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Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus thermophilus HB8

Analyse Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YVP
Type: protein
Length: 182 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MUTT/NUDIX family protein
EC: 3.6.1.-
UniProt: Q5SJY9
Ligands: RBY, MG
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MUTT/NUDIX family protein (EC 3.6.1.-)	protein	182	23% helix, 39% strand	Q5SJY9

Ligands and binding sites

RBY · Methylene adp-beta-xylose · ligand · chains A
MG · Magnesium ion · metal · 3 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	292	0.50	0.73	30	MG, RBY

Compared structures

2YVP · Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus thermophilus HB8 · the same entry in another collection · 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 Q5SJY9
Elsewhere: RCSB PDB 2YVP · PDBe 2YVP · UniProt Q5SJY9

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