Research workbench
Crystal structure of G336V mutant of E.COLI phosphoglycerate dehydrogenase
Analyse Crystal structure of G336V mutant of E.COLI phosphoglycerate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P9E
- Type
- protein
- Length
- 1,619 residues
- Chains
- 4
- 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, PO4, SO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 406 | 33% helix, 20% strand | P0A9T0 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 404 | 34% helix, 20% strand | P0A9T0 |
| D | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 403 | 34% helix, 21% strand | P0A9T0 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains C
- CIT · Citric acid · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.71 | 0.78 | 71 | NAI, PO4 |
| 2 | 669 | 0.71 | 0.78 | 63 | PO4, NAI, CIT |
| 3 | 628 | 0.70 | 0.79 | 66 | PO4, NAI, CIT |
| 4 | 600 | 0.69 | 0.78 | 61 | PO4, NAI |
| 5 | 65 | 0.55 | 0.88 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2716 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2714 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 773 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 715 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 52 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2P9E · Crystal Structure of 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 B against A, TM-score 0.97
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 2P9E · PDBe 2P9E · UniProt P0A9T0
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