Research workbench
Type III-B cmr-beta cryo-EM structure of the apo state
Analyse Type III-B cmr-beta cryo-EM structure of the apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S6B
- Type
- protein + RNA
- Length
- 8,245 residues
- Chains
- 38
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated protein, CMR5 family; CRISPR-associated ramp protein, CMR4 family…
- UniProt
- F0NDX5, F0NDX6, F0NDX1, F0NDX3, F0NDX2, F0NDX7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 9 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated protein, CMR5 family | protein | 153 | 77% helix, 0% strand | F0NDX5 |
| B, C | CRISPR-associated protein, CMR5 family | protein | 154 | 74% helix, 0% strand | F0NDX5 |
| D, E, F, G | CRISPR-associated ramp protein, CMR4 family | protein | 285 | 25% helix, 28% strand | F0NDX6 |
| H | CRISPR-associated protein, CMR3 family | protein | 312 | 17% helix, 33% strand | F0NDX1 |
| I | CRISPR-associated ramp protein, CMR6 family | protein | 284 | 39% helix, 21% strand | F0NDX3 |
| J | CMR1 | protein | 475 | 35% helix, 22% strand | — |
| K | CRISPR-associated protein, CMR2 family | protein | 1024 | 44% helix, 11% strand | F0NDX2 |
| V | Crrna (51-mer) | rna | 51 | — | — |
| M, R, S, Q, P, W, T, Z, Y, r, s, q, p, w, t, z, y, m, L, l, O, o, N, n, x, X | CRISPR-associated protein cmrx | protein | 173 | 19% helix, 30% strand | F0NDX7 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains K
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 | 883 | 0.88 | 0.90 | 98 | empty |
| 2 | 1067 | 0.88 | 0.89 | 114 | empty |
| 3 | 1115 | 0.86 | 0.87 | 131 | empty |
| 4 | 1125 | 0.84 | 0.84 | 112 | empty |
| 5 | 1197 | 0.84 | 0.84 | 77 | empty |
Interfaces
91 interfaces between chains.
- H–K · 2934 Ų buried · 36 hydrogen bonds · protein-protein
- I–J · 2140 Ų buried · 25 hydrogen bonds · protein-protein
- F–G · 1717 Ų buried · 21 hydrogen bonds · protein-protein
- D–I · 1689 Ų buried · 13 hydrogen bonds · protein-protein
- H–V · 1629 Ų buried · 33 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 6S6B · Type III-B Cmr-beta Cryo-EM structure of the Apo state · the same entry in another collection · chain B against B, 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 F0NDX5
- Every structure of UniProt F0NDX6
- Every structure of UniProt F0NDX1
- Every structure of UniProt F0NDX3
- Every structure of UniProt F0NDX2
- Every structure of UniProt F0NDX7
- Elsewhere: RCSB PDB 6S6B · PDBe 6S6B · UniProt F0NDX5 · UniProt F0NDX6 · UniProt F0NDX1 · UniProt F0NDX3 · UniProt F0NDX2 · UniProt F0NDX7
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