MolNFT v1 · #186908 · protein
Dahp synthase complexed with trifluoropyruvate semicarbazone
7RUE · Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive: “Dahp synthase complexed with trifluoropyruvate semicarbazone”. X-ray diffraction, 2 ligands (7QH, MN), 11 pockets (best druggability 0.83). MolNFT v1 #186908 on GenesisL1…
- PDB
- 7RUE
- Type
- protein
- Length
- 1,366 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
- 7QH, MN
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 40% 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 | 339 | 40% helix, 20% strand | P0AB91 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (EC 2.5.1.54) | protein | 345 | 40% helix, 19% strand | P0AB91 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (EC 2.5.1.54) | protein | 340 | 41% helix, 19% strand | P0AB91 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (EC 2.5.1.54) | protein | 342 | 40% helix, 21% strand | P0AB91 |
Ligands and binding sites
- 7QH · (2E)-2-(2-carbamoylhydrazinylidene)-3,3,3-trifluoropropanoic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.83 | 0.86 | 122 | empty |
| 2 | 70 | 0.74 | 0.98 | 16 | empty |
| 3 | 521 | 0.73 | 0.81 | 73 | 7QH |
| 4 | 187 | 0.72 | 0.89 | 38 | empty |
| 5 | 55 | 0.72 | 0.99 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2998 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2800 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 569 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 548 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 56 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7RUE · DAHP synthase complexed with trifluoropyruvate semicarbazone · 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 7RUE · PDBe 7RUE · UniProt P0AB91
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.