MolNFT v1 · #103416 · protein
Crystal structure of S. aureus homoserine dehydrogenase at PH6.5
4PG5: “Crystal structure of S. aureus homoserine dehydrogenase at PH6.5”. X-ray diffraction, 6 pockets (best druggability 0.78). MolNFT v1 #103416 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PG5
- Type
- protein
- Length
- 791 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
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 395 | 37% helix, 28% strand | N6FDB4 |
| B | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 396 | 35% helix, 27% strand | N6FDB4 |
Ligands and binding sites
- ACT · Acetate ion · additive · 11 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.78 | 0.80 | 107 | ACT |
| 2 | 779 | 0.67 | 0.75 | 102 | ACT |
| 3 | 415 | 0.65 | 0.78 | 63 | DMS |
| 4 | 67 | 0.37 | 0.78 | 19 | empty |
| 5 | 85 | 0.34 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1193 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4PG5 · Crystal structure of S. aureus Homoserine Dehydrogenase at pH6.5 · 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 4PG5 · PDBe 4PG5 · UniProt N6FDB4
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