Research workbench
Crystal structure of the acidaminococcus sp. BV3L6 CPF1 rvr variant in complex with crrna and target DNA (tata pam)
Analyse Crystal structure of the acidaminococcus sp. BV3L6 CPF1 rvr variant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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