MolNFT v1 · #184639 · protein + DNA + RNA
Target-bound SPCAS9 complex with AAVS1 chimeric RNA-DNA guide
7OXA: “Target-bound SPCAS9 complex with AAVS1 chimeric RNA-DNA guide”. X-ray diffraction, 2 ligands (K, MG), 20 pockets (best druggability 0.83). MolNFT v1 #184639 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7OXA
- Type
- protein + DNA + RNA
- Length
- 1,439 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimeric RNA-DNA guide; CRISPR-associated endonuclease CAS9/CSN1; AAVS1 target DNA…
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- K, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimeric RNA-DNA guide | rna | 81 | — | — |
| B | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1320 | 48% helix, 12% strand | Q99ZW2 |
| C | AAVS1 target DNA strand | dna | 28 | — | — |
| D | AAVS1 non-target DNA strand | dna | 10 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 14 copies · chains A, B, C
- MG · Magnesium ion · metal · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.83 | 0.85 | 108 | MG, K |
| 2 | 826 | 0.79 | 0.83 | 63 | K |
| 3 | 634 | 0.71 | 0.79 | 79 | empty |
| 4 | 597 | 0.68 | 0.78 | 42 | K |
| 5 | 135 | 0.65 | 0.87 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 6085 Ų buried · 136 hydrogen bonds · protein-nucleic
- B–C · 1686 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 989 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- B–D · 556 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 385 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 7OXA · Target-bound SpCas9 complex with AAVS1 chimeric RNA-DNA guide · the same entry in another collection · chain A against A, TM-score 1.00
- Q99ZW2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9/CSN1 (Q99ZW2) · a predicted model of the same protein · chain B 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 Q99ZW2
- Elsewhere: RCSB PDB 7OXA · PDBe 7OXA · UniProt Q99ZW2
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