MolNFT v1 · #120066 · protein

Crystal structure of a di-nucleotide cyclase vibrio mutant

5GO3 · Cyclic gmp-AMP synthase: “Crystal structure of a di-nucleotide cyclase vibrio mutant”. X-ray diffraction, 7 pockets (best druggability 0.70). MolNFT v1 #120066 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GO3
Type: protein
Length: 726 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic gmp-AMP synthase
EC: 2.7.7.-
UniProt: Q9KVG7
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 56% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic gmp-AMP synthase (EC 2.7.7.-)	protein	362	55% helix, 11% strand	Q9KVG7
B	Cyclic gmp-AMP synthase (EC 2.7.7.-)	protein	364	57% helix, 11% strand	Q9KVG7

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.70	0.78	57	empty
2	744	0.68	0.76	57	empty
3	317	0.63	0.79	42	empty
4	50	0.33	0.78	10	empty
5	50	0.32	0.77	10	empty

Interfaces

1 interface between chains.

A–B · 322 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5GO3 · Crystal structure of a di-nucleotide cyclase Vibrio mutant · 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 0.98

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 Q9KVG7
Elsewhere: RCSB PDB 5GO3 · PDBe 5GO3 · UniProt Q9KVG7

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