MolNFT v1 · #54333 · protein + RNA
Crystal structure of the CSY4-crrna complex, orthorhombic form
2XLK · CSY4 endoribonuclease: “Crystal structure of the CSY4-crrna complex, orthorhombic form”. X-ray diffraction, 7 pockets (best druggability 0.71). MolNFT v1 #54333 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XLK
- Type
- protein + RNA
- Length
- 399 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSY4 endoribonuclease; 5'-R(*CP*UP*GP*CP*CP*GP*UP*AP*UP*AP*GP*GP*CP*A*DG*C)-3'
- UniProt
- A3KUJ4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CSY4 endoribonuclease | protein | 188 | 28% helix, 25% strand | A3KUJ4 |
| B | CSY4 endoribonuclease | protein | 181 | 29% helix, 28% strand | A3KUJ4 |
| C, D | 5'-R(*CP*UP*GP*CP*CP*GP*UP*AP*UP*AP*GP*GP*CP*A*DG*C)-3' | rna | 15 | — | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.71 | 0.77 | 74 | empty |
| 2 | 150 | 0.61 | 0.84 | 31 | empty |
| 3 | 179 | 0.56 | 0.81 | 32 | empty |
| 4 | 127 | 0.46 | 0.78 | 20 | empty |
| 5 | 92 | 0.36 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1086 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–D · 1066 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–B · 569 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2XLK · Crystal structure of the Csy4-crRNA complex, orthorhombic form · the same entry in another collection · chain A against A, TM-score 1.00
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 A3KUJ4
- Elsewhere: RCSB PDB 2XLK · PDBe 2XLK · UniProt A3KUJ4
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