Research workbench
Crystal structure of human PHGDH in complex with Homoharringtonine
Analyse Crystal structure of human PHGDH in complex with Homoharringtonine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EWH
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.99
- Source
- Homo sapiens
- Molecule
- D-3-phosphoglycerate dehydrogenase
- EC
- 1.1.1.95, 1.1.1.399, 1.1.1.37
- UniProt
- O43175
- Ligands
- HMT
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.99 · 1 distinct chain · 28% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 302 | 28% helix, 16% strand | O43175 |
Ligands and binding sites
- HMT · (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.73 | 0.90 | 41 | empty |
| 2 | 267 | 0.66 | 0.83 | 43 | empty |
| 3 | 263 | 0.60 | 0.79 | 35 | HMT |
| 4 | 264 | 0.60 | 0.79 | 37 | HMT |
| 5 | 62 | 0.47 | 0.85 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2603 Ų buried · 35 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 A 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 7EWH · PDBe 7EWH · UniProt O43175
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.