Research workbench
Crystal structure of francisella novicida CAS9 rha in complex with sgrna and target DNA (tgg pam)
Analyse Crystal structure of francisella novicida CAS9 rha in complex with sgrna and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B2Q
- Type
- protein + DNA + RNA
- Length
- 1,587 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9; Guide RNA; Target DNA; DNA…
- EC
- 3.1.-.-
- UniProt
- A0Q5Y3
- Ligands
- CA, NA, ZN, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1455 | 47% helix, 15% strand | A0Q5Y3 |
| B | Guide RNA | rna | 93 | — | — |
| C | Target DNA | dna | 30 | — | — |
| D | DNA (5'-D(*TP*GP*GP*TP*AP*TP*CP*GP*G)-3') | dna | 9 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 17 copies · chains A, B, C
- NA · Sodium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.88 | 0.90 | 110 | CA, EDO |
| 2 | 1092 | 0.85 | 0.87 | 86 | NA, ACT, CA, EDO |
| 3 | 370 | 0.76 | 0.86 | 37 | EDO |
| 4 | 1198 | 0.76 | 0.79 | 118 | EDO |
| 5 | 593 | 0.75 | 0.82 | 85 | CL |
Interfaces
5 interfaces between chains.
- A–B · 7791 Ų buried · 212 hydrogen bonds · protein-nucleic
- A–C · 1991 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 1071 Ų buried · 98 hydrogen bonds · nucleic-nucleic
- A–D · 654 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 417 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Compared structures
- 5B2Q · Crystal structure of Francisella novicida Cas9 RHA in complex with sgRNA and target DNA… · the same entry in another collection · chain D against D, TM-score 1.00
- A0Q5Y3 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9 (A0Q5Y3) · 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 A0Q5Y3
- Elsewhere: RCSB PDB 5B2Q · PDBe 5B2Q · UniProt A0Q5Y3
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