MolNFT v1 · #107129 · protein
Structure of the vibrio cholerae di-nucleotide cyclase (dncv) deletion mutant D-loop
4U0N · Cyclic AMP-gmp synthase: “Structure of the vibrio cholerae di-nucleotide cyclase (dncv) deletion mutant D-loop”. X-ray diffraction, 2 ligands (TLL, MG), 7 pockets (best druggability 0.71). MolNFT v1 #107129 on GenesisL1: 3D…
- PDB
- 4U0N
- Type
- protein
- Length
- 746 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic AMP-gmp synthase
- EC
- 2.7.7.86
- UniProt
- Q9KVG7
- Ligands
- TLL, MG
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclic AMP-gmp synthase (EC 2.7.7.86) | protein | 373 | 54% helix, 12% strand | Q9KVG7 |
Ligands and binding sites
- TLL · N-[4-({[(6S)-2-amino-5-methyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-glutamic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.71 | 0.78 | 58 | empty |
| 2 | 700 | 0.69 | 0.77 | 59 | MG |
| 3 | 653 | 0.68 | 0.77 | 59 | empty |
| 4 | 99 | 0.43 | 0.78 | 13 | empty |
| 5 | 110 | 0.41 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 397 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4U0N · Structure of the Vibrio cholerae di-nucleotide cyclase (DncV) deletion mutant D-loop · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KVG7 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q9KVG7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9KVG7
- Elsewhere: RCSB PDB 4U0N · PDBe 4U0N · UniProt Q9KVG7
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