MolNFT v1 · #15558 · protein
Crystal structure of E24Q mutant of phenylalanine-regulated 3-deoxy-D- arabino-heptulosonate-7-phosphate synthase (dahp synthase) from escherichia COLI in complex with MN2+ and pep
1N8F · Dahp synthetase: “Crystal structure of E24Q mutant of phenylalanine-regulated 3-deoxy-D- arabino-heptulosonate-7-phosphate…”. X-ray diffraction, 3 ligands (PEP, MN, SO4), 14 pockets (best druggability 0.85). MolNFT v1 #15558 on…
- PDB
- 1N8F
- Type
- protein
- Length
- 1,372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dahp synthetase
- EC
- 4.1.2.15
- UniProt
- P0AB91
- Ligands
- PEP, MN, SO4
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dahp synthetase (EC 4.1.2.15) | protein | 343 | 39% helix, 18% strand | P0AB91 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.85 | 0.85 | 139 | empty |
| 2 | 50 | 0.71 | 0.99 | 17 | empty |
| 3 | 51 | 0.70 | 0.98 | 16 | empty |
| 4 | 268 | 0.69 | 0.85 | 49 | SO4, PEP |
| 5 | 279 | 0.68 | 0.84 | 52 | SO4, PEP |
Interfaces
6 interfaces between chains.
- C–D · 2819 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2804 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 577 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 568 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 56 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1N8F · Crystal structure of E24Q mutant of phenylalanine-regulated… · the same entry in another collection · chain D against D, TM-score 1.00
- P0AB91 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase… · 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 P0AB91
- Elsewhere: RCSB PDB 1N8F · PDBe 1N8F · UniProt P0AB91
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