | 47 | empty |
| 4 | 433 | 0.76 | 0.85 | 49 | empty |
| 5 | 1191 | 0.76 | 0.78 | 87 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3060 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 3052 Ų buried · 60 hydrogen bonds · protein-protein
- A–C · 846 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 249 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 244 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 P40830
- Elsewhere: RCSB PDB 4YXQ · PDBe 4YXQ · UniProt P40830
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