Research workbench
Crystal structure of AACC2C1-sgrna-8MER substrate DNA ternary complex
Analyse Crystal structure of AACC2C1-sgrna-8MER substrate DNA ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U31
- Type
- protein + DNA + RNA
- Length
- 1,227 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease C2C1; Sgrna; Target DNA strand; Non-target DNA strand
- EC
- 3.1.-.-
- UniProt
- T0D7A2
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease C2C1 (EC 3.1.-.-) | protein | 1085 | 42% helix, 17% strand | T0D7A2 |
| B | Sgrna | rna | 99 | — | — |
| C | Target DNA strand | dna | 28 | — | — |
| D | Non-target DNA strand | dna | 8 | — | — |
| E | Non-target DNA strand | dna | 7 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.78 | 0.90 | 34 | empty |
| 2 | 345 | 0.76 | 0.87 | 44 | empty |
| 3 | 423 | 0.75 | 0.85 | 45 | empty |
| 4 | 768 | 0.72 | 0.78 | 50 | empty |
| 5 | 535 | 0.71 | 0.81 | 39 | empty |
Interfaces
7 interfaces between chains.
- A–B · 6228 Ų buried · 142 hydrogen bonds · protein-nucleic
- A–C · 2591 Ų buried · 51 hydrogen bonds · protein-nucleic
- A–E · 1250 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 937 Ų buried · 98 hydrogen bonds · nucleic-nucleic
- A–D · 862 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 5U31 · Crystal structure of AacC2c1-sgRNA-8mer substrate DNA ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
- T0D7A2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS12B (T0D7A2) · 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 T0D7A2
- Elsewhere: RCSB PDB 5U31 · PDBe 5U31 · UniProt T0D7A2
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