Research workbench
Crystal structure of DCAS9 in complex with sgrna and DNA (cga pam)
Analyse Crystal structure of DCAS9 in complex with sgrna and DNA (cga pam) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K57
- Type
- protein + DNA + RNA
- Length
- 1,435 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgrna; CRISPR-associated endonuclease CAS9; Target DNA; Non-target DNA
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sgrna | rna | 81 | — | — |
| B | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1315 | 49% helix, 11% strand | Q99ZW2 |
| C | Target DNA | dna | 28 | — | — |
| D | Non-target DNA | dna | 11 | — | — |
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 | 793 | 0.80 | 0.83 | 75 | empty |
| 2 | 831 | 0.79 | 0.83 | 86 | empty |
| 3 | 790 | 0.79 | 0.82 | 78 | empty |
| 4 | 432 | 0.77 | 0.86 | 37 | empty |
| 5 | 525 | 0.69 | 0.79 | 55 | empty |
Interfaces
5 interfaces between chains.
- A–B · 6053 Ų buried · 133 hydrogen bonds · protein-nucleic
- B–C · 1684 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–C · 970 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- B–D · 577 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 390 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Compared structures
- 6K57 · Crystal structure of dCas9 in complex with sgRNA and DNA (CGA PAM) · the same entry in another collection · chain A against A, TM-score 1.00
- Q99ZW2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9/CSN1 (Q99ZW2) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q99ZW2
- Elsewhere: RCSB PDB 6K57 · PDBe 6K57 · UniProt Q99ZW2
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