Research workbench

Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A

Analyse Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BGP
Type: protein
Length: 1,244 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.75
Source: Homo sapiens
Molecule: Calpain-3
EC: 3.4.22.54
UniProt: P20807
Ligands: CA, CL
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · resolution 2.75 · 3 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Calpain-3 (EC 3.4.22.54)	protein	303	31% helix, 23% strand	P20807
B, D	Calpain-3 (EC 3.4.22.54)	protein	314	30% helix, 23% strand	P20807
C	Calpain-3 (EC 3.4.22.54)	protein	313	31% helix, 23% strand	P20807

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, B, C, D
CL · Chloride ion · ion · 4 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1097	0.83	0.85	99	empty
2	921	0.80	0.83	82	empty
3	1133	0.77	0.79	87	empty
4	351	0.73	0.85	33	empty
5	93	0.40	0.77	19	empty

Interfaces

3 interfaces between chains.

A–B · 1411 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1320 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 486 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6BGP · Crystal structure of human calpain-3 protease core mutant-C129A · the same entry in another collection · chain D against D, TM-score 1.00
P20807 · AlphaFold monomer V2.0 prediction for calpain-3 (P20807) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P20807
Elsewhere: RCSB PDB 6BGP · PDBe 6BGP · UniProt P20807

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