Research workbench
Crystal structure of phenylalanine-regulated 3-deoxy-D- arabino-heptulosonate-7-phosphate synthase (dahp synthase) from E.COLI complexed with MN2+, pep, and phe
Analyse Crystal structure of phenylalanine-regulated 3-deoxy-D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KFL
- Type
- protein
- Length
- 2,800 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
- EC
- 4.1.2.15
- UniProt
- P00886
- Ligands
- PHE, PEP, MN, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (EC 4.1.2.15) | protein | 350 | 41% helix, 18% strand | P00886 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PEP · Phosphoenolpyruvate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.80 | 0.98 | 34 | empty |
| 2 | 118 | 0.79 | 0.98 | 27 | empty |
| 3 | 560 | 0.79 | 0.85 | 90 | PEP |
| 4 | 564 | 0.79 | 0.85 | 89 | PEP |
| 5 | 345 | 0.78 | 0.88 | 52 | PEP |
Interfaces
13 interfaces between chains.
- G–H · 3654 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 3602 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 3573 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 3558 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 522 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified (engineered).
Compared structures
- 1KFL · Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
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 P00886
- Elsewhere: RCSB PDB 1KFL · PDBe 1KFL · UniProt P00886
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