MolNFT v1 · #163905 · protein + RNA
Cryo-EM structure of the type III-B cmr-beta bound to cognate target RNA and amppnp, state 1, in the presence of ssdna
6SHB · CRISPR-associated protein, CMR5 family: “Cryo-EM structure of the type III-B cmr-beta bound to cognate target RNA and amppnp, state 1, in the presence…”. Electron microscopy, 3 ligands (ANP, MN, ZN), 20 pockets (best druggability…
- PDB
- 6SHB
- Type
- protein + RNA
- Length
- 8,271 residues
- Chains
- 39
- 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, F0NDX3, F0NDX4, F0NDX7, F0NDX2, F0NDX1
- Ligands
- ANP, MN, ZN
- Pockets
- 20 · best druggability 0.87
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 | 77% helix, 1% strand | F0NDX5 |
| B, C | CRISPR-associated protein, CMR5 family | protein | 154 | 80% helix, 0% strand | F0NDX5 |
| D, E, F, G | CRISPR-associated ramp protein, CMR4 family | protein | 285 | 29% helix, 32% strand | F0NDX6 |
| I | CRISPR-associated ramp protein, CMR6 family | protein | 284 | 40% helix, 19% strand | F0NDX3 |
| J | CMR1,CRISPR-associated ramp protein, CMR1 family | protein | 475 | 35% helix, 19% strand | F0NDX4 |
| U | Cognate target RNA (43-mer) | rna | 43 | — | — |
| V | Crrna (49-mer) | rna | 49 | — | — |
| L, M, N, O, P, Q, R, S, T, W, X, l, m, n, o, p, q, r, s, t, w, x, Z, z, Y, y | CRISPR-associated protein cmrx | protein | 173 | 12% helix, 29% strand | F0NDX7 |
| K | CRISPR-associated protein, CMR2 family | protein | 1009 | 41% helix, 12% strand | F0NDX2 |
| H | CRISPR-associated protein, CMR3 family | protein | 312 | 22% helix, 34% strand | F0NDX1 |
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 | 622 | 0.87 | 0.92 | 93 | empty |
| 2 | 937 | 0.86 | 0.88 | 99 | ANP, MN |
| 3 | 992 | 0.86 | 0.87 | 108 | empty |
| 4 | 342 | 0.86 | 0.96 | 59 | empty |
| 5 | 413 | 0.85 | 0.94 | 51 | empty |
Interfaces
103 interfaces between chains.
- K–H · 2517 Ų buried · 25 hydrogen bonds · protein-protein
- I–J · 2034 Ų buried · 23 hydrogen bonds · protein-protein
- U–V · 1725 Ų buried · 146 hydrogen bonds · nucleic-nucleic
- D–I · 1666 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1559 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6SHB · 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 F0NDX3
- Every structure of UniProt F0NDX4
- Every structure of UniProt F0NDX7
- Every structure of UniProt F0NDX2
- Every structure of UniProt F0NDX1
- Elsewhere: RCSB PDB 6SHB · PDBe 6SHB · UniProt F0NDX5 · UniProt F0NDX6 · UniProt F0NDX3 · UniProt F0NDX4 · UniProt F0NDX7 · UniProt F0NDX2 · UniProt F0NDX1
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