MolNFT v1 · #114120 · protein + DNA + RNA
Crystal structure of francisella novicida CAS9 in complex with sgrna and target DNA (tga pam)
5B2P · CRISPR-associated endonuclease CAS9: “Crystal structure of francisella novicida CAS9 in complex with sgrna and target DNA (tga pam)”. X-ray diffraction, 4 ligands (CA, NA, ZN), 20 pockets (best druggability 0.85). MolNFT v1 #114120…
- PDB
- 5B2P
- 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 0.85
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*AP*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 · 23 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.85 | 0.87 | 83 | NA, CA, ACT |
| 2 | 452 | 0.82 | 0.90 | 57 | EDO |
| 3 | 751 | 0.81 | 0.84 | 79 | EDO |
| 4 | 367 | 0.80 | 0.90 | 40 | CA, EDO |
| 5 | 218 | 0.73 | 0.89 | 37 | empty |
Interfaces
5 interfaces between chains.
- A–B · 7791 Ų buried · 211 hydrogen bonds · protein-nucleic
- A–C · 2004 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–C · 1073 Ų buried · 89 hydrogen bonds · nucleic-nucleic
- A–D · 709 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 404 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 5B2P · Crystal structure of Francisella novicida Cas9 in complex with sgRNA and target DNA (TGA… · the same entry in another collection · chain A against A, 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 5B2P · PDBe 5B2P · UniProt A0Q5Y3
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