Research workbench
Crystal structure of active caspase-6 bound with ac-veid-cho
Analyse Crystal structure of active caspase-6 bound with ac-veid-cho in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 439 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 425 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
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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