MolNFT v1 · #151605 · protein
The crystal structure of type II dehydroquinase from psychromonas ingrahamii 37, 40% ethanol as cryoprotectant
6HSR · 3-dehydroquinate dehydratase: “The crystal structure of type II dehydroquinase from psychromonas ingrahamii 37, 40% ethanol as cryoprotectant”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.66). MolNFT v1 #151605…
- PDB
- 6HSR
- 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 0.66
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 148 | 49% 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 | 48% helix, 19% strand | A1SZA3 |
| D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 152 | 47% helix, 18% strand | A1SZA3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- EOH · Ethanol · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.66 | 0.79 | 32 | EOH, SO4 |
| 2 | 474 | 0.66 | 0.78 | 39 | EOH, SO4 |
| 3 | 368 | 0.64 | 0.79 | 32 | EOH, SO4 |
| 4 | 144 | 0.61 | 0.84 | 30 | empty |
| 5 | 136 | 0.50 | 0.79 | 23 | empty |
Interfaces
4 interfaces between chains.
- B–D · 839 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 755 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 755 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 748 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6HSR · The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37, 40%… · 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 0.95
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 6HSR · PDBe 6HSR · UniProt A1SZA3
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