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Cathepsin B in complex with darpin 8H6

Analyse Cathepsin B in complex with darpin 8H6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MBM
Type: protein
Length: 837 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin B; Darpin 8H6
EC: 3.4.22.1
UniProt: P07858
Pockets: 9 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cathepsin B (EC 3.4.22.1)	protein	256	26% helix, 23% strand	P07858
B	Cathepsin B (EC 3.4.22.1)	protein	255	25% helix, 20% strand	P07858
C, D	Darpin 8H6	protein	163	58% helix, 1% strand	—

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	289	0.73	0.87	29	empty
2	253	0.68	0.84	29	empty
3	244	0.66	0.83	42	empty
4	190	0.60	0.82	35	empty
5	176	0.53	0.79	25	empty

Interfaces

3 interfaces between chains.

B–D · 1114 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 1054 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 377 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 2 modified (disulfide, methylation).

Compared structures

5MBM · Cathepsin B in complex with DARPin 8h6 · 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 5MBM · PDBe 5MBM · UniProt P07858

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