Research workbench
The allosteric ligand site in the vmax-type cooperative enzyme phosphoglycerate dehydrogenase
Analyse The allosteric ligand site in the vmax-type cooperative enzyme phosphoglycerate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PSD
- Type
- protein
- Length
- 808 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-3-phosphoglycerate dehydrogenase (phosphoglycerate dehydrogenase)
- EC
- 1.1.1.95
- UniProt
- P0A9T0
- Ligands
- NAD, SER
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-3-phosphoglycerate dehydrogenase (phosphoglycerate dehydrogenase) (EC 1.1.1.95) | protein | 404 | 33% helix, 21% strand | P0A9T0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SER · Serine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.69 | 0.78 | 59 | NAD |
| 2 | 676 | 0.68 | 0.77 | 57 | NAD |
| 3 | 142 | 0.56 | 0.82 | 21 | empty |
| 4 | 162 | 0.55 | 0.80 | 29 | empty |
| 5 | 159 | 0.50 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2702 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 1PSD · The allosteric ligand site in the vmax-type cooperative enzyme phosphoglycerate… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A9T0 · AlphaFold monomer V2.0 prediction for D-3-phosphoglycerate dehydrogenase (P0A9T0) · a predicted model of the same protein · chain B 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 P0A9T0
- Elsewhere: RCSB PDB 1PSD · PDBe 1PSD · UniProt P0A9T0
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