MolNFT v1 · #162125 · protein + DNA
Structure of clostridium butyricum argonaute bound to a guide DNA (5' deoxycytidine) and a 19-mer target DNA
6QZK: “Structure of clostridium butyricum argonaute bound to a guide DNA (5' deoxycytidine) and a 19-mer target DNA”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.82). MolNFT v1 #162125 on GenesisL1: 3D structure…
- PDB
- 6QZK
- Type
- protein + DNA
- Length
- 780 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clostridium butyricum argonaute; Sidna guide (5'…
- Ligands
- MG
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clostridium butyricum argonaute | protein | 746 | 28% helix, 25% strand | — |
| B | Sidna guide (5'- D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)- 3') | dna | 16 | — | — |
| C | DNA target (5'- D(T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*T)-3') | dna | 18 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.82 | 0.84 | 54 | FMT |
| 2 | 503 | 0.70 | 0.80 | 37 | empty |
| 3 | 380 | 0.62 | 0.78 | 35 | empty |
| 4 | 134 | 0.60 | 0.85 | 21 | empty |
| 5 | 142 | 0.58 | 0.83 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1774 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 1744 Ų buried · 43 hydrogen bonds · protein-nucleic
- B–C · 685 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Compared structures
- 6QZK · Structure of Clostridium butyricum Argonaute bound to a guide DNA (5' deoxycytidine) and… · 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 6QZK · PDBe 6QZK
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