Research workbench

RNase PO1 complexed with 3'GMP

Analyse RNase PO1 complexed with 3'GMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WR2
Type: protein
Length: 606 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanyl-specific ribonuclease PO1
EC: 4.6.1.24
UniProt: P81762
Ligands: 3GP
Pockets: 8 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Guanyl-specific ribonuclease PO1 (EC 4.6.1.24)	protein	101	12% helix, 33% strand	P81762

Ligands and binding sites

3GP · Guanosine-3'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	265	0.62	0.80	36	empty
2	204	0.60	0.81	34	empty
3	258	0.51	0.74	32	3GP
4	163	0.45	0.75	26	3GP
5	81	0.35	0.75	14	3GP

Interfaces

8 interfaces between chains.

A–F · 328 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 312 Å² buried · 0 hydrogen bonds · protein-protein
E–F · 311 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 290 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 267 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

3WR2 · RNase Po1 complexed with 3'GMP · the same entry in another collection · chain C against C, TM-score 1.00
P81762 · AlphaFold monomer V2.0 prediction for guanyl-specific ribonuclease PO1 (P81762) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P81762
Elsewhere: RCSB PDB 3WR2 · PDBe 3WR2 · UniProt P81762

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.