Research workbench
The closed form of serine dehydrogenase complexed with NADP+
Analyse The closed form of serine dehydrogenase complexed with NADP+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ASV
- Type
- protein
- Length
- 1,488 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- Ligands
- NAP, PO4
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 248 | 45% helix, 15% strand | — |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.87 | 0.93 | 43 | empty |
| 2 | 424 | 0.80 | 0.88 | 51 | NAP, PO4 |
| 3 | 513 | 0.79 | 0.86 | 54 | NAP, PO4 |
| 4 | 363 | 0.79 | 0.89 | 50 | NAP, PO4 |
| 5 | 490 | 0.79 | 0.86 | 50 | NAP, PO4 |
Interfaces
10 interfaces between chains.
- C–D · 2067 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2046 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 2035 Ų buried · 38 hydrogen bonds · protein-protein
- C–F · 1446 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1443 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3ASV · The Closed form of serine dehydrogenase complexed with NADP+ · 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
- Elsewhere: RCSB PDB 3ASV · PDBe 3ASV
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