Research workbench
Cryo-EM structure of type III-a csm-CTR1 complex, amppnp bound
Analyse Cryo-EM structure of type III-a csm-CTR1 complex, amppnp bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IFK
- Type
- protein + RNA
- Length
- 2,323 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
- ANP, MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 9 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type III-a CRISPR-associated protein CSM1 | protein | 734 | 44% helix, 12% strand | A0A2U2M0F3 |
| D, C | Type III-a CRISPR-associated protein CSM2 | protein | 121 | 62% helix, 2% strand | A0A2U2M049 |
| G | Type III-a CRISPR-associated ramp protein CSM3 | protein | 217 | 15% helix, 24% strand | A0A2U2M035 |
| F | Type III-a CRISPR-associated ramp protein CSM3 | protein | 216 | 25% helix, 26% strand | A0A2U2M035 |
| E | Type III-a CRISPR-associated ramp protein CSM3 | protein | 207 | 24% helix, 25% strand | A0A2U2M035 |
| B | Type III-a CRISPR-associated ramp protein CSM4 | protein | 295 | 16% helix, 17% strand | A0A2U2M037 |
| H | Type III-a CRISPR-associated ramp protein CSM5 | protein | 345 | 25% helix, 17% strand | A0A2U2M038 |
| N | Crrna | rna | 34 | — | — |
| J | CTR1 | rna | 33 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · 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 | 1053 | 0.89 | 0.91 | 113 | empty |
| 2 | 294 | 0.85 | 0.95 | 40 | empty |
| 3 | 406 | 0.84 | 0.93 | 43 | empty |
| 4 | 842 | 0.82 | 0.85 | 67 | empty |
| 5 | 231 | 0.81 | 0.95 | 38 | empty |
Interfaces
34 interfaces between chains.
- A–B · 1714 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1557 Ų buried · 15 hydrogen bonds · protein-protein
- B–N · 1557 Ų buried · 42 hydrogen bonds · protein-nucleic
- E–B · 1489 Ų buried · 17 hydrogen bonds · protein-protein
- F–E · 1450 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6IFK · Cryo-EM structure of type III-A Csm-CTR1 complex, AMPPNP 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 6IFK · PDBe 6IFK · UniProt A0A2U2M0F3 · UniProt A0A2U2M049 · UniProt A0A2U2M035 · UniProt A0A2U2M037 · UniProt A0A2U2M038
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