Research workbench
Crystal structure of CSM1-CSM4 cassette in complex with one ATP
Analyse Crystal structure of CSM1-CSM4 cassette in complex with one ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O7D
- Type
- protein
- Length
- 950 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-a); CSM4
- EC
- 3.1.-.-, 2.7.7.-
- UniProt
- B6YWB8, B6YWC1
- Ligands
- ATP, MN
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-a) (EC 3.1.-.-, 2.7.7.-) | protein | 708 | 46% helix, 15% strand | B6YWB8 |
| B | CSM4 | protein | 242 | 29% helix, 29% strand | B6YWC1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.85 | 0.87 | 91 | ATP, MN |
| 2 | 265 | 0.54 | 0.76 | 31 | empty |
| 3 | 90 | 0.51 | 0.83 | 22 | empty |
| 4 | 108 | 0.45 | 0.78 | 20 | empty |
| 5 | 87 | 0.43 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1289 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6O7D · Crystal structure of Csm1-Csm4 cassette in complex with one ATP · the same entry in another collection · chain A against A, TM-score 1.00
- B6YWB8 · AlphaFold monomer V2.0 prediction for CRISPR system single-strand- specific… · a predicted model of the same protein · chain A against A, TM-score 0.99
- B6YWC1 · AlphaFold monomer V2.0 prediction for CRISPR system cms protein CSM4 (B6YWC1) · a predicted model of the same protein · chain B 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 B6YWB8
- Every structure of UniProt B6YWC1
- Elsewhere: RCSB PDB 6O7D · PDBe 6O7D · UniProt B6YWB8 · UniProt B6YWC1
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