MolNFT v1 · #163938 · protein + RNA
Cryo-EM structure of the type III-B cmr-beta bound to cognate target RNA
6SIC · CRISPR-associated protein, CMR5 family: “Cryo-EM structure of the type III-B cmr-beta bound to cognate target RNA”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.89). MolNFT v1 #163938 on GenesisL1: 3D…
- PDB
- 6SIC
- Type
- protein + RNA
- Length
- 7,577 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, F0NDX4, F0NDX2, F0NDX7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 10 distinct chains · 37% helix, 17% 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 | 72% helix, 1% strand | F0NDX5 |
| D, E, F, G | CRISPR-associated ramp protein, CMR4 family | protein | 285 | 25% helix, 32% strand | F0NDX6 |
| H | CRISPR-associated protein, CMR3 family | protein | 312 | 23% helix, 27% strand | F0NDX1 |
| I | CRISPR-associated ramp protein, CMR6 family | protein | 284 | 41% helix, 18% strand | F0NDX3 |
| J | CRISPR-associated ramp protein, CMR1 family | protein | 475 | 34% helix, 20% strand | F0NDX4 |
| K | CRISPR-associated protein, CMR2 family | protein | 1009 | 38% helix, 10% strand | F0NDX2 |
| L, M, N, O, P, Q, R, S, T, W, l, m, n, o, p, q, r, s, t, w, X, x | CRISPR-associated protein cmrx | protein | 173 | 14% helix, 27% strand | F0NDX7 |
| U | Cognate target RNA | rna | 42 | — | — |
| V | Crrna | rna | 48 | — | — |
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 | 1174 | 0.89 | 0.91 | 146 | empty |
| 2 | 899 | 0.86 | 0.87 | 93 | empty |
| 3 | 1101 | 0.85 | 0.87 | 121 | empty |
| 4 | 1187 | 0.85 | 0.86 | 86 | empty |
| 5 | 672 | 0.85 | 0.90 | 47 | empty |
Interfaces
101 interfaces between chains.
- H–K · 2645 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 2094 Ų buried · 21 hydrogen bonds · protein-protein
- D–I · 1764 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1730 Ų buried · 16 hydrogen bonds · protein-protein
- U–V · 1725 Ų buried · 166 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 6SIC · Cryo-EM structure of the Type III-B Cmr-beta bound to cognate target RNA · 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 F0NDX4
- Every structure of UniProt F0NDX2
- Every structure of UniProt F0NDX7
- Elsewhere: RCSB PDB 6SIC · PDBe 6SIC · UniProt F0NDX5 · UniProt F0NDX6 · UniProt F0NDX1 · UniProt F0NDX3 · UniProt F0NDX4 · UniProt F0NDX2 · UniProt F0NDX7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.