Research workbench
Hyperthermophilic archaeal homoserine dehydrogenase in complex with NADPH
Analyse Hyperthermophilic archaeal homoserine dehydrogenase in complex with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XB1
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 319AA long hypothetical homoserine dehydrogenase
- UniProt
- O58802
- Ligands
- NDP, NA
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 319AA long hypothetical homoserine dehydrogenase | protein | 319 | 40% helix, 24% strand | O58802 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.64 | 0.77 | 56 | NDP, MPD |
| 2 | 501 | 0.63 | 0.76 | 56 | NDP, MPD |
| 3 | 134 | 0.43 | 0.76 | 17 | empty |
| 4 | 76 | 0.32 | 0.74 | 16 | empty |
| 5 | 62 | 0.31 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1642 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4XB1 · Hyperthermophilic archaeal homoserine dehydrogenase in complex with NADPH · 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 O58802
- Elsewhere: RCSB PDB 4XB1 · PDBe 4XB1 · UniProt O58802
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