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Structure of human calpain 9 in complex with leupeptin

Analyse Structure of human calpain 9 in complex with leupeptin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P0R
Type: protein
Length: 644 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calpain-9; Leupeptin
EC: 3.4.22.52
UniProt: O14815
Ligands: ACE, CA
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Calpain-9 (EC 3.4.22.52)	protein	319	30% helix, 22% strand	O14815
D, E	Leupeptin	protein	3	0% helix, 33% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, D, E
CA · Calcium ion · metal · 5 copies · chains A, B

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

Pockets

6 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	446	0.77	0.85	31	empty
2	72	0.72	0.97	12	empty
3	124	0.42	0.76	28	empty
4	74	0.39	0.78	14	empty
5	95	0.36	0.75	21	empty

Interfaces

5 interfaces between chains.

A–B · 1311 Å² buried · 23 hydrogen bonds · protein-protein
B–E · 372 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 357 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 76 Å² buried · 1 hydrogen bond · protein-protein
B–D · 64 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).

Compared structures

2P0R · Structure of Human Calpain 9 in complex with Leupeptin · the same entry in another collection · chain A against A, TM-score 1.00
O14815 · AlphaFold monomer V2.0 prediction for calpain-9 (O14815) · 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 O14815
Elsewhere: RCSB PDB 2P0R · PDBe 2P0R · UniProt O14815

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