Research workbench
Target-bound SPCAS9 complex with trac full RNA guide
Analyse Target-bound SPCAS9 complex with trac full RNA guide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OX8
- Type
- protein + DNA + RNA
- Length
- 1,450 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgrna; CRISPR-associated endonuclease CAS9/CSN1; Trac target DNA strand; Trac non-target…
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- K, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sgrna | rna | 82 | — | — |
| B | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1330 | 49% helix, 12% strand | Q99ZW2 |
| C | Trac target DNA strand | dna | 28 | — | — |
| D | Trac non-target DNA strand | dna | 10 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 12 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.78 | 0.80 | 81 | K |
| 2 | 1116 | 0.78 | 0.80 | 90 | K |
| 3 | 833 | 0.76 | 0.81 | 58 | K |
| 4 | 1087 | 0.76 | 0.79 | 109 | K |
| 5 | 474 | 0.75 | 0.84 | 38 | MG, K |
Interfaces
5 interfaces between chains.
- A–B · 6162 Ų buried · 127 hydrogen bonds · protein-nucleic
- B–C · 1676 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 1019 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- B–D · 554 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 410 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Compared structures
- 7OX8 · Target-bound SpCas9 complex with TRAC full RNA 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 0.98
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 7OX8 · PDBe 7OX8 · UniProt Q99ZW2
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