Research workbench
Crystal structure of an archaeal CRISPR-associated CAS6 nuclease
Analyse Crystal structure of an archaeal CRISPR-associated CAS6 nuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZFV
- Type
- protein
- Length
- 1,027 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endoribonuclease CAS6 1
- EC
- 3.1.-.-
- UniProt
- Q97Y96
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endoribonuclease CAS6 1 (EC 3.1.-.-) | protein | 259 | 29% helix, 36% strand | Q97Y96 |
| B | CRISPR-associated endoribonuclease CAS6 1 (EC 3.1.-.-) | protein | 258 | 29% helix, 37% strand | Q97Y96 |
| C | CRISPR-associated endoribonuclease CAS6 1 (EC 3.1.-.-) | protein | 248 | 30% helix, 35% strand | Q97Y96 |
| D | CRISPR-associated endoribonuclease CAS6 1 (EC 3.1.-.-) | protein | 262 | 28% helix, 34% strand | Q97Y96 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.77 | 0.81 | 81 | empty |
| 2 | 146 | 0.73 | 0.92 | 41 | empty |
| 3 | 173 | 0.57 | 0.81 | 29 | empty |
| 4 | 215 | 0.51 | 0.76 | 35 | empty |
| 5 | 103 | 0.49 | 0.81 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1423 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 911 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 429 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3ZFV · Crystal structure of an archaeal CRISPR-associated Cas6 nuclease · the same entry in another collection · chain D against D, TM-score 1.00
- Q97Y96 · AlphaFold monomer V2.0 prediction for CRISPR-associated endoribonuclease CAS6 1 (Q97Y96) · a predicted model of the same protein · chain D 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 Q97Y96
- Elsewhere: RCSB PDB 3ZFV · PDBe 3ZFV · UniProt Q97Y96
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