MolNFT v1 · #178092 · protein
The crystal structure of the immature holo-enzyme of homoserine dehydrogenase complexed with NADP and 1,4-butandiol from the hyperthermophilic archaeon sulfurisphaera tokodaii.
7F4C: “The crystal structure of the immature holo-enzyme of homoserine dehydrogenase complexed with NADP and…”. X-ray diffraction, 1 ligand (NAP), 3 pockets (best druggability 0.69). MolNFT v1 #178092 on GenesisL1: 3D structure, binding…
- PDB
- 7F4C
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoserine dehydrogenase
- EC
- 1.1.1.3
- UniProt
- F9VNG5
- Ligands
- NAP
- Pockets
- 3 · best druggability 0.69
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 | 300 | 39% helix, 22% strand | F9VNG5 |
| B | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 287 | 38% helix, 22% strand | F9VNG5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- BU1 · 1,4-butanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.69 | 0.82 | 52 | NAP, BU1 |
| 2 | 354 | 0.68 | 0.82 | 50 | NAP, BU1 |
| 3 | 445 | 0.60 | 0.75 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 1516 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7F4C · The crystal structure of the immature holo-enzyme of homoserine dehydrogenase complexed… · 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 F9VNG5
- Elsewhere: RCSB PDB 7F4C · PDBe 7F4C · UniProt F9VNG5
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