MolNFT v1 · #163615 · protein + RNA
Cryo-EM structure of the type III-B cmr-beta bound to cognate target RNA and amppnp, state 1
6S8B · CRISPR-associated protein, CMR5 family: “Cryo-EM structure of the type III-B cmr-beta bound to cognate target RNA and amppnp, state 1”. Electron microscopy, 3 ligands (ANP, MN, ZN), 20 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 6S8B
- Type
- protein + RNA
- Length
- 7,572 residues
- Chains
- 35
- 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, F0NDX7, F0NDX2
- Ligands
- ANP, MN, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 10 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated protein, CMR5 family | protein | 153 | 78% helix, 0% strand | F0NDX5 |
| B, C | CRISPR-associated protein, CMR5 family | protein | 154 | 77% helix, 1% strand | F0NDX5 |
| D, E, F, G | CRISPR-associated ramp protein, CMR4 family | protein | 285 | 27% helix, 32% strand | F0NDX6 |
| H | CRISPR-associated protein, CMR3 family | protein | 304 | 24% helix, 35% strand | F0NDX1 |
| I | CRISPR-associated ramp protein, CMR6 family | protein | 284 | 43% helix, 19% strand | F0NDX3 |
| J | CMR1 | protein | 475 | 34% helix, 21% strand | — |
| U | Cognate target RNA (46-mer) | rna | 44 | — | — |
| V | Crrna | rna | 49 | — | — |
| L, M, N, O, P, Q, R, S, T, W, X, l, m, n, o, p, q, r, s, t, w, x | CRISPR-associated protein cmrx | protein | 173 | 12% helix, 31% strand | F0NDX7 |
| K | CRISPR-associated protein, CMR2 family | protein | 1009 | 42% helix, 11% strand | F0NDX2 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains K
- MN · Manganese (II) ion · metal · 3 copies · chains K
- 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 | 963 | 0.89 | 0.91 | 121 | empty |
| 2 | 939 | 0.86 | 0.88 | 92 | empty |
| 3 | 504 | 0.84 | 0.90 | 81 | empty |
| 4 | 698 | 0.84 | 0.88 | 76 | empty |
| 5 | 526 | 0.83 | 0.89 | 49 | empty |
Interfaces
101 interfaces between chains.
- H–K · 2301 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 1971 Ų buried · 25 hydrogen bonds · protein-protein
- U–V · 1728 Ų buried · 143 hydrogen bonds · nucleic-nucleic
- D–I · 1659 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1637 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6S8B · Cryo-EM structure of the Type III-B Cmr-beta bound to cognate target RNA and AMPPnP… · 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 F0NDX7
- Every structure of UniProt F0NDX2
- Elsewhere: RCSB PDB 6S8B · PDBe 6S8B · UniProt F0NDX5 · UniProt F0NDX6 · UniProt F0NDX1 · UniProt F0NDX3 · UniProt F0NDX7 · UniProt F0NDX2
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