Research workbench

RRNA N-glycosylase rta

Analyse RRNA N-glycosylase rta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GU4
Type: protein
Length: 522 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin; Gly-phe-gly-leu-phe-asp
EC: 3.2.2.22
UniProt: P02879
Pockets: 2 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ricin (EC 3.2.2.22)	protein	255	42% helix, 22% strand	P02879
C, D	Gly-phe-gly-leu-phe-asp	protein	6	67% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · chains B

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	858	0.79	0.82	102	empty
2	66	0.34	0.76	13	empty

Interfaces

3 interfaces between chains.

A–B · 672 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 422 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 418 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5GU4 · rRNA N-glycosylase RTA · 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 P02879
Elsewhere: RCSB PDB 5GU4 · PDBe 5GU4 · UniProt P02879

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