Research workbench
Crystal structure of L-lysine dehydrogenase from hyperthermophilic archaeon pyrococcus horikoshii
Analyse Crystal structure of L-lysine dehydrogenase from hyperthermophilic archaeon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ABI
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein PH1688
- EC
- 1.4.1.18
- UniProt
- O59312
- Ligands
- NAD, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein PH1688 (EC 1.4.1.18) | protein | 349 | 39% helix, 28% strand | O59312 |
| B | Putative uncharacterized protein PH1688 (EC 1.4.1.18) | protein | 345 | 38% helix, 28% strand | O59312 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.73 | 0.78 | 81 | NAD |
| 2 | 376 | 0.72 | 0.84 | 55 | SO4, NAD |
| 3 | 134 | 0.48 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 678 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ABI · Crystal Structure of L-Lysine Dehydrogenase from Hyperthermophilic Archaeon Pyrococcus… · 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 O59312
- Elsewhere: RCSB PDB 3ABI · PDBe 3ABI · UniProt O59312
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