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Crystal structure of the apoform of the D-erythrose-4-phosphate dehydrogenase from E. COLI
Analyse Crystal structure of the apoform of the D-erythrose-4-phosphate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X5J
- Type
- protein
- Length
- 1,310 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-erythrose-4-phosphate dehydrogenase
- EC
- 1.2.1.72
- UniProt
- P0A9B6
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 324 | 32% helix, 28% strand | P0A9B6 |
| P | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 328 | 32% helix, 28% strand | P0A9B6 |
| Q | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 328 | 32% helix, 29% strand | P0A9B6 |
| R | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 330 | 34% helix, 28% strand | P0A9B6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains O, P, Q, R
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 | 1179 | 0.76 | 0.79 | 113 | PO4 |
| 2 | 626 | 0.74 | 0.81 | 92 | PO4 |
| 3 | 837 | 0.71 | 0.77 | 80 | PO4 |
| 4 | 374 | 0.59 | 0.76 | 41 | PO4 |
| 5 | 50 | 0.36 | 0.80 | 18 | empty |
Interfaces
6 interfaces between chains.
- O–P · 2050 Ų buried · 34 hydrogen bonds · protein-protein
- Q–R · 2048 Ų buried · 27 hydrogen bonds · protein-protein
- O–R · 820 Ų buried · 5 hydrogen bonds · protein-protein
- P–Q · 730 Ų buried · 2 hydrogen bonds · protein-protein
- O–Q · 623 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2X5J · Crystal structure of the Apoform of the D-Erythrose-4-phosphate dehydrogenase from E. coli · the same entry in another collection · chain R against R, TM-score 1.00
- P0A9B6 · AlphaFold monomer V2.0 prediction for D-erythrose-4-phosphate dehydrogenase (P0A9B6) · a predicted model of the same protein · chain O 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 P0A9B6
- Elsewhere: RCSB PDB 2X5J · PDBe 2X5J · UniProt P0A9B6
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