MolNFT v1 · #77634 · protein
Substrate fingerprint and the structure of NADP+ dependent serine dehydrogenase from saccharomyces cerevisiae complexed with NADP+
3RKU · Oxidoreductase YMR226C: “Substrate fingerprint and the structure of NADP+ dependent serine dehydrogenase from saccharomyces cerevisiae…”. X-ray diffraction, 1 ligand (NAP), 14 pockets (best druggability 0.84). MolNFT v1 #77634 on…
- PDB
- 3RKU
- Type
- protein
- Length
- 1,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase YMR226C
- EC
- 1.-.-.-
- UniProt
- Q05016
- Ligands
- NAP
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Oxidoreductase YMR226C (EC 1.-.-.-) | protein | 268 | 46% helix, 19% strand | Q05016 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.84 | 0.85 | 92 | empty |
| 2 | 464 | 0.78 | 0.86 | 53 | NAP |
| 3 | 474 | 0.78 | 0.86 | 52 | NAP |
| 4 | 477 | 0.78 | 0.86 | 54 | NAP |
| 5 | 447 | 0.77 | 0.86 | 55 | NAP |
Interfaces
6 interfaces between chains.
- A–C · 1692 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1691 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1432 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1416 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 156 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3RKU · Substrate Fingerprint and the Structure of NADP+ Dependent Serine Dehydrogenase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05016 · AlphaFold monomer V2.0 prediction for NADP-dependent 3-hydroxy acid dehydrogenase (Q05016) · 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 Q05016
- Elsewhere: RCSB PDB 3RKU · PDBe 3RKU · UniProt Q05016
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