Research workbench
Crystal structure of S. aureus homoserine dehydrogenase at PH6.0
Analyse Crystal structure of S. aureus homoserine dehydrogenase at PH6.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PG4
- Type
- protein
- Length
- 777 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoserine dehydrogenase
- EC
- 1.1.1.3
- UniProt
- N6FDB4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 394 | 37% helix, 28% strand | N6FDB4 |
| B | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 383 | 37% helix, 28% strand | N6FDB4 |
Ligands and binding sites
- ACT · Acetate ion · additive · 17 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.73 | 0.76 | 131 | empty |
| 2 | 883 | 0.69 | 0.75 | 98 | ACT |
| 3 | 139 | 0.47 | 0.78 | 34 | DMS |
| 4 | 50 | 0.34 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 973 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4PG4 · Crystal structure of S. aureus Homoserine Dehydrogenase at pH6.0 · the same entry in another collection · chain A 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 N6FDB4
- Elsewhere: RCSB PDB 4PG4 · PDBe 4PG4 · UniProt N6FDB4
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