MolNFT v1 · #38690 · protein

Crystal strusture of caspase-3 with inhibitor ac-vdvad-cho

2H65 · Caspase-3, P17 subunit: “Crystal strusture of caspase-3 with inhibitor ac-vdvad-cho”. X-ray diffraction, 1 ligand (ACE), 3 pockets (best druggability 0.64). MolNFT v1 #38690 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2H65
Type: protein
Length: 476 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3, P17 subunit; Caspase-3, P12 subunit; Ac-vdvad-cho
EC: 3.4.22.-
UniProt: P42574
Ligands: ACE
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 5 distinct chains · 28% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3, P17 subunit (EC 3.4.22.-)	protein	140	26% helix, 30% strand	P42574
B	Caspase-3, P12 subunit (EC 3.4.22.-)	protein	93	33% helix, 19% strand	P42574
C	Caspase-3, P17 subunit (EC 3.4.22.-)	protein	141	25% helix, 30% strand	P42574
D	Caspase-3, P12 subunit (EC 3.4.22.-)	protein	92	34% helix, 21% strand	P42574
E, F	Ac-vdvad-cho	protein	5	0% helix, 60% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains B, E, D, F

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	306	0.64	0.80	32	empty
2	54	0.31	0.76	19	empty
3	51	0.27	0.74	19	empty

Interfaces

10 interfaces between chains.

C–D · 2232 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2198 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 1392 Å² buried · 22 hydrogen bonds · protein-protein
B–E · 454 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 451 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2H65 · Crystal strusture of caspase-3 with inhibitor Ac-VDVAD-Cho · the same entry in another collection · chain F against F, 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 0.99

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 P42574
Elsewhere: RCSB PDB 2H65 · PDBe 2H65 · UniProt P42574

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