MolNFT v1 · #126884 · protein + DNA + RNA
Structure of the CPF1 endonuclease R-loop complex after DNA cleavage
5MGA · CRISPR-associated endonuclease CPF1: “Structure of the CPF1 endonuclease R-loop complex after DNA cleavage”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.80). MolNFT v1 #126884 on GenesisL1: 3D structure…
- PDB
- 5MGA
- Type
- protein + DNA + RNA
- Length
- 1,260 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CPF1; RNA (40-mer); DNA (26-mer); DNA…
- EC
- 3.1.-.-
- UniProt
- A0Q7Q2
- Ligands
- MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CPF1 (EC 3.1.-.-) | protein | 1182 | 41% helix, 11% strand | A0Q7Q2 |
| B | RNA (40-mer) | rna | 40 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
| D | DNA (5'-D(P*CP*GP*TP*TP*AP*GP*AP*GP*AP*AP*GP*T)-3') | dna | 12 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.80 | 0.86 | 64 | empty |
| 2 | 700 | 0.78 | 0.83 | 63 | empty |
| 3 | 1114 | 0.75 | 0.78 | 77 | empty |
| 4 | 77 | 0.72 | 0.96 | 19 | empty |
| 5 | 571 | 0.72 | 0.80 | 47 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3705 Ų buried · 96 hydrogen bonds · protein-nucleic
- A–C · 2313 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–D · 1176 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 952 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- C–D · 246 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Compared structures
- 5MGA · Structure of the Cpf1 endonuclease R-loop complex after DNA cleavage · the same entry in another collection · chain A against A, TM-score 1.00
- A0Q7Q2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS12A (A0Q7Q2) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 A0Q7Q2
- Elsewhere: RCSB PDB 5MGA · PDBe 5MGA · UniProt A0Q7Q2
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