MolNFT v1 · #145715 · protein
Crystal structure phgdh in complex with NADH and 3-phosphoglycerate at 1.77 a resolution
6CWA · D-3-phosphoglycerate dehydrogenase: “Crystal structure phgdh in complex with NADH and 3-phosphoglycerate at 1.77 a resolution”. X-ray diffraction, 2 ligands (3PG, NAI), 7 pockets (best druggability 0.66). MolNFT v1 #145715 on…
- PDB
- 6CWA
- Type
- protein
- Length
- 578 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
- 3PG, NAI
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% 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 | 299 | 39% helix, 18% strand | O43175 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 279 | 37% helix, 18% strand | O43175 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · 2 copies · chains A, B
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.66 | 0.82 | 46 | 3PG, NAI |
| 2 | 133 | 0.65 | 0.87 | 30 | empty |
| 3 | 259 | 0.64 | 0.82 | 45 | 3PG, NAI |
| 4 | 68 | 0.47 | 0.83 | 23 | empty |
| 5 | 79 | 0.34 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2565 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 6CWA · Crystal structure phgdh in complex with NADH and 3-phosphoglycerate at 1.77 a resolution · the same entry in another collection · chain A against A, TM-score 1.00
- 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 6CWA · PDBe 6CWA · UniProt O43175
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