MolNFT v1 · #72843 · protein
Crystal structure of human ligand-free mature caspase-6 with intersubunit linker attached
3NKF: “Crystal structure of human ligand-free mature caspase-6 with intersubunit linker attached”. X-ray diffraction, 19 pockets (best druggability 0.82). MolNFT v1 #72843 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NKF
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-6
- EC
- 3.4.22.59
- UniProt
- P55212
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-6 (EC 3.4.22.59) | protein | 219 | 36% helix, 19% strand | P55212 |
| B | Caspase-6 (EC 3.4.22.59) | protein | 213 | 39% helix, 19% strand | P55212 |
| C | Caspase-6 (EC 3.4.22.59) | protein | 222 | 35% helix, 19% strand | P55212 |
| D | Caspase-6 (EC 3.4.22.59) | protein | 220 | 36% helix, 18% strand | P55212 |
Pockets
19 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.82 | 0.86 | 68 | empty |
| 2 | 218 | 0.67 | 0.84 | 33 | empty |
| 3 | 354 | 0.63 | 0.78 | 43 | empty |
| 4 | 198 | 0.58 | 0.80 | 28 | empty |
| 5 | 70 | 0.46 | 0.83 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1435 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1245 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 328 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 305 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 183 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3NKF · Crystal structure of human ligand-free mature caspase-6 with intersubunit linker attached · the same entry in another collection · chain D against D, TM-score 1.00
- P55212 · AlphaFold monomer V2.0 prediction for caspase-6 (P55212) · a predicted model of the same protein · chain D against A, TM-score 0.88
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 3NKF · PDBe 3NKF · UniProt P55212
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