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Crystal structure of the complex of ribosome inactivating protein from momordica balsamina with pyrimidine-2,4-dione at 1.70 ångström resolution

Analyse Crystal structure of the complex of ribosome inactivating protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y48
Type: protein
Length: 246 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosome inactivating protein
EC: 3.2.2.22
UniProt: D9J2T9
Ligands: URA, NAG
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosome inactivating protein (EC 3.2.2.22)	protein	246	42% helix, 25% strand	D9J2T9

Ligands and binding sites

URA · Uracil · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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	135	0.52	0.80	18	URA
2	69	0.37	0.77	16	empty

Modifications

Observed in the structure: 1 glycan (N-glycosylation).

Compared structures

5Y48 · Crystal structure of the complex of Ribosome inactivating protein from Momordica… · 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 D9J2T9
Elsewhere: RCSB PDB 5Y48 · PDBe 5Y48 · UniProt D9J2T9

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