MolNFT v1 · #175889 · protein

Apo-form cyclic trinucleotide synthase cdnd

7D4S · Cyclic AMP-AMP-gmp synthase: “Apo-form cyclic trinucleotide synthase cdnd”. X-ray diffraction, 2 ligands (APC, MG), 2 pockets (best druggability 0.72). MolNFT v1 #175889 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7D4S
Type: protein
Length: 345 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic AMP-AMP-gmp synthase
EC: 2.7.7.-
UniProt: P0DSP4
Ligands: APC, MG
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic AMP-AMP-gmp synthase (EC 2.7.7.-)	protein	345	49% helix, 12% strand	P0DSP4

Ligands and binding sites

APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A
MG · Magnesium ion · metal · 4 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	810	0.72	0.77	53	APC, MG
2	51	0.31	0.77	12	empty

Compared structures

7D4S · apo-form cyclic trinucleotide synthase CdnD · the same entry in another collection · chain A against A, TM-score 1.00
P0DSP4 · AlphaFold monomer V2.0 prediction for cyclic AMP-AMP-gmp synthase (P0DSP4) · 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 P0DSP4
Elsewhere: RCSB PDB 7D4S · PDBe 7D4S · UniProt P0DSP4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.