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1.65 ångström resolution crystal structure of type II 3-dehydroquinate dehydratase (aroq) from yersinia pestis
Analyse 1.65 ångström resolution crystal structure of type II 3-dehydroquinate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LWZ
- Type
- protein
- Length
- 586 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
- Q8ZAX1
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 146 | 50% helix, 19% strand | Q8ZAX1 |
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 145 | 47% helix, 19% strand | Q8ZAX1 |
| C | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 148 | 46% helix, 18% strand | Q8ZAX1 |
| D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 147 | 45% helix, 18% strand | Q8ZAX1 |
Ligands and binding sites
- GOL · Glycerol · additive · 17 copies · chains A, D, B, C
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · chains 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 | 105 | 0.76 | 0.96 | 29 | BME, GOL |
| 2 | 334 | 0.71 | 0.84 | 28 | GOL |
| 3 | 355 | 0.71 | 0.83 | 29 | GOL |
| 4 | 404 | 0.70 | 0.81 | 33 | GOL |
| 5 | 178 | 0.61 | 0.83 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–D · 848 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 728 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 712 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 711 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 3LWZ · 1.65 Angstrom Resolution Crystal Structure of Type II 3-Dehydroquinate Dehydratase (aroQ)… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8ZAX1 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (Q8ZAX1) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8ZAX1
- Elsewhere: RCSB PDB 3LWZ · PDBe 3LWZ · UniProt Q8ZAX1
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