MolNFT v1 · #113966 · protein + DNA + RNA
Crystal structure of staphylococcus aureus CAS9 in complex with sgrna and target DNA (ttgggt pam)
5AXW · CRISPR-associated endonuclease CAS9: “Crystal structure of staphylococcus aureus CAS9 in complex with sgrna and target DNA (ttgggt pam)”. X-ray diffraction, 2 ligands (NA, PO4), 20 pockets (best druggability 0.84). MolNFT v1 #113966…
- PDB
- 5AXW
- Type
- protein + DNA + RNA
- Length
- 1,151 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9; RNA (73-mer); DNA (28-mer); DNA…
- EC
- 3.1.-.-
- UniProt
- J7RUA5
- Ligands
- NA, PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1043 | 45% helix, 15% strand | J7RUA5 |
| B | RNA (73-mer) | rna | 72 | — | — |
| C | DNA (28-mer) | dna | 28 | — | — |
| D | DNA (5'-D(*TP*TP*GP*GP*GP*TP*AP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C, B
- PO4 · Phosphate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.84 | 0.86 | 76 | empty |
| 2 | 999 | 0.74 | 0.78 | 47 | empty |
| 3 | 224 | 0.72 | 0.88 | 32 | EDO |
| 4 | 305 | 0.67 | 0.82 | 39 | empty |
| 5 | 272 | 0.62 | 0.81 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4991 Ų buried · 130 hydrogen bonds · protein-nucleic
- A–C · 1600 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 996 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- A–D · 696 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 360 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Compared structures
- 5AXW · Crystal structure of Staphylococcus aureus Cas9 in complex with sgRNA and target DNA… · the same entry in another collection · chain A against A, TM-score 1.00
- J7RUA5 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9 (J7RUA5) · a predicted model of the same protein · chain A 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 J7RUA5
- Elsewhere: RCSB PDB 5AXW · PDBe 5AXW · UniProt J7RUA5
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