Research workbench
Type III-a csm complex, cryo-EM structure of csm-ntr, ATP bound
Analyse Type III-a csm complex, cryo-EM structure of csm-ntr, ATP bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IFR
- Type
- protein + RNA
- Length
- 2,286 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
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 29% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type III-a CRISPR-associated protein CSM1 | protein | 694 | 43% helix, 9% strand | A0A2U2M0F3 |
| D, C | Type III-a CRISPR-associated protein CSM2 | protein | 121 | 61% helix, 2% strand | A0A2U2M049 |
| G | Type III-a CRISPR-associated ramp protein CSM3 | protein | 217 | 19% helix, 24% strand | A0A2U2M035 |
| F | Type III-a CRISPR-associated ramp protein CSM3 | protein | 217 | 17% helix, 27% strand | A0A2U2M035 |
| E | Type III-a CRISPR-associated ramp protein CSM3 | protein | 205 | 18% helix, 22% strand | A0A2U2M035 |
| B | Type III-a CRISPR-associated ramp protein CSM4 | protein | 288 | 17% helix, 19% strand | A0A2U2M037 |
| H | Type III-a CRISPR-associated ramp protein CSM5 | protein | 353 | 21% helix, 15% strand | A0A2U2M038 |
| N | Type III-a CRISPR-CAS interference complex, crrna | rna | 35 | — | — |
| J | Type III-a CRISPR-CAS interference complex, ntr | rna | 35 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · 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 | 1012 | 0.85 | 0.86 | 82 | empty |
| 2 | 365 | 0.84 | 0.94 | 42 | empty |
| 3 | 237 | 0.83 | 0.96 | 28 | empty |
| 4 | 601 | 0.83 | 0.89 | 54 | empty |
| 5 | 1196 | 0.82 | 0.83 | 99 | empty |
Interfaces
34 interfaces between chains.
- G–H · 1558 Ų buried · 17 hydrogen bonds · protein-protein
- B–N · 1542 Ų buried · 45 hydrogen bonds · protein-nucleic
- E–B · 1532 Ų buried · 21 hydrogen bonds · protein-protein
- G–F · 1435 Ų buried · 6 hydrogen bonds · protein-protein
- F–E · 1370 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6IFR · Type III-A Csm complex, Cryo-EM structure of Csm-NTR, 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 6IFR · PDBe 6IFR · UniProt A0A2U2M0F3 · UniProt A0A2U2M049 · UniProt A0A2U2M035 · UniProt A0A2U2M037 · UniProt A0A2U2M038
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