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Crystal structure of vibrio cholerae dncv 3'-deoxy ATP bound form

Analyse Crystal structure of vibrio cholerae dncv 3'-deoxy ATP bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XJ4
Type: protein
Length: 372 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic AMP-gmp synthase
EC: 2.7.7.-
UniProt: Q9KVG7
Ligands: 3AT, MG
Pockets: 1 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic AMP-gmp synthase (EC 2.7.7.-)	protein	372	55% helix, 14% strand	Q9KVG7

Ligands and binding sites

3AT · 3'-deoxyadenosine-5'-triphosphate · ligand · 2 copies · chains A
MG · Magnesium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 5 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	724	0.69	0.77	55	3AT, MG

Compared structures

4XJ4 · Crystal structure of Vibrio cholerae DncV 3'-deoxy ATP bound form · 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 A 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 4XJ4 · PDBe 4XJ4 · UniProt Q9KVG7

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