MolNFT v1 · #4684 · protein

Calpain domain VI with calcium bound

1DVI: “Calpain domain VI with calcium bound”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.77). MolNFT v1 #4684 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1DVI
Type: protein
Length: 346 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calpain
UniProt: Q64537
Ligands: CA
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Calpain	protein	173	64% helix, 6% strand	Q64537

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, B

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	134	0.77	0.95	27	empty
2	170	0.50	0.78	22	empty
3	155	0.50	0.78	21	empty
4	116	0.45	0.78	20	empty
5	112	0.44	0.78	18	empty

Interfaces

1 interface between chains.

A–B · 2201 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

1DVI · Calpain domain VI with calcium bound · the same entry in another collection · chain A against A, TM-score 1.00
Q64537 · AlphaFold monomer V2.0 prediction for calpain small subunit 1 (Q64537) · 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 Q64537
Elsewhere: RCSB PDB 1DVI · PDBe 1DVI · UniProt Q64537

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