MolNFT v1 · #90540 · protein

Crystal structure of the complex of type I ribosome inactivating protein in complex with 7N-methyl-8-hydroguanosine-5-P-diphosphate at 1.77 a

4EMF · RRNA N-glycosidase: “Crystal structure of the complex of type I ribosome inactivating protein in complex with…”. X-ray diffraction, 2 ligands (M7G, NAG), 1 pocket (best druggability 0.47). MolNFT v1 #90540 on GenesisL1: 3D…

PDB: 4EMF
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: M7G, NAG
Pockets: 1 · best druggability 0.47

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RRNA N-glycosidase (EC 3.2.2.22)	protein	246	42% helix, 25% strand	D9J2T9

Ligands and binding sites

M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · chains A
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

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	132	0.47	0.78	19	M7G

Modifications

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

Compared structures

4EMF · Crystal structure of the complex of type I Ribosome inactivating protein in complex with… · 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 4EMF · PDBe 4EMF · UniProt D9J2T9

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