Research workbench
CAS9:GRNA in complex with 18-20MM DNA, 1 minute time-point, kinked active conformation
Analyse CAS9:GRNA in complex with 18-20MM DNA, 1 minute time-point, kinked active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S4X
- Type
- protein + DNA + RNA
- Length
- 1,515 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9/CSN1; Grna; Ts; Nts
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1354 | 47% helix, 12% strand | Q99ZW2 |
| B | Grna | rna | 98 | — | — |
| C | Ts | dna | 16 | — | — |
| c | Ts | dna | 20 | — | — |
| D | Nts | dna | 27 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, D, C, c, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.84 | 0.85 | 104 | empty |
| 2 | 498 | 0.82 | 0.89 | 45 | MG |
| 3 | 882 | 0.76 | 0.80 | 74 | empty |
| 4 | 770 | 0.74 | 0.79 | 57 | empty |
| 5 | 229 | 0.73 | 0.89 | 30 | empty |
Interfaces
9 interfaces between chains.
- A–B · 7548 Ų buried · 166 hydrogen bonds · protein-nucleic
- A–D · 2042 Ų buried · 46 hydrogen bonds · protein-nucleic
- A–c · 1934 Ų buried · 39 hydrogen bonds · protein-nucleic
- B–c · 870 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- A–C · 701 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 7S4X · Cas9:gRNA in complex with 18-20MM DNA, 1 minute time-point, kinked active conformation · the same entry in another collection · chain B against B, 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 A against A, TM-score 0.84
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 7S4X · PDBe 7S4X · UniProt Q99ZW2
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