Research workbench
Caspase-6 in complex with Z-vad-fmk inhibitor
Analyse Caspase-6 in complex with Z-vad-fmk inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QNW
- Type
- protein
- Length
- 897 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-6; Z-vad-fmk
- EC
- 3.4.22.59
- UniProt
- P55212
- Ligands
- PHQ, CF0
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-6 (EC 3.4.22.59) | protein | 134 | 37% helix, 20% strand | P55212 |
| B | Caspase-6 (EC 3.4.22.59) | protein | 93 | 29% helix, 14% strand | P55212 |
| C, E, G | Caspase-6 (EC 3.4.22.59) | protein | 133 | 39% helix, 23% strand | P55212 |
| D | Caspase-6 (EC 3.4.22.59) | protein | 92 | 32% helix, 15% strand | P55212 |
| F | Caspase-6 (EC 3.4.22.59) | protein | 86 | 30% helix, 15% strand | P55212 |
| H | Caspase-6 (EC 3.4.22.59) | protein | 84 | 31% helix, 15% strand | P55212 |
| X, Y, Z | Z-vad-fmk | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 3 copies · chains B, X, D, Y, H, Z
- CF0 · Fluoromethane · ion · 3 copies · chains A, B, X, C, D, Y, G, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.81 | 0.82 | 97 | empty |
| 2 | 611 | 0.71 | 0.79 | 63 | empty |
| 3 | 69 | 0.56 | 0.88 | 18 | empty |
| 4 | 95 | 0.56 | 0.85 | 22 | empty |
| 5 | 229 | 0.49 | 0.74 | 36 | empty |
Interfaces
22 interfaces between chains.
- A–B · 1678 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1664 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1654 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1618 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 947 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
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 3QNW · PDBe 3QNW · UniProt P55212
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.