MolNFT v1 · #103419 · protein
Crystal structure of S. aureus homoserine dehydrogenase at PH8.5
4PG8: “Crystal structure of S. aureus homoserine dehydrogenase at PH8.5”. X-ray diffraction, 7 pockets (best druggability 0.78). MolNFT v1 #103419 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PG8
- Type
- protein
- Length
- 787 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
- 7 · 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 | 399 | 38% helix, 27% strand | N6FDB4 |
| B | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 388 | 35% helix, 27% strand | N6FDB4 |
Ligands and binding sites
- ACT · Acetate ion · additive · 16 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains B
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.78 | 0.80 | 114 | empty |
| 2 | 556 | 0.60 | 0.73 | 74 | ACT |
| 3 | 194 | 0.44 | 0.74 | 29 | ACT |
| 4 | 76 | 0.35 | 0.76 | 20 | empty |
| 5 | 73 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1134 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4PG8 · Crystal structure of S. aureus Homoserine Dehydrogenase at pH8.5 · 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 4PG8 · PDBe 4PG8 · UniProt N6FDB4
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