Research workbench
Crystal structure of serine bound G336V mutant of E.COLI phosphoglycerate dehydrogenase
Analyse Crystal structure of serine bound G336V mutant of E.COLI phosphoglycerate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P9C
- Type
- protein
- Length
- 810 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
- P0A9T0
- Ligands
- NAI, SER
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 405 | 34% helix, 21% strand | P0A9T0 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- SER · Serine · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.72 | 0.79 | 69 | NAI |
| 2 | 620 | 0.70 | 0.78 | 60 | NAI |
| 3 | 187 | 0.55 | 0.79 | 34 | empty |
| 4 | 143 | 0.51 | 0.79 | 32 | empty |
| 5 | 82 | 0.44 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2725 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 2P9C · Crystal structure of serine bound G336V mutant of E.coli phosphoglycerate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- P0A9T0 · AlphaFold monomer V2.0 prediction for D-3-phosphoglycerate dehydrogenase (P0A9T0) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0A9T0
- Elsewhere: RCSB PDB 2P9C · PDBe 2P9C · UniProt P0A9T0
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