Research workbench
Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog
Analyse Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X1L
- Type
- protein + DNA + RNA
- Length
- 2,524 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.096
- Source
- Archaeoglobus fulgidus DSM 4304; Pyrococcus furiosus DSM 3638; SYNTHETIC…
- Molecule
- CRISPR system Cmr subunit Cmr2; CRISPR system Cmr subunit Cmr3; Cmr4; CRISPR system Cmr…
- UniProt
- Q8U1S6, Q8U1S7, O28416, O28417, O28418
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.096 · 10 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR system Cmr subunit Cmr2 | protein | 573 | 59% helix, 15% strand | Q8U1S6 |
| B | CRISPR system Cmr subunit Cmr3 | protein | 319 | 16% helix, 43% strand | Q8U1S7 |
| C | Cmr4 | protein | 322 | 35% helix, 30% strand | O28416 |
| D | Cmr4 | protein | 331 | 33% helix, 28% strand | O28416 |
| E | Cmr4 | protein | 330 | 32% helix, 29% strand | O28416 |
| F | CRISPR system Cmr subunit Cmr5 | protein | 146 | 73% helix, 0% strand | O28417 |
| G | CRISPR system Cmr subunit Cmr5 | protein | 152 | 70% helix, 0% strand | O28417 |
| H | Cmr6 | protein | 297 | 46% helix, 18% strand | O28418 |
| I | RNA (32-mer) | rna | 32 | — | — |
| J | DNA (5'-D(*TP*GP*CP*TP*CP*TP*CP*AP*GP*CP*CP*GP*CP*AP*AP*GP*GP*AP*CP*CP*GP*CP*AP*TP*AP*CP*TP*AP*CP*AP*A)-3') | dna | 22 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 826 | 0.87 | 0.90 | 103 | empty |
| 2 | 733 | 0.85 | 0.88 | 69 | empty |
| 3 | 290 | 0.83 | 0.94 | 54 | empty |
| 4 | 371 | 0.83 | 0.93 | 50 | empty |
| 5 | 876 | 0.80 | 0.83 | 83 | empty |
Interfaces
35 interfaces between chains.
- A–B · 2241 Ų buried · 27 hydrogen bonds · protein-protein
- E–H · 2061 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1606 Ų buried · 24 hydrogen bonds · protein-protein
- B–I · 1595 Ų buried · 52 hydrogen bonds · protein-nucleic
- D–E · 1518 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3X1L · Crystal structure of the CRISPR-CAS RNA silencing cmr complex bound to a target analog · the same entry in another collection · chain J against J, TM-score 1.00
- Q8U1S6 · AlphaFold monomer V2.0 prediction for CRISPR system cmr subunit CMR2 (Q8U1S6) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O28417 · AlphaFold monomer V2.0 prediction for CRISPR system cmr subunit CMR5 (O28417) · a predicted model of the same protein · chain F against A, TM-score 0.98
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 Q8U1S6
- Every structure of UniProt Q8U1S7
- Every structure of UniProt O28416
- Every structure of UniProt O28417
- Every structure of UniProt O28418
- Elsewhere: RCSB PDB 3X1L · PDBe 3X1L · UniProt Q8U1S6 · UniProt Q8U1S7 · UniProt O28416 · UniProt O28417 · UniProt O28418
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