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Caspases from scleractinian coral

Analyse Caspases from scleractinian coral in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WI4
Type: protein
Length: 481 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; ACE-devd inhibitor
Ligands: ACE
Pockets: 1 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Caspase-3	protein	233	28% helix, 24% strand	—
C	Caspase-3	protein	7	0% helix, 0% strand	—
D, E	ACE-devd inhibitor	protein	4	0% helix, 50% strand	—

Ligands and binding sites

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

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	568	0.74	0.81	50	empty

Interfaces

4 interfaces between chains.

A–B · 1503 Å² buried · 30 hydrogen bonds · protein-protein
B–E · 470 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 468 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 394 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6WI4 · Caspases from Scleractinian Coral · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6WI4 · PDBe 6WI4

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