MolNFT v1 · #16323 · protein
Crystal structure of 3-dehydroquinate synthase (dhqs) in complex with ZN2+, ADP and carbaphosphonate
1NVF: “Crystal structure of 3-dehydroquinate synthase (dhqs) in complex with ZN2+, ADP and carbaphosphonate”. X-ray diffraction, 4 ligands (ADP, CRB, ZN), 8 pockets (best druggability 0.78). MolNFT v1 #16323 on GenesisL1: 3D structure…
- PDB
- 1NVF
- Type
- protein
- Length
- 1,164 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate synthase
- EC
- 4.2.3.4
- UniProt
- P07547
- Ligands
- ADP, CRB, ZN, CL
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 388 | 50% helix, 18% strand | P07547 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- CRB · [1R-(1alpha,3beta,4alpha,5beta)]-5-(phosphonomethyl)-1,3,4-trihydroxycyclohexane-1-carboxylic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.78 | 0.84 | 70 | ZN, ADP, CRB |
| 2 | 448 | 0.77 | 0.85 | 54 | ADP, CRB |
| 3 | 596 | 0.75 | 0.82 | 57 | ADP, CRB |
| 4 | 82 | 0.63 | 0.90 | 17 | CL |
| 5 | 168 | 0.48 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1673 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1NVF · Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, ADP and… · the same entry in another collection · chain A against A, TM-score 1.00
- P07547 · AlphaFold monomer V2.0 prediction for pentafunctional arom polypeptide (P07547) · 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 P07547
- Elsewhere: RCSB PDB 1NVF · PDBe 1NVF · UniProt P07547
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