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Crystal structure of saccharomyces cerevisiae DCP2 nudix domain in complex with mg

Analyse Crystal structure of saccharomyces cerevisiae DCP2 nudix domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K6E
Type: protein
Length: 144 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRNA-decapping enzyme subunit 2
EC: 3.-.-.-
UniProt: P53550
Ligands: MG
Pockets: 1 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MRNA-decapping enzyme subunit 2 (EC 3.-.-.-)	protein	144	28% helix, 32% strand	P53550

Ligands and binding sites

MG · Magnesium ion · metal · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.36	0.74	19	empty

Compared structures

4K6E · Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg · the same entry in another collection · chain A against A, TM-score 1.00
P53550 · AlphaFold monomer V2.0 prediction for M7GPPPN-mRNA hydrolase (P53550) · 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 P53550
Elsewhere: RCSB PDB 4K6E · PDBe 4K6E · UniProt P53550

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