MolNFT v1 · #111005 · protein
Crystal structure of oxidized homoserine dehydrogenase of sulfolobus tokodaii
4YDR: “Crystal structure of oxidized homoserine dehydrogenase of sulfolobus tokodaii”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.63). MolNFT v1 #111005 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YDR
- Type
- protein
- Length
- 604 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
- NA
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 304 | 38% helix, 21% strand | F9VNG5 |
| B | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 300 | 38% helix, 22% strand | F9VNG5 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.63 | 0.76 | 59 | empty |
| 2 | 427 | 0.63 | 0.77 | 35 | empty |
| 3 | 289 | 0.53 | 0.75 | 37 | empty |
| 4 | 71 | 0.30 | 0.74 | 21 | empty |
| 5 | 54 | 0.26 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1468 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4YDR · Crystal structure of oxidized homoserine dehydrogenase of Sulfolobus tokodaii · 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 4YDR · PDBe 4YDR · UniProt F9VNG5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.