Research workbench
Structure of nuclease in complex with associated protein
Analyse Structure of nuclease in complex with associated protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XBL
- Type
- protein + RNA
- Length
- 1,489 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9/CSN1; Associated protein; RNA (98-mer)
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1320 | 45% helix, 12% strand | Q99ZW2 |
| D | Associated protein | protein | 81 | 31% helix, 16% strand | — |
| B | RNA (98-mer) | rna | 88 | — | — |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.86 | 0.89 | 101 | empty |
| 2 | 396 | 0.77 | 0.87 | 41 | empty |
| 3 | 1089 | 0.75 | 0.78 | 89 | empty |
| 4 | 391 | 0.75 | 0.86 | 50 | empty |
| 5 | 58 | 0.69 | 0.97 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 6360 Ų buried · 126 hydrogen bonds · protein-nucleic
- A–D · 1764 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5XBL · Structure of nuclease in complex with associated protein · 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 A against A, TM-score 0.79
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 5XBL · PDBe 5XBL · UniProt Q99ZW2
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