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Crystal structure of ribosome inactivating protein from momordica balsamina with highly ordered water structure in the substrate binding site

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

PDB: 4L66
Type: protein
Length: 246 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RRNA N-glycosidase
EC: 3.2.2.22
UniProt: D9J2T9
Ligands: NAG
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RRNA N-glycosidase (EC 3.2.2.22)	protein	246	43% helix, 25% strand	D9J2T9

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
GOL · Glycerol · additive · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	124	0.48	0.79	20	empty
2	52	0.32	0.76	12	empty

Modifications

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

Compared structures

4L66 · Crystal structure of Ribosome inactivating protein from Momordica balsamina with highly… · 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 4L66 · PDBe 4L66 · UniProt D9J2T9

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