Research workbench
Crystal structure of type I-D CRISPR-CAS nuclease CAS10D in complex with the SIRV3 ACRID1 (GP02) anti-CRISPR protein
Analyse Crystal structure of type I-D CRISPR-CAS nuclease CAS10D in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6THH
- Type
- protein
- Length
- 1,008 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SIRV3 ACRID1 (GP02) anti-CRISPR protein; CRISPR-associated protein, csca
- UniProt
- A0A1B3SN05, M9U4Y8
- Ligands
- ZN, PO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SIRV3 ACRID1 (GP02) anti-CRISPR protein | protein | 96 | 20% helix, 59% strand | A0A1B3SN05 |
| C | CRISPR-associated protein, csca | protein | 816 | 55% helix, 6% strand | M9U4Y8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.82 | 0.83 | 116 | empty |
| 2 | 237 | 0.72 | 0.87 | 44 | empty |
| 3 | 410 | 0.70 | 0.81 | 56 | empty |
| 4 | 329 | 0.61 | 0.78 | 25 | empty |
| 5 | 78 | 0.50 | 0.84 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1009 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 692 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 6THH · Crystal structure of type I-D CRISPR-Cas nuclease Cas10d in complex with the SIRV3 AcrID1… · 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 A0A1B3SN05
- Every structure of UniProt M9U4Y8
- Elsewhere: RCSB PDB 6THH · PDBe 6THH · UniProt A0A1B3SN05 · UniProt M9U4Y8
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