MolNFT v1 · #60226 · protein
Crystal structure of 3-dehydroquinate synthase (DHQS)FROM helicobacter pylori
3CLH: “Crystal structure of 3-dehydroquinate synthase (DHQS)FROM helicobacter pylori”. X-ray diffraction, 2 ligands (NAD, ZN), 6 pockets (best druggability 0.74). MolNFT v1 #60226 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3CLH
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate synthase
- EC
- 4.2.3.4
- UniProt
- P56081
- Ligands
- NAD, ZN
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 308 | 45% helix, 19% strand | P56081 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.74 | 0.78 | 65 | ZN, NAD |
| 2 | 824 | 0.74 | 0.79 | 58 | ZN, NAD |
| 3 | 191 | 0.68 | 0.85 | 30 | empty |
| 4 | 92 | 0.36 | 0.74 | 18 | empty |
| 5 | 60 | 0.31 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1013 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3CLH · Crystal structure of 3-dehydroquinate synthase (DHQS)from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
- P56081 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate synthase (P56081) · a predicted model of the same protein · chain B 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 P56081
- Elsewhere: RCSB PDB 3CLH · PDBe 3CLH · UniProt P56081
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