MolNFT v1 · #175594 · protein
The crystal structure of human phgdh from biortus.
7CVP · D-3-phosphoglycerate dehydrogenase: “The crystal structure of human phgdh from biortus.”. X-ray diffraction, 1 ligand (NAD), 4 pockets (best druggability 0.66). MolNFT v1 #175594 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7CVP
- Type
- protein
- Length
- 496 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
- NAD
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 254 | 38% helix, 19% strand | O43175 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 242 | 38% helix, 14% strand | O43175 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.66 | 0.79 | 69 | NAD |
| 2 | 483 | 0.66 | 0.78 | 62 | NAD |
| 3 | 53 | 0.26 | 0.74 | 15 | empty |
| 4 | 53 | 0.26 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2525 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
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 7CVP · PDBe 7CVP · UniProt O43175
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