MolNFT v1 · #142752 · protein + DNA + RNA
Crystal structure of XCAS9 in complex with sgrna and target DNA (aag pam)
6AEB · RNA (95-mer): “Crystal structure of XCAS9 in complex with sgrna and target DNA (aag pam)”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #142752 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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