Research workbench
Crystal structure of LBUCAS13A-crrna-target RNA ternary complex
Analyse Crystal structure of LBUCAS13A-crrna-target RNA ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XWP
- Type
- protein + RNA
- Length
- 2,414 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; RNA (59-mer); RNA (30-mer)
- UniProt
- C7NBY4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 1125 | 60% helix, 6% strand | C7NBY4 |
| C, E | RNA (59-mer) | rna | 58 | — | — |
| D | RNA (30-mer) | rna | 30 | — | — |
| F | RNA (30-mer) | rna | 29 | — | — |
| B | Uncharacterized protein | protein | 1114 | 61% helix, 7% strand | C7NBY4 |
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 | 515 | 0.87 | 0.93 | 54 | empty |
| 2 | 512 | 0.87 | 0.93 | 51 | empty |
| 3 | 1186 | 0.86 | 0.87 | 100 | empty |
| 4 | 1114 | 0.83 | 0.85 | 75 | empty |
| 5 | 148 | 0.79 | 0.97 | 38 | empty |
Interfaces
9 interfaces between chains.
- A–C · 5562 Ų buried · 108 hydrogen bonds · protein-nucleic
- E–B · 5324 Ų buried · 99 hydrogen bonds · protein-nucleic
- A–D · 1910 Ų buried · 27 hydrogen bonds · protein-nucleic
- F–B · 1727 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 1307 Ų buried · 119 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 42 modified (engineered).
Compared structures
- 5XWP · Crystal structure of LbuCas13a-crRNA-target RNA ternary complex · the same entry in another collection · chain B against B, TM-score 1.00
- C7NBY4 · AlphaFold monomer V2.0 prediction for CRISPR-associated endoribonuclease CAS13A (C7NBY4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 C7NBY4
- Elsewhere: RCSB PDB 5XWP · PDBe 5XWP · UniProt C7NBY4
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