MolNFT v1 · #169327 · protein

Caspase-3 in complex with ketomethylene inhibitor reveals tetrahedral adduct

6X8I: “Caspase-3 in complex with ketomethylene inhibitor reveals tetrahedral adduct”. X-ray diffraction, 1 ligand (ACE), 1 pocket (best druggability 0.65). MolNFT v1 #169327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6X8I
Type: protein
Length: 475 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; Ketomethylene inhibitor
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Caspase-3 (EC 3.4.22.56)	protein	141	28% helix, 32% strand	P42574
C	Caspase-3 (EC 3.4.22.56)	protein	93	33% helix, 20% strand	P42574
D	Caspase-3 (EC 3.4.22.56)	protein	92	34% helix, 21% strand	P42574
E, F	Ketomethylene inhibitor	protein	4	0% helix, 50% strand	—

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	303	0.65	0.81	34	empty

Interfaces

10 interfaces between chains.

A–C · 2190 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 2128 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 1405 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 437 Å² buried · 11 hydrogen bonds · protein-protein
D–F · 434 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6X8I · Caspase-3 in complex with ketomethylene inhibitor reveals tetrahedral adduct · 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 0.99

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 6X8I · PDBe 6X8I · UniProt P42574

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