MolNFT v1 · #167141 · protein + DNA + RNA
Cryo-EM structure of cascade-tniq-dsdna ternary complex
6VBW · DNA (5'- D(*GP*CP*AP*GP*TP*CP*AP*TP*CP*AP*CP*CP*AP*AP*TP*TP*…: “Cryo-EM structure of cascade-tniq-dsdna ternary complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #167141 on GenesisL1: 3D…
- PDB
- 6VBW
- Type
- protein + DNA + RNA
- Length
- 3,449 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*GP*CP*AP*GP*TP*CP*AP*TP*CP*AP*CP*CP*AP*AP*TP*TP*TP*AP*TP*TP*TP*A)- 3'); DNA…
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 12 distinct chains · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | DNA (5'- D(*GP*CP*AP*GP*TP*CP*AP*TP*CP*AP*CP*CP*AP*AP*TP*TP*TP*AP*TP*TP*TP*A)- 3') | dna | 7 | — | — |
| L | DNA (100-mer) | dna | 39 | — | — |
| K | RNA (61-mer) | rna | 60 | — | — |
| A | CAS8 | protein | 450 | 22% helix, 23% strand | — |
| B | CAS7 | protein | 338 | 22% helix, 23% strand | — |
| C | CAS7 | protein | 339 | 25% helix, 22% strand | — |
| D, F | CAS7 | protein | 341 | 23% helix, 26% strand | — |
| E | CAS7 | protein | 340 | 25% helix, 25% strand | — |
| G | CAS7 | protein | 307 | 27% helix, 23% strand | — |
| H | CAS6 | protein | 135 | 24% helix, 17% strand | — |
| I | Tniq | protein | 374 | 37% helix, 7% strand | — |
| J | Tniq | protein | 378 | 38% helix, 9% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains I, J
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 | 930 | 0.83 | 0.85 | 85 | empty |
| 2 | 474 | 0.80 | 0.87 | 57 | empty |
| 3 | 956 | 0.79 | 0.82 | 85 | empty |
| 4 | 928 | 0.79 | 0.82 | 84 | empty |
| 5 | 387 | 0.79 | 0.88 | 38 | empty |
Interfaces
37 interfaces between chains.
- D–E · 2205 Ų buried · 21 hydrogen bonds · protein-protein
- F–E · 2188 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2153 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2148 Ų buried · 25 hydrogen bonds · protein-protein
- F–G · 2130 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6VBW · Cryo-EM structure of Cascade-TniQ-dsDNA ternary complex · the same entry in another collection · chain M against M, 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
- Elsewhere: RCSB PDB 6VBW · PDBe 6VBW
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