MolNFT v1 · #45963 · protein

Catalytic domain of human calpain 8

2NQA · Calpain-8: “Catalytic domain of human calpain 8”. X-ray diffraction, 2 ligands (ACE, CA), 6 pockets (best druggability 0.83). MolNFT v1 #45963 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2NQA
Type: protein
Length: 634 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calpain-8; Leupeptin inhibitor
EC: 3.4.22.53
UniProt: A6NHC0
Ligands: ACE, CA
Pockets: 6 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Calpain-8 (EC 3.4.22.53)	protein	310	30% helix, 24% strand	A6NHC0
B	Calpain-8 (EC 3.4.22.53)	protein	318	29% helix, 23% strand	A6NHC0
D, E	Leupeptin inhibitor	protein	3	0% helix, 33% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, B, 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	330	0.83	0.93	71	empty
2	283	0.67	0.83	48	ACE
3	136	0.65	0.87	27	empty
4	133	0.61	0.86	31	empty
5	182	0.52	0.78	29	ACE

Interfaces

5 interfaces between chains.

A–B · 1131 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 359 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 342 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 115 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 110 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified, 2 covalent (oxidation, covalent ligand, nonstandard).

Compared structures

2NQA · Catalytic Domain of Human Calpain 8 · the same entry in another collection · chain A against A, TM-score 1.00
A6NHC0 · AlphaFold monomer V2.0 prediction for calpain-8 (A6NHC0) · a predicted model of the same protein · chain B 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 A6NHC0
Elsewhere: RCSB PDB 2NQA · PDBe 2NQA · UniProt A6NHC0

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