Research workbench
Crystal structure of XCAS9 in complex with sgrna and DNA (tgg pam)
Analyse Crystal structure of XCAS9 in complex with sgrna and DNA (tgg pam) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K4P
- Type
- protein + DNA + RNA
- Length
- 1,443 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgrna; DNA (28-mer); Non-targeted DNA; CRISPR-associated endonuclease CAS9/CSN1
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sgrna | rna | 81 | — | — |
| C | DNA (28-mer) | dna | 28 | — | — |
| D | Non-targeted DNA | dna | 11 | — | — |
| B | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1323 | 47% helix, 11% strand | Q99ZW2 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains 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 | 659 | 0.84 | 0.88 | 68 | empty |
| 2 | 966 | 0.76 | 0.79 | 92 | empty |
| 3 | 1039 | 0.76 | 0.79 | 83 | empty |
| 4 | 965 | 0.75 | 0.79 | 48 | empty |
| 5 | 559 | 0.72 | 0.81 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5976 Ų buried · 141 hydrogen bonds · protein-nucleic
- C–B · 1657 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 975 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- D–B · 602 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 379 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Compared structures
- 6K4P · Crystal structure of xCas9 in complex with sgRNA and DNA (TGG PAM) · 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 6K4P · PDBe 6K4P · UniProt Q99ZW2
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