Research workbench

Cathepsin B complexed with dipeptidyl nitrile inhibitor

Analyse Cathepsin B complexed with dipeptidyl nitrile inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1GMY
Type: protein
Length: 760 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin B
EC: 3.4.22.1
UniProt: P07858
Ligands: AEM, APD, DFA
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cathepsin B (EC 3.4.22.1)	protein	254	28% helix, 22% strand	P07858
B, C	Cathepsin B (EC 3.4.22.1)	protein	253	27% helix, 24% strand	P07858

Ligands and binding sites

AEM · 2-aminoethanimidic acid · ligand · 3 copies · chains A, B, C
APD · 3-methylphenylalanine · ligand · 3 copies · chains A, B, C
DFA · Diphenylacetic acid · ligand · 3 copies · chains A, B, C

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1145	0.78	0.80	109	AEM, APD, DFA
2	294	0.65	0.81	38	empty
3	187	0.49	0.76	36	AEM, APD
4	121	0.38	0.74	16	empty
5	64	0.37	0.78	16	empty

Interfaces

2 interfaces between chains.

A–B · 657 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 353 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 3 covalent (disulfide, covalent ligand).

Compared structures

1GMY · Cathepsin B complexed with dipeptidyl nitrile inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P07858 · AlphaFold monomer V2.0 prediction for cathepsin B (P07858) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P07858
Elsewhere: RCSB PDB 1GMY · PDBe 1GMY · UniProt P07858

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