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The crystal structure of type II dehydroquinase from psychromonas ingrahamii 37, crystal form 2
Analyse The crystal structure of type II dehydroquinase from psychromonas ingrahamii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HSU
- Type
- protein
- Length
- 1,802 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- A1SZA3
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 148 | 46% helix, 19% strand | A1SZA3 |
| B, C, H, I | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 150 | 45% helix, 19% strand | A1SZA3 |
| D, G | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 152 | 47% helix, 18% strand | A1SZA3 |
| F, J, K | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 151 | 45% helix, 19% strand | A1SZA3 |
| L | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 149 | 46% helix, 19% strand | A1SZA3 |
Ligands and binding sites
- TLA · L(+)-tartaric acid · additive · 12 copies · chains A, G, B, J, C, D, I, E, K, F, H, L
- GOL · Glycerol · additive · chains B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.71 | 0.88 | 37 | empty |
| 2 | 249 | 0.70 | 0.85 | 40 | empty |
| 3 | 435 | 0.69 | 0.80 | 35 | TLA |
| 4 | 459 | 0.68 | 0.80 | 36 | TLA |
| 5 | 528 | 0.68 | 0.78 | 46 | TLA |
Interfaces
18 interfaces between chains.
- F–K · 873 Ų buried · 19 hydrogen bonds · protein-protein
- C–J · 871 Ų buried · 20 hydrogen bonds · protein-protein
- B–G · 866 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 862 Ų buried · 17 hydrogen bonds · protein-protein
- E–H · 854 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6HSU · The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37, crystal… · the same entry in another collection · chain L against L, TM-score 1.00
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 6HSU · PDBe 6HSU · UniProt A1SZA3
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