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Baranase crosslinked by glutaraldehyde

Analyse Baranase crosslinked by glutaraldehyde in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KCH
Type: protein
Length: 324 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease
EC: 3.1.27.-
UniProt: P00648
Ligands: PTD
Pockets: 1 · best druggability 0.53

Structure

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

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

Ligands and binding sites

PTD · Pentanedial · ligand · 3 copies · chains A, B, 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	338	0.53	0.73	36	empty

Interfaces

3 interfaces between chains.

B–C · 194 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 14 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 13 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

3KCH · Baranase crosslinked by glutaraldehyde · 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 P00648
Elsewhere: RCSB PDB 3KCH · PDBe 3KCH · UniProt P00648

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