Research workbench
Dahp synthase complex with trifluoropyruvate oxime
Analyse Dahp synthase complex with trifluoropyruvate oxime in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RUD
- Type
- protein
- Length
- 1,369 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive
- EC
- 2.5.1.54
- UniProt
- P0AB91
- Ligands
- 7QE
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (EC 2.5.1.54) | protein | 341 | 40% helix, 20% strand | P0AB91 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (EC 2.5.1.54) | protein | 343 | 40% helix, 18% strand | P0AB91 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (EC 2.5.1.54) | protein | 343 | 38% helix, 20% strand | P0AB91 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (EC 2.5.1.54) | protein | 342 | 39% helix, 19% strand | P0AB91 |
Ligands and binding sites
- 7QE · (2Z)-3,3,3-trifluoro-2-(hydroxyimino)propanoic acid · ligand · 3 copies · chains 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.83 | 0.86 | 106 | empty |
| 2 | 63 | 0.73 | 0.99 | 18 | empty |
| 3 | 54 | 0.70 | 0.97 | 16 | empty |
| 4 | 50 | 0.69 | 0.98 | 17 | empty |
| 5 | 398 | 0.68 | 0.81 | 57 | 7QE |
Interfaces
6 interfaces between chains.
- A–B · 2994 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2862 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 577 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 566 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 63 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 7RUD · PDBe 7RUD · UniProt P0AB91
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