Research workbench
Thermotoga maritima DAH7P synthase in complex with inhibitor
Analyse Thermotoga maritima DAH7P synthase in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PG9
- Type
- protein
- Length
- 2,704 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase
- EC
- 2.5.1.54
- UniProt
- Q9WYH8
- Ligands
- TYR, NO3, AZI, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 338 | 37% helix, 21% strand | Q9WYH8 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 8 copies · chains A, F, B, G, C, E, D, H
- NO3 · Nitrate ion · ion · 4 copies · chains A, B, F, G, C, D, E, H
- AZI · Azide ion · ion · 2 copies · chains A, B, G
- CL · Chloride ion · ion · chains B
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 | 705 | 0.79 | 0.84 | 85 | empty |
| 2 | 466 | 0.79 | 0.87 | 73 | empty |
| 3 | 606 | 0.78 | 0.84 | 62 | CL |
| 4 | 89 | 0.77 | 0.98 | 20 | NO3 |
| 5 | 760 | 0.77 | 0.81 | 64 | empty |
Interfaces
14 interfaces between chains.
- B–F · 1880 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1846 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 1511 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1403 Ų buried · 8 hydrogen bonds · protein-protein
- E–H · 1379 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3PG9 · Thermotoga maritima DAH7P synthase in complex with inhibitor · the same entry in another collection · chain C against C, TM-score 1.00
- Q9WYH8 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase (Q9WYH8) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q9WYH8
- Elsewhere: RCSB PDB 3PG9 · PDBe 3PG9 · UniProt Q9WYH8
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