MolNFT v1 · #16321 · protein
Crystal structure of 3-dehydroquinate synthase (dhqs) in complex with ZN2+ and carbaphosphonate
1NVD: “Crystal structure of 3-dehydroquinate synthase (dhqs) in complex with ZN2+ and carbaphosphonate”. X-ray diffraction, 3 ligands (CRB, ZN, CL), 6 pockets (best druggability 0.80). MolNFT v1 #16321 on GenesisL1: 3D structure, binding…
- PDB
- 1NVD
- Type
- protein
- Length
- 767 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
- P07547
- Ligands
- CRB, ZN, CL
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 385 | 52% helix, 18% strand | P07547 |
| B | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 382 | 52% helix, 18% strand | P07547 |
Ligands and binding sites
- CRB · [1R-(1alpha,3beta,4alpha,5beta)]-5-(phosphonomethyl)-1,3,4-trihydroxycyclohexane-1-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.80 | 0.84 | 98 | ZN, CRB |
| 2 | 440 | 0.75 | 0.84 | 50 | CRB |
| 3 | 280 | 0.62 | 0.80 | 53 | empty |
| 4 | 86 | 0.61 | 0.89 | 18 | CL |
| 5 | 60 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1695 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1NVD · Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+ 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 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 P07547
- Elsewhere: RCSB PDB 1NVD · PDBe 1NVD · UniProt P07547
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