Research workbench
Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with GDD-04-35
Analyse Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VA1
- Type
- protein
- Length
- 765 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.74
- Source
- Homo sapiens
- Molecule
- D-3-phosphoglycerate dehydrogenase
- EC
- 1.1.1.95, 1.1.1.399, 1.1.1.37
- UniProt
- O43175
- Ligands
- 5YP
- Pockets
- 7 · best druggability 0.32
Structure
x-ray diffraction · resolution 1.74 · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 190 | 38% helix, 18% strand | O43175 |
| A | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 193 | 39% helix, 18% strand | O43175 |
| C | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 192 | 38% helix, 18% strand | O43175 |
Ligands and binding sites
- 5YP · 4-[(3-ethanoylphenyl)sulfamoyl]-~{N}-[4-(3-fluorophenyl)-1,3-thiazol-2-yl]benzamide · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.32 | 0.76 | 17 | empty |
| 2 | 52 | 0.32 | 0.77 | 14 | empty |
| 3 | 54 | 0.32 | 0.76 | 13 | empty |
| 4 | 57 | 0.31 | 0.75 | 16 | 5YP |
| 5 | 68 | 0.28 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–A · 2462 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2445 Ų buried · 45 hydrogen bonds · protein-protein
- B–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- O43175 · AlphaFold monomer V2.0 prediction for D-3-phosphoglycerate dehydrogenase (O43175) · a predicted model of the same protein · chain C 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 O43175
- Elsewhere: RCSB PDB 7VA1 · PDBe 7VA1 · UniProt O43175
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