MolNFT v1 · #55710 · protein
Crystal structure of the 3-dehydroquinate dehydratase from aquifex aeolicus VF5
2YSW: “Crystal structure of the 3-dehydroquinate dehydratase from aquifex aeolicus VF5”. X-ray diffraction, 4 pockets (best druggability 0.60). MolNFT v1 #55710 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YSW
- Type
- protein
- Length
- 657 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- O66440
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 219 | 43% helix, 22% strand | O66440 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.60 | 0.79 | 28 | empty |
| 2 | 262 | 0.59 | 0.79 | 32 | empty |
| 3 | 218 | 0.53 | 0.77 | 25 | empty |
| 4 | 158 | 0.43 | 0.75 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1273 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 193 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2YSW · Crystal Structure of the 3-dehydroquinate dehydratase from Aquifex aeolicus VF5 · the same entry in another collection · chain C against C, TM-score 1.00
- O66440 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (O66440) · a predicted model of the same protein · chain A 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 O66440
- Elsewhere: RCSB PDB 2YSW · PDBe 2YSW · UniProt O66440
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