Research workbench
Crystal structure of AMP-bound saccharopine dehydrogenase (L-lys forming) from saccharomyces cerevisiae
Analyse Crystal structure of AMP-bound saccharopine dehydrogenase (L-lys forming) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QRK
- Type
- protein
- Length
- 365 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saccharopine dehydrogenase [NAD+, L-lysine-forming
- EC
- 1.5.1.7
- UniProt
- P38998
- Ligands
- AMP
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Saccharopine dehydrogenase [NAD+, L-lysine-forming (EC 1.5.1.7) | protein | 365 | 38% helix, 13% strand | P38998 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.64 | 0.75 | 39 | empty |
| 2 | 59 | 0.34 | 0.77 | 16 | empty |
| 3 | 58 | 0.32 | 0.76 | 17 | AMP |
Compared structures
- 2QRK · Crystal Structure of AMP-bound Saccharopine Dehydrogenase (L-Lys Forming) from… · the same entry in another collection · chain A against A, TM-score 1.00
- P38998 · AlphaFold monomer V2.0 prediction for saccharopine dehydrogenase [NAD(+)… · 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 P38998
- Elsewhere: RCSB PDB 2QRK · PDBe 2QRK · UniProt P38998
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