MolNFT v1 · #152711 · protein + RNA
Cryo-EM structure of csm effector complex
6IQW · CSM1: “Cryo-EM structure of csm effector complex”. Electron microscopy, 1 ligand (ATP), 20 pockets (best druggability 0.84). MolNFT v1 #152711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IQW
- Type
- protein + RNA
- Length
- 2,097 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSM1; CSM2; CSM3; CSM4; CSM5; RNA (5'- R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*…
- UniProt
- B6YWB8, B6YWB9, B6YWC0, B6YWC1, B6YWC2
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 7 distinct chains · 34% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CSM1 | protein | 771 | 41% helix, 12% strand | B6YWB8 |
| B | CSM2 | protein | 134 | 68% helix, 0% strand | B6YWB9 |
| C | CSM3 | protein | 274 | 25% helix, 14% strand | B6YWC0 |
| D | CSM3 | protein | 271 | 26% helix, 14% strand | B6YWC0 |
| E | CSM4 | protein | 277 | 13% helix, 15% strand | B6YWC1 |
| F | CSM5 | protein | 346 | 37% helix, 17% strand | B6YWC2 |
| I | RNA (5'- R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*CP*CP*CP*UP* UP*C)-3') | rna | 24 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.84 | 0.85 | 100 | empty |
| 2 | 773 | 0.81 | 0.84 | 63 | ATP |
| 3 | 548 | 0.78 | 0.85 | 66 | empty |
| 4 | 101 | 0.77 | 0.98 | 28 | empty |
| 5 | 509 | 0.76 | 0.83 | 57 | empty |
Interfaces
18 interfaces between chains.
- C–D · 2168 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 1729 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 1511 Ų buried · 15 hydrogen bonds · protein-protein
- E–I · 1396 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–I · 1293 Ų buried · 31 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6IQW · Cryo-EM structure of Csm effector complex · the same entry in another collection · chain I against I, 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 0.98
- B6YWC1 · AlphaFold monomer V2.0 prediction for CRISPR system cms protein CSM4 (B6YWC1) · a predicted model of the same protein · chain E against A, TM-score 0.93
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 B6YWB9
- Every structure of UniProt B6YWC0
- Every structure of UniProt B6YWC1
- Every structure of UniProt B6YWC2
- Elsewhere: RCSB PDB 6IQW · PDBe 6IQW · UniProt B6YWB8 · UniProt B6YWB9 · UniProt B6YWC0 · UniProt B6YWC1 · UniProt B6YWC2
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