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Crystal structure of caspase-7 incomplex with acetyl-yvad- cho

Analyse Crystal structure of caspase-7 incomplex with acetyl-yvad- cho in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IBC
Type: protein
Length: 473 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-7; Acetyl-yvad-cho
EC: 3.4.22.60
UniProt: P55210
Ligands: ACE
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 28% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-7 (EC 3.4.22.60)	protein	140	28% helix, 28% strand	P55210
B	Caspase-7 (EC 3.4.22.60)	protein	92	28% helix, 18% strand	P55210
D	Caspase-7 (EC 3.4.22.60)	protein	93	28% helix, 22% strand	P55210
E, F	Acetyl-yvad-cho	protein	4	0% helix, 50% 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

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	544	0.78	0.84	43	empty
2	52	0.36	0.80	15	empty

Interfaces

10 interfaces between chains.

A–B · 2291 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 2255 Å² buried · 38 hydrogen bonds · protein-protein
B–D · 1425 Å² buried · 18 hydrogen bonds · protein-protein
D–F · 406 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 400 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3IBC · Crystal Structure of Caspase-7 incomplex with Acetyl-YVAD-CHO · the same entry in another collection · chain F against F, TM-score 1.00
P55210 · AlphaFold monomer V2.0 prediction for caspase-7 (P55210) · 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 P55210
Elsewhere: RCSB PDB 3IBC · PDBe 3IBC · UniProt P55210

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