Research workbench

X-ray crystal structure analysis of bovine spleen cathepsin B-CA078 complex

Analyse X-ray crystal structure analysis of bovine spleen cathepsin B-CA078 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DCD
Type: protein
Length: 251 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin B
EC: 3.4.22.1
Ligands: 78A, PO4
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cathepsin B (EC 3.4.22.1)	protein	251	27% helix, 25% strand	—

Ligands and binding sites

78A · N-({(2S,3S)-3-[(benzylamino)carbonyl]oxiran-2-yl}carbonyl)-L-isoleucyl-L-proline · ligand · chains A
PO4 · Phosphate ion · ion · chains A
GOL · Glycerol · additive · chains A

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	176	0.48	0.76	27	78A
2	51	0.36	0.80	19	empty
3	51	0.25	0.73	16	empty

Modifications

Observed in the structure: 7 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

2DCD · X-ray crystal structure analysis of bovine spleen cathepsin B-CA078 complex · 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
Elsewhere: RCSB PDB 2DCD · PDBe 2DCD

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