MolNFT v1 · #121944 · protein

Caspase 3 V266D

5IAB · Caspase-3: “Caspase 3 V266D”. X-ray diffraction, 2 ligands (ACE, 0QE), 2 pockets (best druggability 0.62). MolNFT v1 #121944 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IAB
Type: protein
Length: 477 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; ACE-asp-glu-val-ask
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE, 0QE
Pockets: 2 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3 (EC 3.4.22.56)	protein	235	29% helix, 27% strand	P42574
C	Caspase-3 (EC 3.4.22.56)	protein	234	29% helix, 27% strand	P42574
D, E	ACE-asp-glu-val-ask	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains C, D, A, E
0QE · Chloromethane · ligand · 2 copies · chains C, D, A, E
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	275	0.62	0.80	34	empty
2	90	0.36	0.75	19	empty

Interfaces

3 interfaces between chains.

A–C · 2211 Å² buried · 47 hydrogen bonds · protein-protein
C–D · 476 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 475 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

5IAB · Caspase 3 V266D · the same entry in another collection · chain A against A, TM-score 1.00
P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · a predicted model of the same protein · chain C 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 P42574
Elsewhere: RCSB PDB 5IAB · PDBe 5IAB · UniProt P42574

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