Research workbench
Target DNA-bound V. cholerae tniq-cascade complex, closed conformation
Analyse Target DNA-bound V. cholerae tniq-cascade complex, closed conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PIJ
- Type
- protein + DNA + RNA
- Length
- 3,548 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAS7 type I-F CRISPR-associated protein CSY3; CAS5_8 naturally occurring fusion protein…
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 12 distinct chains · 24% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CAS7 type I-F CRISPR-associated protein CSY3 | protein | 351 | 25% helix, 21% strand | — |
| B, E | CAS7 type I-F CRISPR-associated protein CSY3 | protein | 339 | 24% helix, 23% strand | — |
| C | CAS7 type I-F CRISPR-associated protein CSY3 | protein | 340 | 24% helix, 24% strand | — |
| D | CAS7 type I-F CRISPR-associated protein CSY3 | protein | 338 | 26% helix, 24% strand | — |
| F | CAS7 type I-F CRISPR-associated protein CSY3 | protein | 310 | 24% helix, 25% strand | — |
| G | CAS5_8 naturally occurring fusion protein | protein | 511 | 19% helix, 18% strand | — |
| H | Type I-F CRISPR-associated endoribonuclease CAS6/CSY4 | protein | 197 | 19% helix, 14% strand | — |
| I | Tniq monomer I | protein | 358 | 30% helix, 3% strand | — |
| J | Tniq monomer 2 | protein | 369 | 28% helix, 3% strand | — |
| 1 | Guide RNA | rna | 60 | — | — |
| 2 | Targeting strand ssdna | dna | 27 | — | — |
| 3 | Non-targeting strand ssdna | dna | 9 | — | — |
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 | 916 | 0.86 | 0.88 | 98 | empty |
| 2 | 779 | 0.84 | 0.87 | 94 | empty |
| 3 | 976 | 0.79 | 0.81 | 75 | empty |
| 4 | 273 | 0.79 | 0.90 | 48 | empty |
| 5 | 1100 | 0.79 | 0.81 | 101 | empty |
Interfaces
36 interfaces between chains.
- C–D · 2251 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2240 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2226 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2151 Ų buried · 17 hydrogen bonds · protein-protein
- A–G · 2113 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6PIJ · Target DNA-bound V. cholerae TniQ-Cascade complex, closed conformation · the same entry in another collection · chain A against A, 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 6PIJ · PDBe 6PIJ
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