Research workbench
Crystal structure of XCAS9 in complex with sgrna and target DNA (aag pam)
Analyse Crystal structure of XCAS9 in complex with sgrna and target DNA (aag pam) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AEB
- Type
- protein + DNA + RNA
- Length
- 2,906 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (95-mer); DNA (25-mer); DNA (5'-D(*AP*AP*AP*AP*AP*GP*TP*AP*TP*TP*G)-3'); DNA nuclease
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | RNA (95-mer) | rna | 95 | — | — |
| C, G | DNA (25-mer) | dna | 25 | — | — |
| D, H | DNA (5'-D(*AP*AP*AP*AP*AP*GP*TP*AP*TP*TP*G)-3') | dna | 11 | — | — |
| B, F | DNA nuclease (EC 3.1.-.-) | protein | 1322 | 45% helix, 13% strand | Q99ZW2 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.83 | 0.86 | 96 | empty |
| 2 | 1109 | 0.82 | 0.84 | 101 | empty |
| 3 | 877 | 0.74 | 0.79 | 64 | empty |
| 4 | 850 | 0.73 | 0.78 | 87 | empty |
| 5 | 1028 | 0.73 | 0.76 | 91 | empty |
Interfaces
11 interfaces between chains.
- A–B · 6453 Ų buried · 167 hydrogen bonds · protein-nucleic
- E–F · 6452 Ų buried · 152 hydrogen bonds · protein-nucleic
- G–F · 1389 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–B · 1361 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 829 Ų buried · 76 hydrogen bonds · nucleic-nucleic
Compared structures
- 6AEB · Crystal structure of xCas9 in complex with sgRNA and target DNA (AAG PAM) · the same entry in another collection · chain F against F, 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 F against A, TM-score 0.95
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 6AEB · PDBe 6AEB · UniProt Q99ZW2
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