MolNFT v1 · #158875 · protein + RNA
Crystal structure of CSM1-CSM4 cassette in complex with pppapapa
6O78 · CRISPR system single-strand-specific deoxyribonuclease…: “Crystal structure of CSM1-CSM4 cassette in complex with pppapapa”. X-ray diffraction, 1 ligand (MN), 13 pockets (best druggability 0.82). MolNFT v1 #158875 on GenesisL1: 3D…
- PDB
- 6O78
- Type
- protein + RNA
- Length
- 947 residues
- Chains
- 3
- 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
- MN
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% 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 | 700 | 46% helix, 15% strand | B6YWB8 |
| B | CSM4 | protein | 244 | 28% helix, 31% strand | B6YWC1 |
| E | RNA (5'-D(*(ATP))-R(P*AP*A)-3') | rna | 3 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.82 | 0.83 | 93 | empty |
| 2 | 122 | 0.79 | 0.97 | 24 | empty |
| 3 | 209 | 0.58 | 0.79 | 26 | empty |
| 4 | 213 | 0.53 | 0.77 | 23 | empty |
| 5 | 135 | 0.52 | 0.80 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1380 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 762 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–E · 138 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 6O78 · Crystal structure of Csm1-Csm4 cassette in complex with pppApApA · 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 6O78 · PDBe 6O78 · UniProt B6YWB8 · UniProt B6YWC1
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