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Crystal structure of active caspase-6 in complex with ac-veid-cho inhibitor

Analyse Crystal structure of active caspase-6 in complex with ac-veid-cho inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3P4U
Type: protein
Length: 486 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-6; Ac-veid-cho inhibitor
EC: 3.4.22.59
UniProt: P55212
Ligands: ACE
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-6 (EC 3.4.22.59)	protein	145	27% helix, 27% strand	P55212
B, D	Caspase-6 (EC 3.4.22.59)	protein	94	32% helix, 20% strand	P55212
E, F	Ac-veid-cho inhibitor	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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	341	0.69	0.82	42	empty
2	67	0.62	0.91	24	empty
3	95	0.38	0.76	24	empty
4	95	0.36	0.75	21	empty

Interfaces

10 interfaces between chains.

A–B · 2342 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 2333 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 1294 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 551 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 534 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified, 2 covalent (artifact, covalent ligand, nonstandard).

Compared structures

3P4U · Crystal structure of active caspase-6 in complex with Ac-VEID-CHO inhibitor · the same entry in another collection · chain F against F, TM-score 1.00
P55212 · AlphaFold monomer V2.0 prediction for caspase-6 (P55212) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P55212
Elsewhere: RCSB PDB 3P4U · PDBe 3P4U · UniProt P55212

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