MolNFT v1 · #142757 · protein + DNA + RNA
Crystal structure of XCAS9 in complex with sgrna and target DNA (gat pam)
6AEG · RNA (95-mer): “Crystal structure of XCAS9 in complex with sgrna and target DNA (gat pam)”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #142757 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AEG
- Type
- protein + DNA + RNA
- Length
- 1,453 residues
- Chains
- 4
- 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*GP*AP*TP*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 · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (95-mer) | rna | 95 | — | — |
| C | DNA (25-mer) | dna | 25 | — | — |
| D | DNA (5'-D(*AP*AP*AP*GP*AP*TP*TP*AP*TP*TP*G)-3') | dna | 11 | — | — |
| B | DNA nuclease (EC 3.1.-.-) | protein | 1322 | 48% helix, 13% strand | Q99ZW2 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.83 | 0.84 | 101 | empty |
| 2 | 896 | 0.74 | 0.78 | 79 | empty |
| 3 | 692 | 0.72 | 0.79 | 54 | empty |
| 4 | 970 | 0.72 | 0.76 | 76 | empty |
| 5 | 1063 | 0.71 | 0.75 | 63 | empty |
Interfaces
5 interfaces between chains.
- A–B · 6494 Ų buried · 155 hydrogen bonds · protein-nucleic
- C–B · 1417 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 834 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- D–B · 542 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 372 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Compared structures
- 6AEG · Crystal structure of xCas9 in complex with sgRNA and target DNA (GAT 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 0.95
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 6AEG · PDBe 6AEG · UniProt Q99ZW2
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