Research workbench
Homoserine dehydrogenase in complex with suicide inhibitor complex NAD-5-hydroxy-4-oxonorvaline
Analyse Homoserine dehydrogenase in complex with suicide inhibitor complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q7G
- Type
- protein
- Length
- 716 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoserine dehydrogenase
- EC
- 1.1.1.3
- UniProt
- P31116
- Ligands
- NHO, NA
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Homoserine dehydrogenase (EC 1.1.1.3) | protein | 358 | 40% helix, 19% strand | P31116 |
Ligands and binding sites
- NHO · Nicotinamide-adenine-dinucleotide-5-hydroxy-4-oxonorvaline · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.79 | 0.81 | 88 | empty |
| 2 | 342 | 0.60 | 0.78 | 40 | empty |
| 3 | 335 | 0.56 | 0.75 | 44 | NHO |
| 4 | 64 | 0.44 | 0.82 | 14 | empty |
| 5 | 124 | 0.43 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1751 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1Q7G · Homoserine Dehydrogenase in complex with suicide inhibitor complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P31116 · AlphaFold monomer V2.0 prediction for homoserine dehydrogenase (P31116) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P31116
- Elsewhere: RCSB PDB 1Q7G · PDBe 1Q7G · UniProt P31116
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