Research workbench
Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 1-methyl-3-phenyl-1H-pyrazol-5-amine
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
- 5NZO
- Type
- protein
- Length
- 390 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-3-phosphoglycerate dehydrogenase
- EC
- 1.1.1.95, 1.1.1.399, 1.1.1.37
- UniProt
- O43175
- Ligands
- 9EZ
- Pockets
- 5 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 195 | 38% helix, 17% strand | O43175 |
Ligands and binding sites
- 9EZ · 2-methyl-5-phenyl-pyrazol-3-amine · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.38 | 0.75 | 23 | empty |
| 2 | 87 | 0.36 | 0.76 | 28 | empty |
| 3 | 84 | 0.35 | 0.76 | 23 | empty |
| 4 | 65 | 0.32 | 0.75 | 17 | 9EZ |
| 5 | 56 | 0.28 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 2552 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 5NZO · Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- O43175 · AlphaFold monomer V2.0 prediction for D-3-phosphoglycerate dehydrogenase (O43175) · a predicted model of the same protein · chain B 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
- Every structure of UniProt O43175
- Elsewhere: RCSB PDB 5NZO · PDBe 5NZO · UniProt O43175
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