MolNFT v1 · #114121 · protein + DNA + RNA
Crystal structure of francisella novicida CAS9 rha in complex with sgrna and target DNA (tgg pam)
5B2Q · CRISPR-associated endonuclease CAS9: “Crystal structure of francisella novicida CAS9 rha in complex with sgrna and target DNA (tgg pam)”. X-ray diffraction, 4 ligands (CA, NA, ZN), 20 pockets (best druggability 0.88). MolNFT v1…
- 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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