MolNFT v1 · #127768 · protein
Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with NAD and L-tartrate
5N6C · D-3-phosphoglycerate dehydrogenase: “Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with NAD and L-tartrate”. X-ray diffraction, 1 ligand (NAD), 4 pockets (best druggability 0.66). MolNFT v1 #127768 on…
- PDB
- 5N6C
- Type
- protein
- Length
- 599 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
- UniProt
- O43175
- Ligands
- NAD
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 300 | 40% helix, 18% strand | O43175 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 299 | 40% helix, 18% strand | O43175 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 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 | 434 | 0.66 | 0.79 | 55 | NAD |
| 2 | 295 | 0.64 | 0.81 | 48 | TLA, NAD |
| 3 | 196 | 0.48 | 0.76 | 33 | empty |
| 4 | 99 | 0.37 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2560 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 5N6C · Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with NAD and… · 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 5N6C · PDBe 5N6C · UniProt O43175
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