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Barnase cross-linked with glutaraldehyde soaked in 6M urea

Analyse Barnase cross-linked with glutaraldehyde soaked in 6M urea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F56
Type: protein
Length: 324 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.955
Source: Bacillus amyloliquefaciens
Molecule: Ribonuclease
EC: 3.1.27.-
UniProt: P00648
Ligands: URE, ZN
Pockets: 1 · best druggability 0.57

Structure

x-ray diffraction · resolution 1.955 · 1 distinct chain · 22% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Ribonuclease (EC 3.1.27.-)	protein	108	22% helix, 23% strand	P00648

Ligands and binding sites

URE · Urea · ligand · 11 copies · chains A, C, B
ZN · Zinc ion · metal · chains A, C

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	400	0.57	0.75	35	URE

Interfaces

3 interfaces between chains.

B–C · 202 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 55 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 17 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2F56 · Barnase cross-linked with glutaraldehyde soaked in 6M urea · the same entry in another collection · chain A against A, TM-score 1.00
P00648 · AlphaFold monomer V2.0 prediction for ribonuclease (P00648) · 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 P00648
Elsewhere: RCSB PDB 2F56 · PDBe 2F56 · UniProt P00648

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