Research workbench
Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-hydroxybenzisoxazole
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
- 5NZP
- 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
- 9EW
- Pockets
- 4 · best druggability 0.42
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
- 9EW · 1,2-benzoxazol-3-ol · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.42 | 0.75 | 31 | 9EW |
| 2 | 135 | 0.40 | 0.75 | 36 | empty |
| 3 | 103 | 0.35 | 0.74 | 23 | empty |
| 4 | 51 | 0.32 | 0.77 | 15 | 9EW |
Interfaces
1 interface between chains.
- B–A · 2568 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 5NZP · 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 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 5NZP · PDBe 5NZP · UniProt O43175
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