Research workbench
DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase complexed with Mn(II), PEP, and Pi in unbound:(bound)2:other Conformations
Analyse DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8E0X
- Type
- protein
- Length
- 1,371 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.97
- Source
- Escherichia coli K-12
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
- EC
- 2.5.1.54
- UniProt
- P0AB91
- Ligands
- PEP, MN, PO4
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · resolution 1.97 · 4 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive (EC 2.5.1.54) | protein | 344 | 39% helix, 18% strand | P0AB91 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive (EC 2.5.1.54) | protein | 345 | 40% helix, 17% strand | P0AB91 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive (EC 2.5.1.54) | protein | 341 | 39% helix, 19% strand | P0AB91 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive (EC 2.5.1.54) | protein | 341 | 40% helix, 18% strand | P0AB91 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.82 | 0.91 | 53 | empty |
| 2 | 192 | 0.81 | 0.95 | 40 | empty |
| 3 | 111 | 0.76 | 0.96 | 28 | empty |
| 4 | 389 | 0.75 | 0.86 | 53 | empty |
| 5 | 66 | 0.71 | 0.97 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3253 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2744 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 585 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 581 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 88 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 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 8E0X · PDBe 8E0X · UniProt P0AB91
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