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Crystal structure of yeast YMX7, an ADP-ribose-1''-monophosphatase

Analyse Crystal structure of yeast YMX7, an ADP-ribose-1''-monophosphatase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NJR
Type: protein
Length: 249 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 32.1 kda protein in ADH3-RCA1 intergenic region
UniProt: Q04299
Ligands: XYL
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	32.1 kda protein in ADH3-RCA1 intergenic region	protein	249	45% helix, 13% strand	Q04299

Ligands and binding sites

XYL · Xylitol · ligand · 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	197	0.67	0.85	30	XYL

Modifications

Observed in the structure: 9 modified, 1 disulfide (engineered, disulfide).

Compared structures

1NJR · Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase · the same entry in another collection · chain A against A, TM-score 1.00
Q04299 · AlphaFold monomer V2.0 prediction for probable ADP-ribose 1''-phosphate phosphatase… · 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 Q04299
Elsewhere: RCSB PDB 1NJR · PDBe 1NJR · UniProt Q04299

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