MolNFT v1 · #139482 · protein + DNA + RNA
Crystal structure of the acidaminococcus sp. BV3L6 CPF1 rvr variant in complex with crrna and target DNA (tata pam)
5XH6 · CRISPR-associated endonuclease CPF1: “Crystal structure of the acidaminococcus sp. BV3L6 CPF1 rvr variant in complex with crrna and target DNA…”. X-ray diffraction, 2 ligands (NA, CL), 20 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 5XH6
- Type
- protein + DNA + RNA
- Length
- 1,362 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CPF1; Crrna; Target DNA strand; Non-target DNA strand
- EC
- 3.1.-.-
- UniProt
- U2UMQ6
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CPF1 (EC 3.1.-.-) | protein | 1283 | 48% helix, 14% strand | U2UMQ6 |
| B | Crrna | rna | 39 | — | — |
| C | Target DNA strand | dna | 30 | — | — |
| D | Non-target DNA strand | dna | 10 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B, C
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.82 | 0.92 | 51 | EDO |
| 2 | 831 | 0.78 | 0.82 | 60 | EDO, NA |
| 3 | 702 | 0.72 | 0.79 | 56 | NA |
| 4 | 573 | 0.66 | 0.77 | 50 | EDO |
| 5 | 722 | 0.66 | 0.75 | 71 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 3805 Ų buried · 96 hydrogen bonds · protein-nucleic
- A–C · 2401 Ų buried · 48 hydrogen bonds · protein-nucleic
- B–C · 927 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- A–D · 650 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 450 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Compared structures
- 5XH6 · Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with crRNA… · 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 5XH6 · PDBe 5XH6 · UniProt U2UMQ6
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