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Crystal structure of a ribonuclease a-onconase chimera

Analyse Crystal structure of a ribonuclease a-onconase chimera in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QMN
Type: protein
Length: 366 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease pancreatic
EC: 3.1.27.5
UniProt: P61824
Ligands: PO4
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Ribonuclease pancreatic (EC 3.1.27.5)	protein	122	21% helix, 36% strand	P61824

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains A, B, C

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

Pockets

3 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	154	0.43	0.75	21	empty
2	79	0.42	0.80	15	empty
3	60	0.29	0.75	15	empty

Interfaces

3 interfaces between chains.

A–B · 332 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 209 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 105 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

6QMN · Crystal structure of a Ribonuclease A-Onconase chimera · the same entry in another collection · chain A against A, TM-score 1.00
P61824 · AlphaFold monomer V2.0 prediction for ribonuclease pancreatic (P61824) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P61824
Elsewhere: RCSB PDB 6QMN · PDBe 6QMN · UniProt P61824

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