MolNFT v1 · #184636 · protein + DNA + RNA
Target-bound SPCAS9 complex with trac chimeric RNA-DNA guide
7OX7: “Target-bound SPCAS9 complex with trac chimeric RNA-DNA guide”. X-ray diffraction, 2 ligands (K, MG), 20 pockets (best druggability 0.77). MolNFT v1 #184636 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7OX7
- Type
- protein + DNA + RNA
- Length
- 1,442 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; Trac target DNA strand…
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- K, MG
- Pockets
- 20 · best druggability 0.77
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 | 1323 | 48% 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 · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.77 | 0.83 | 75 | K |
| 2 | 502 | 0.74 | 0.83 | 44 | empty |
| 3 | 689 | 0.74 | 0.81 | 54 | MG, K |
| 4 | 873 | 0.73 | 0.78 | 73 | K |
| 5 | 669 | 0.72 | 0.79 | 86 | empty |
Interfaces
5 interfaces between chains.
- A–B · 6123 Ų buried · 131 hydrogen bonds · protein-nucleic
- B–C · 1684 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 1000 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- B–D · 547 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 399 Ų buried · 27 hydrogen bonds · nucleic-nucleic
Compared structures
- 7OX7 · Target-bound SpCas9 complex with TRAC 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 7OX7 · PDBe 7OX7 · UniProt Q99ZW2
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