MolNFT v1 · #109995 · protein

Crystal structure of escherichia COLI dncv 3'-deoxy GTP bound form

4XJ6 · VC0179-like protein: “Crystal structure of escherichia COLI dncv 3'-deoxy GTP bound form”. X-ray diffraction, 2 ligands (GH3, MG), 2 pockets (best druggability 0.72). MolNFT v1 #109995 on GenesisL1: 3D structure, binding sites and…

PDB: 4XJ6
Type: protein
Length: 370 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VC0179-like protein
UniProt: Q6XGD8
Ligands: GH3, MG
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VC0179-like protein	protein	370	56% helix, 14% strand	Q6XGD8

Ligands and binding sites

GH3 · 3'-deoxy-guanosine-5'-triphosphate · ligand · 2 copies · chains A
MG · Magnesium ion · metal · 2 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	758	0.72	0.78	55	MG, GH3
2	66	0.37	0.78	12	empty

Compared structures

4XJ6 · Crystal structure of Escherichia coli DncV 3'-deoxy GTP bound form · the same entry in another collection · chain A against A, TM-score 1.00
Q6XGD8 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q6XGD8) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q6XGD8
Elsewhere: RCSB PDB 4XJ6 · PDBe 4XJ6 · UniProt Q6XGD8

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