Research workbench
The crystal structure of type II dehydroquinase from psychromonas ingrahamii 37 crystal form 1
Analyse The crystal structure of type II dehydroquinase from psychromonas ingrahamii 37… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HSQ
- Type
- protein
- Length
- 600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- A1SZA3
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 148 | 46% helix, 19% strand | A1SZA3 |
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 151 | 46% helix, 19% strand | A1SZA3 |
| C | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 149 | 46% helix, 19% strand | A1SZA3 |
| D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 152 | 44% helix, 18% strand | A1SZA3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.70 | 0.86 | 40 | empty |
| 2 | 490 | 0.67 | 0.78 | 40 | SO4, GOL |
| 3 | 370 | 0.66 | 0.80 | 29 | SO4, GOL |
| 4 | 354 | 0.66 | 0.80 | 29 | SO4, GOL |
| 5 | 127 | 0.55 | 0.82 | 34 | empty |
Interfaces
4 interfaces between chains.
- B–D · 838 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 776 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 771 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 759 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6HSQ · The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37 crystal… · the same entry in another collection · chain D against D, TM-score 1.00
- A1SZA3 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (A1SZA3) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 A1SZA3
- Elsewhere: RCSB PDB 6HSQ · PDBe 6HSQ · UniProt A1SZA3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.