MolNFT v1 · #158872 · protein + RNA
Crystal structure of CSM1-CSM4 cassette in complex with pppapa
6O75 · CRISPR system single-strand-specific deoxyribonuclease…: “Crystal structure of CSM1-CSM4 cassette in complex with pppapa”. X-ray diffraction, 1 ligand (MN), 18 pockets (best druggability 0.82). MolNFT v1 #158872 on GenesisL1: 3D…
- PDB
- 6O75
- Type
- protein + RNA
- Length
- 967 residues
- Chains
- 4
- 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
- 18 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% 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 | 710 | 48% helix, 15% strand | B6YWB8 |
| B | CSM4 | protein | 253 | 27% helix, 34% strand | B6YWC1 |
| C, D | RNA (5'-D(*(ATP))-R(P*A)-3') | rna | 2 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.82 | 0.97 | 37 | empty |
| 2 | 351 | 0.81 | 0.91 | 30 | empty |
| 3 | 998 | 0.72 | 0.76 | 64 | empty |
| 4 | 462 | 0.70 | 0.81 | 53 | empty |
| 5 | 138 | 0.48 | 0.78 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1403 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 560 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 474 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 173 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- B–C · 145 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified, 1 disulfide (nucleotide modification, disulfide).
Compared structures
- 6O75 · Crystal structure of Csm1-Csm4 cassette in complex with pppApA · 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 6O75 · PDBe 6O75 · UniProt B6YWB8 · UniProt B6YWC1
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