MolNFT v1 · #121927 · protein

Caspase 3 V266C

5I9T · Caspase-3: “Caspase 3 V266C”. X-ray diffraction, 2 ligands (ACE, 0QE), 2 pockets (best druggability 0.63). MolNFT v1 #121927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I9T
Type: protein
Length: 486 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 0.63

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-3 (EC 3.4.22.56)	protein	239	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 · ion · 2 copies · chains C, D, A, E
ACT · Acetate ion · 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	283	0.63	0.80	34	empty
2	54	0.31	0.76	18	empty

Interfaces

3 interfaces between chains.

A–C · 2208 Å² buried · 42 hydrogen bonds · protein-protein
C–D · 472 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 471 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).

Compared structures

5I9T · Caspase 3 V266C · 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 A 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 5I9T · PDBe 5I9T · UniProt P42574

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