MolNFT v1 · #18674 · protein
Rat liver L-serine dehydratase- complex with pyridoxyl-(O-methyl- serine)-5-monophosphate
1PWH: “Rat liver L-serine dehydratase- complex with pyridoxyl-(O-methyl- serine)-5-monophosphate”. X-ray diffraction, 2 ligands (PLV, K), 20 pockets (best druggability 0.79). MolNFT v1 #18674 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1PWH
- Type
- protein
- Length
- 1,308 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-serine dehydratase
- EC
- 4.3.1.17
- UniProt
- P09367
- Ligands
- PLV, K
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-serine dehydratase (EC 4.3.1.17) | protein | 327 | 45% helix, 15% strand | P09367 |
Ligands and binding sites
- PLV · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-O-methyl-L-serine · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.79 | 0.98 | 34 | PLV |
| 2 | 96 | 0.78 | 0.98 | 30 | PLV |
| 3 | 134 | 0.77 | 0.95 | 42 | PLV |
| 4 | 107 | 0.77 | 0.97 | 33 | PLV |
| 5 | 741 | 0.74 | 0.79 | 95 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1416 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1301 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1271 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1PWH · Rat Liver L-Serine Dehydratase- Complex with PYRIDOXYL-(O-METHYL-SERINE)-5-MONOPHOSPHATE · the same entry in another collection · chain C against C, TM-score 1.00
- P09367 · AlphaFold monomer V2.0 prediction for L-serine DEHYDRATASE/L-threonine deaminase (P09367) · a predicted model of the same protein · chain C 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 P09367
- Elsewhere: RCSB PDB 1PWH · PDBe 1PWH · UniProt P09367
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