MolNFT v1 · #34314 · protein

X-ray crystal structure analysis of bovine spleen cathepsin B-CA059 complex

2DC8: “X-ray crystal structure analysis of bovine spleen cathepsin B-CA059 complex”. X-ray diffraction, 2 ligands (59A, PO4), 2 pockets (best druggability 0.46). MolNFT v1 #34314 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2DC8
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: 59A, PO4
Pockets: 2 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cathepsin B (EC 3.4.22.1)	protein	251	26% helix, 26% strand	—

Ligands and binding sites

59A · N-{[(2S,3S)-3-(ethoxycarbonyl)oxiran-2-yl]carbonyl}-L-isoleucine · 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

2 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	186	0.46	0.75	29	59A
2	52	0.25	0.73	15	empty

Modifications

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

Compared structures

2DC8 · X-ray crystal structure analysis of bovine spleen cathepsin B-CA059 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 2DC8 · PDBe 2DC8

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