Research workbench
Crystal structure of acidaminococcus sp. CPF1 in complex with crrna and target DNA
Analyse Crystal structure of acidaminococcus sp. CPF1 in complex with crrna and target… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B43
- Type
- protein + DNA + RNA
- Length
- 1,352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CPF1; RNA (43-mer); DNA (34-mer); DNA…
- EC
- 3.1.-.-
- UniProt
- U2UMQ6
- Ligands
- NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CPF1 (EC 3.1.-.-) | protein | 1272 | 48% helix, 13% strand | U2UMQ6 |
| B | RNA (43-mer) | rna | 40 | — | — |
| C | DNA (34-mer) | dna | 30 | — | — |
| D | DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*TP*TP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.81 | 0.88 | 52 | empty |
| 2 | 894 | 0.79 | 0.82 | 62 | EDO |
| 3 | 463 | 0.72 | 0.82 | 41 | empty |
| 4 | 84 | 0.68 | 0.93 | 25 | empty |
| 5 | 440 | 0.59 | 0.75 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3722 Ų buried · 91 hydrogen bonds · protein-nucleic
- A–C · 2341 Ų buried · 47 hydrogen bonds · protein-nucleic
- B–C · 920 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- A–D · 651 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 449 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Compared structures
- 5B43 · Crystal structure of Acidaminococcus sp. Cpf1 in complex with crRNA and target DNA · the same entry in another collection · chain A against A, TM-score 1.00
- U2UMQ6 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS12A (U2UMQ6) · a predicted model of the same protein · 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
- Every structure of UniProt U2UMQ6
- Elsewhere: RCSB PDB 5B43 · PDBe 5B43 · UniProt U2UMQ6
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