MolNFT v1 · #178091 · protein
The crystal structure of the immature apo-enzyme of homoserine dehydrogenase from the hyperthermophilic archaeon sulfurisphaera tokodaii.
7F4B: “The crystal structure of the immature apo-enzyme of homoserine dehydrogenase from the hyperthermophilic…”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.68). MolNFT v1 #178091 on GenesisL1: 3D structure, binding…
- PDB
- 7F4B
- Type
- protein
- Length
- 596 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoserine dehydrogenase
- EC
- 1.1.1.3
- Ligands
- MG
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 304 | 38% helix, 22% strand | — |
| B | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 292 | 39% helix, 22% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.68 | 0.81 | 39 | empty |
| 2 | 411 | 0.62 | 0.77 | 50 | empty |
| 3 | 203 | 0.44 | 0.73 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 1452 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7F4B · The crystal structure of the immature apo-enzyme of homoserine dehydrogenase from the… · 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
- Elsewhere: RCSB PDB 7F4B · PDBe 7F4B
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