MolNFT v1 · #139483 · protein + DNA + RNA
Crystal structure of the acidaminococcus sp. BV3L6 CPF1 rr variant in complex with crrna and target DNA (tcca pam)
5XH7 · CRISPR-associated endonuclease CPF1: “Crystal structure of the acidaminococcus sp. BV3L6 CPF1 rr variant in complex with crrna and target DNA (tcca…”. X-ray diffraction, 2 ligands (NA, CL), 19 pockets (best druggability 0.82).…
- PDB
- 5XH7
- 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
- 19 · 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 · 16 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.82 | 0.90 | 47 | EDO |
| 2 | 1171 | 0.78 | 0.80 | 73 | EDO, NA |
| 3 | 487 | 0.72 | 0.82 | 45 | NA |
| 4 | 104 | 0.67 | 0.91 | 30 | empty |
| 5 | 719 | 0.67 | 0.75 | 73 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 3819 Ų buried · 95 hydrogen bonds · protein-nucleic
- A–C · 2520 Ų buried · 54 hydrogen bonds · protein-nucleic
- B–C · 931 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–D · 721 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 448 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Compared structures
- 5XH7 · Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RR 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 5XH7 · PDBe 5XH7 · UniProt U2UMQ6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.