MolNFT v1 · #114165 · protein + DNA + RNA
Crystal structure of acidaminococcus sp. CPF1 in complex with crrna and target DNA
5B43 · CRISPR-associated endonuclease CPF1: “Crystal structure of acidaminococcus sp. CPF1 in complex with crrna and target DNA”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.81). MolNFT v1 #114165 on GenesisL1: 3D…
- 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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