MolNFT v1 · #19754 · protein

Crystal structure of the complex of caspase-8 with the tetrapeptide inhibitor ACE-ietd-aldehyde

1QTN: “Crystal structure of the complex of caspase-8 with the tetrapeptide inhibitor ACE-ietd-aldehyde”. X-ray diffraction, 1 ligand (ACE), 2 pockets (best druggability 0.45). MolNFT v1 #19754 on GenesisL1: 3D structure, binding sites and…

PDB: 1QTN
Type: protein
Length: 246 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-8; Acetyl-ile-glu-thr-asp-aldehyde
EC: 3.4.22.-
UniProt: Q14790
Ligands: ACE
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-8 (EC 3.4.22.-)	protein	152	31% helix, 23% strand	Q14790
B	Caspase-8 (EC 3.4.22.-)	protein	90	33% helix, 21% strand	Q14790
C	Acetyl-ile-glu-thr-asp-aldehyde	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains B, C
DTD · Dithiane diol · additive · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	144	0.45	0.76	19	empty
2	104	0.39	0.76	20	DTD

Interfaces

3 interfaces between chains.

A–B · 2327 Å² buried · 41 hydrogen bonds · protein-protein
B–C · 348 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 262 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).

Compared structures

1QTN · Crystal structure of the complex of caspase-8 with the tetrapeptide inhibitor… · the same entry in another collection · chain C against C, TM-score 1.00
Q14790 · AlphaFold monomer V2.0 prediction for caspase-8 (Q14790) · 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 Q14790
Elsewhere: RCSB PDB 1QTN · PDBe 1QTN · UniProt Q14790

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