Research workbench
Cryo-EM structure of ST1CAS9-sgrna-TDNA20-ACRIIA6 dimeric assembly.
Analyse Cryo-EM structure of ST1CAS9-sgrna-TDNA20-ACRIIA6 dimeric assembly. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RJA
- Type
- protein + DNA + RNA
- Length
- 2,190 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ACRIIA6; CRISPR-associated endonuclease CAS9 1; RNA (78-mer); TDNA20
- EC
- 3.1.-.-
- UniProt
- A0A2U7VKE8, Q03LF7
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ACRIIA6 | protein | 183 | 50% helix, 17% strand | A0A2U7VKE8 |
| C, F | CRISPR-associated endonuclease CAS9 1 (EC 3.1.-.-) | protein | 815 | 38% helix, 18% strand | Q03LF7 |
| D, G | RNA (78-mer) | rna | 78 | — | — |
| E, H | TDNA20 | dna | 19 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.84 | 0.85 | 88 | empty |
| 2 | 1175 | 0.84 | 0.85 | 89 | empty |
| 3 | 1119 | 0.84 | 0.86 | 68 | empty |
| 4 | 1155 | 0.84 | 0.85 | 72 | empty |
| 5 | 747 | 0.83 | 0.87 | 101 | empty |
Interfaces
13 interfaces between chains.
- C–D · 5980 Ų buried · 106 hydrogen bonds · protein-nucleic
- F–G · 5934 Ų buried · 103 hydrogen bonds · protein-nucleic
- A–C · 1377 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1371 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1263 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6RJA · Cryo-EM structure of St1Cas9-sgRNA-tDNA20-AcrIIA6 dimeric assembly. · the same entry in another collection · chain H against H, TM-score 1.00
- Q03LF7 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9 1 (Q03LF7) · a predicted model of the same protein · chain F against A, TM-score 0.93
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 A0A2U7VKE8
- Every structure of UniProt Q03LF7
- Elsewhere: RCSB PDB 6RJA · PDBe 6RJA · UniProt A0A2U7VKE8 · UniProt Q03LF7
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