Research workbench
The active form of phosphoglycerate dehydrogenase
Analyse The active form of phosphoglycerate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YBA
- Type
- protein
- Length
- 1,624 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-3-phosphoglycerate dehydrogenase
- EC
- 1.1.1.95
- UniProt
- P08328
- Ligands
- UNL, AKG, NAD, PO4
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 406 | 34% helix, 21% strand | P08328 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 7 copies · chains A, B, C, D
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.70 | 0.78 | 67 | AKG, NAD, PO4 |
| 2 | 619 | 0.70 | 0.78 | 70 | PO4, AKG, NAD |
| 3 | 635 | 0.70 | 0.78 | 68 | AKG, NAD, PO4 |
| 4 | 587 | 0.68 | 0.77 | 65 | PO4, AKG, NAD |
| 5 | 65 | 0.56 | 0.88 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2767 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2724 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 824 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 742 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 1YBA · The active form of phosphoglycerate dehydrogenase · the same entry in another collection · chain D against D, 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
- Every structure of UniProt P08328
- Elsewhere: RCSB PDB 1YBA · PDBe 1YBA · UniProt P08328
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