Research workbench
Crystal structure of phenylalanine-regulated 3-deoxy-D- arabino-heptulosonate-7-phosphate synthase from escherichia COLI complexed with PB2+ and pep
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
- 1QR7
- Type
- protein
- Length
- 1,353 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine-regulated 3-deoxy-D-arabino- heptulosonate-7-phosphate synthase
- EC
- 4.1.2.15
- UniProt
- P0AB91
- Ligands
- PEP, PB, SO4
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Phenylalanine-regulated 3-deoxy-D-arabino- heptulosonate-7-phosphate synthase (EC 4.1.2.15) | protein | 338 | 40% helix, 19% strand | P0AB91 |
| D | Phenylalanine-regulated 3-deoxy-D-arabino- heptulosonate-7-phosphate synthase (EC 4.1.2.15) | protein | 339 | 40% helix, 19% strand | P0AB91 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- PB · Lead (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.78 | 0.81 | 90 | empty |
| 2 | 51 | 0.71 | 0.98 | 16 | empty |
| 3 | 119 | 0.60 | 0.86 | 24 | PB, SO4, PEP |
| 4 | 162 | 0.59 | 0.83 | 23 | empty |
| 5 | 152 | 0.59 | 0.83 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2881 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2854 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 571 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 546 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 57 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1QR7 · Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate… · 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 D 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 1QR7 · PDBe 1QR7 · UniProt P0AB91
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