MolNFT v1 · #152376 · protein + RNA
Crystal structure of type III-a CRISPR csm complex
6IFN · Type III-a CRISPR-associated protein CSM1: “Crystal structure of type III-a CRISPR csm complex”. X-ray diffraction, 2 ligands (ZN, MN), 20 pockets (best druggability 0.82). MolNFT v1 #152376 on GenesisL1: 3D structure, binding sites…
- PDB
- 6IFN
- Type
- protein + RNA
- Length
- 2,313 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type III-a CRISPR-associated protein CSM1; Type III-a CRISPR-associated ramp protein…
- UniProt
- A0A2U2M0F3, A0A2U2M035, A0A2U2M037, A0A2U2M049, A0A2U2M038
- Ligands
- ZN, MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type III-a CRISPR-associated protein CSM1 | protein | 733 | 51% helix, 14% strand | A0A2U2M0F3 |
| F, G | Type III-a CRISPR-associated ramp protein CSM3 | protein | 220 | 28% helix, 30% strand | A0A2U2M035 |
| B | Type III-a CRISPR-associated ramp protein CSM4 | protein | 297 | 23% helix, 29% strand | A0A2U2M037 |
| E | Type III-a CRISPR-associated ramp protein CSM3 | protein | 219 | 29% helix, 31% strand | A0A2U2M035 |
| C | Type III-a CRISPR-associated protein CSM2 | protein | 124 | 70% helix, 2% strand | A0A2U2M049 |
| D | Type III-a CRISPR-associated protein CSM2 | protein | 123 | 67% helix, 3% strand | A0A2U2M049 |
| H | Type III-a CRISPR-associated ramp protein CSM5 | protein | 345 | 23% helix, 23% strand | A0A2U2M038 |
| N | RNA (32-mer) | rna | 32 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.82 | 0.85 | 120 | empty |
| 2 | 162 | 0.82 | 0.97 | 42 | empty |
| 3 | 190 | 0.81 | 0.96 | 36 | empty |
| 4 | 218 | 0.79 | 0.93 | 42 | empty |
| 5 | 214 | 0.78 | 0.92 | 31 | empty |
Interfaces
23 interfaces between chains.
- A–B · 1678 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 1560 Ų buried · 20 hydrogen bonds · protein-protein
- B–N · 1443 Ų buried · 33 hydrogen bonds · protein-nucleic
- F–E · 1419 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1346 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6IFN · Crystal structure of Type III-A CRISPR Csm complex · 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 A0A2U2M0F3
- Every structure of UniProt A0A2U2M035
- Every structure of UniProt A0A2U2M037
- Every structure of UniProt A0A2U2M049
- Every structure of UniProt A0A2U2M038
- Elsewhere: RCSB PDB 6IFN · PDBe 6IFN · UniProt A0A2U2M0F3 · UniProt A0A2U2M035 · UniProt A0A2U2M037 · UniProt A0A2U2M049 · UniProt A0A2U2M038
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