MolNFT v1 · #49548 · protein
Crystal structure of oxalylglycine-bound saccharopine dehydrogenase (L-lys forming) from saccharomyces cerevisiae
2QRL · Saccharopine dehydrogenase, NAD+, L-lysine-forming: “Crystal structure of oxalylglycine-bound saccharopine dehydrogenase (L-lys forming) from saccharomyces…”. X-ray diffraction, 1 ligand (OGA), 2 pockets (best druggability 0.61).…
- PDB
- 2QRL
- Type
- protein
- Length
- 371 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
- OGA
- Pockets
- 2 · best druggability 0.61
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 | 371 | 38% helix, 13% strand | P38998 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.61 | 0.76 | 49 | OGA |
| 2 | 106 | 0.47 | 0.80 | 24 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2QRL · Crystal Structure of Oxalylglycine-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 0.98
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 2QRL · PDBe 2QRL · UniProt P38998
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