MolNFT v1 · #152389 · protein + RNA
Type III-a csm complex, cryo-EM structure of csm-CTR1, ATP bound
6IG0 · Type III-a CRISPR-associated protein CSM1: “Type III-a csm complex, cryo-EM structure of csm-CTR1, ATP bound”. Electron microscopy, 3 ligands (ATP, MG, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #152389 on GenesisL1: 3D…
- PDB
- 6IG0
- Type
- protein + RNA
- Length
- 2,325 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type III-a CRISPR-associated protein CSM1; Type III-a CRISPR-associated protein CSM2…
- UniProt
- A0A2U2M0F3, A0A2U2M049, A0A2U2M035, A0A2U2M037, A0A2U2M038
- Ligands
- ATP, MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 30% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type III-a CRISPR-associated protein CSM1 | protein | 737 | 43% helix, 11% strand | A0A2U2M0F3 |
| D, C | Type III-a CRISPR-associated protein CSM2 | protein | 121 | 67% helix, 2% strand | A0A2U2M049 |
| G | Type III-a CRISPR-associated ramp protein CSM3 | protein | 217 | 14% helix, 22% strand | A0A2U2M035 |
| F | Type III-a CRISPR-associated ramp protein CSM3 | protein | 216 | 22% helix, 24% strand | A0A2U2M035 |
| E | Type III-a CRISPR-associated ramp protein CSM3 | protein | 207 | 20% helix, 24% strand | A0A2U2M035 |
| B | Type III-a CRISPR-associated ramp protein CSM4 | protein | 295 | 17% helix, 16% strand | A0A2U2M037 |
| H | Type III-a CRISPR-associated ramp protein CSM5 | protein | 344 | 23% helix, 16% strand | A0A2U2M038 |
| N | Crrna | rna | 34 | — | — |
| J | CTR1 | rna | 33 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
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 | 1115 | 0.87 | 0.89 | 117 | empty |
| 2 | 358 | 0.84 | 0.94 | 42 | empty |
| 3 | 1014 | 0.84 | 0.85 | 75 | empty |
| 4 | 787 | 0.83 | 0.86 | 61 | empty |
| 5 | 173 | 0.82 | 0.97 | 41 | empty |
Interfaces
35 interfaces between chains.
- A–B · 1745 Ų buried · 17 hydrogen bonds · protein-protein
- B–N · 1546 Ų buried · 39 hydrogen bonds · protein-nucleic
- E–B · 1546 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1536 Ų buried · 19 hydrogen bonds · protein-protein
- F–E · 1443 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6IG0 · Type III-A Csm complex, Cryo-EM structure of Csm-CTR1, ATP bound · 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 A0A2U2M049
- Every structure of UniProt A0A2U2M035
- Every structure of UniProt A0A2U2M037
- Every structure of UniProt A0A2U2M038
- Elsewhere: RCSB PDB 6IG0 · PDBe 6IG0 · UniProt A0A2U2M0F3 · UniProt A0A2U2M049 · UniProt A0A2U2M035 · UniProt A0A2U2M037 · UniProt A0A2U2M038
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