Research workbench
Structure of the mini-RNA-guided endonuclease CRISPR-CAS_PHI3
Analyse Structure of the mini-RNA-guided endonuclease CRISPR-CAS_PHI3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ODF
- Type
- protein + DNA + RNA
- Length
- 781 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAS_PHI3; DNA (5'- D(P*GP*TP*AP*TP*CP*CP*CP*AP*TP*TP*AP*CP*CP*AP*GP*CP*TP*GP*AP*AP*TP*TP…
- Ligands
- NI, ZN
- Pockets
- 14 · best druggability 0.79
Structure
electron microscopy · 5 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CAS_PHI3 | protein | 703 | 43% helix, 12% strand | — |
| E | DNA (5'- D(P*GP*TP*AP*TP*CP*CP*CP*AP*TP*TP*AP*CP*CP*AP*GP*CP*TP*GP*AP*AP*TP*TP *AP*C)-3') | dna | 24 | — | — |
| G | DNA (5'-D(P*GP*TP*AP*AP*TP*TP*CP*AP*G)-3') | dna | 9 | — | — |
| C | DNA (5'-D(P*GP*G)-3') | dna | 2 | — | — |
| F | RNA (43-mer) | rna | 43 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.79 | 0.84 | 73 | empty |
| 2 | 529 | 0.72 | 0.81 | 45 | empty |
| 3 | 661 | 0.69 | 0.77 | 41 | empty |
| 4 | 153 | 0.65 | 0.87 | 27 | empty |
| 5 | 67 | 0.64 | 0.92 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–F · 4271 Ų buried · 105 hydrogen bonds · protein-nucleic
- A–E · 1472 Ų buried · 13 hydrogen bonds · protein-nucleic
- E–F · 762 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- A–G · 576 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 345 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 7ODF · Structure of the mini-RNA-guided endonuclease CRISPR-Cas_phi3 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7ODF · PDBe 7ODF
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