MolNFT v1 · #73803 · protein

Crystal structure of active caspase-6 bound with ac-veid-cho

3OD5: “Crystal structure of active caspase-6 bound with ac-veid-cho”. X-ray diffraction, 1 ligand (ACE), 4 pockets (best druggability 0.77). MolNFT v1 #73803 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3OD5
Type: protein
Length: 488 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-6; Peptide aldehyde inhibitor ac-veid-cho
EC: 3.4.22.59
UniProt: P55212
Ligands: ACE
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Caspase-6 (EC 3.4.22.59)	protein	240	29% helix, 24% strand	P55212
C, D	Peptide aldehyde inhibitor ac-veid-cho	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
CAC · Cacodylate ion · additive · 8 copies · chains A, C, B, D

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	512	0.77	0.84	49	CAC
2	64	0.59	0.91	21	empty
3	145	0.44	0.75	25	empty
4	95	0.39	0.76	21	empty

Interfaces

3 interfaces between chains.

A–B · 2384 Å² buried · 38 hydrogen bonds · protein-protein
B–D · 439 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 425 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3OD5 · Crystal structure of active caspase-6 bound with Ac-VEID-CHO · the same entry in another collection · chain A against A, TM-score 1.00
P55212 · AlphaFold monomer V2.0 prediction for caspase-6 (P55212) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 3OD5 · PDBe 3OD5 · UniProt P55212

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