Research workbench

Binding of nonnatural 3'-nucleotides to ribonuclease a

Analyse Binding of nonnatural 3'-nucleotides to ribonuclease a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1W4P
Type: protein
Length: 248 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pancreatic ribonuclease a
EC: 3.1.27.5
UniProt: P61823
Ligands: UM3
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pancreatic ribonuclease a (EC 3.1.27.5)	protein	124	21% helix, 35% strand	P61823

Ligands and binding sites

UM3 · 2'-deoxyuridine 3'-monophosphate · ligand · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	189	0.50	0.77	29	empty

Interfaces

1 interface between chains.

A–B · 335 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1W4P · Binding of Nonnatural 3'-Nucleotides to Ribonuclease A · 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 P61823
Elsewhere: RCSB PDB 1W4P · PDBe 1W4P · UniProt P61823

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