MolNFT v1 · #143974 · protein

Caspase-3 mutant- T245A

6BFK: “Caspase-3 mutant- T245A”. X-ray diffraction, 3 ligands (ACE, NA, 0QE), 3 pockets (best druggability 0.65). MolNFT v1 #143974 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6BFK
Type: protein
Length: 481 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; Ac-asp-glu-val-asp-cmk
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE, NA, 0QE
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Caspase-3 (EC 3.4.22.56)	protein	143	27% helix, 30% strand	P42574
C	Caspase-3 (EC 3.4.22.56)	protein	94	33% helix, 18% strand	P42574
D	Caspase-3 (EC 3.4.22.56)	protein	93	33% helix, 18% strand	P42574
F, E	Ac-asp-glu-val-asp-cmk	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains C, F, D, E
NA · Sodium ion · metal · 5 copies · chains A, C, B, D
0QE · Chloromethane · ion · 2 copies · chains A, C, F, B, E

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

Pockets

3 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	305	0.65	0.80	38	empty
2	63	0.32	0.76	13	empty
3	50	0.28	0.75	12	empty

Interfaces

10 interfaces between chains.

B–D · 2274 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 2261 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 1429 Å² buried · 18 hydrogen bonds · protein-protein
C–F · 406 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 405 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

6BFK · Caspase-3 Mutant- T245A · 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 1.00

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 6BFK · PDBe 6BFK · UniProt P42574

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