Research workbench
Crystal structure of SPCAS9-ng
Analyse Crystal structure of SPCAS9-ng in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AI6
- Type
- protein + DNA + RNA
- Length
- 1,439 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9/CSN1; RNA (81-mer); DNA (28-mer); DNA (8-mer)
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- K, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1322 | 48% helix, 12% strand | Q99ZW2 |
| B | RNA (81-mer) | rna | 81 | — | — |
| C | DNA (28-mer) | dna | 28 | — | — |
| D | DNA (8-mer) | dna | 8 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 10 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.82 | 0.83 | 101 | K, MG |
| 2 | 957 | 0.75 | 0.79 | 74 | EDO |
| 3 | 859 | 0.74 | 0.78 | 89 | K |
| 4 | 838 | 0.72 | 0.78 | 30 | empty |
| 5 | 897 | 0.72 | 0.77 | 79 | empty |
Interfaces
5 interfaces between chains.
- A–B · 6008 Ų buried · 126 hydrogen bonds · protein-nucleic
- A–C · 1551 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 1003 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- A–D · 567 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 360 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 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 0.99
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 6AI6 · PDBe 6AI6 · UniProt Q99ZW2
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