MolNFT v1 · #53792 · protein
Structure of an active site mutant of the D-erythrose-4-phosphate dehydrogenase from E. COLI
2X5K: “Structure of an active site mutant of the D-erythrose-4-phosphate dehydrogenase from E. COLI”. X-ray diffraction, 1 ligand (CL), 11 pockets (best druggability 0.74). MolNFT v1 #53792 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2X5K
- Type
- protein
- Length
- 1,342 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
- CL
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 333 | 32% helix, 28% strand | P0A9B6 |
| P | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 338 | 31% helix, 28% strand | P0A9B6 |
| Q | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 337 | 34% helix, 26% strand | P0A9B6 |
| R | D-erythrose-4-phosphate dehydrogenase (EC 1.2.1.72) | protein | 334 | 32% helix, 30% strand | P0A9B6 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains O, R, P, Q
- GOL · Glycerol · additive · 6 copies · chains O, P, R
- EDO · 1,2-ethanediol · additive · 5 copies · chains O, P, Q, R
- PGE · Triethylene glycol · additive · 4 copies · chains O, P, Q
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains P, Q, R
- PG4 · Tetraethylene glycol · additive · chains O, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.74 | 0.84 | 53 | empty |
| 2 | 1009 | 0.74 | 0.77 | 101 | CL |
| 3 | 625 | 0.73 | 0.80 | 64 | empty |
| 4 | 386 | 0.70 | 0.82 | 64 | empty |
| 5 | 392 | 0.68 | 0.81 | 42 | empty |
Interfaces
6 interfaces between chains.
- O–P · 2023 Ų buried · 28 hydrogen bonds · protein-protein
- Q–R · 2021 Ų buried · 30 hydrogen bonds · protein-protein
- P–Q · 1263 Ų buried · 10 hydrogen bonds · protein-protein
- O–R · 1048 Ų buried · 9 hydrogen bonds · protein-protein
- O–Q · 595 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2X5K · Structure of an active site mutant of the D-Erythrose-4-Phosphate Dehydrogenase from E.… · 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 Q 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 2X5K · PDBe 2X5K · UniProt P0A9B6
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