Research workbench
Crystal structure of staphylococcus aureus CAS9 in complex with sgrna and target DNA (ttgggt pam)
Analyse Crystal structure of staphylococcus aureus CAS9 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
- 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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