MolNFT v1 · #6074 · protein

Crystal structure of caspase-7 in complex with acetyl-asp-glu-val-asp- cho

1F1J · Caspase-7 protease: “Crystal structure of caspase-7 in complex with acetyl-asp-glu-val-asp- cho”. X-ray diffraction, 2 ligands (ACE, SO4), 2 pockets (best druggability 0.75). MolNFT v1 #6074 on GenesisL1: 3D structure, binding sites…

PDB: 1F1J
Type: protein
Length: 469 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-7 protease; ACE-asp-glu-val-asp-cho
EC: 3.4.22.-
UniProt: P55210
Ligands: ACE, SO4
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-7 protease (EC 3.4.22.-)	protein	230	31% helix, 27% strand	P55210
B	Caspase-7 protease (EC 3.4.22.-)	protein	231	32% helix, 28% strand	P55210
C, D	ACE-asp-glu-val-asp-cho	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
SO4 · Sulfate ion · ion · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	475	0.75	0.83	45	empty
2	53	0.48	0.86	17	empty

Interfaces

3 interfaces between chains.

A–B · 2061 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 455 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 452 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1F1J · Crystal structure of caspase-7 in complex with acetyl-asp-glu-val-asp-cho · the same entry in another collection · chain A against A, TM-score 1.00
P55210 · AlphaFold monomer V2.0 prediction for caspase-7 (P55210) · a predicted model of the same protein · chain B 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 P55210
Elsewhere: RCSB PDB 1F1J · PDBe 1F1J · UniProt P55210

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