Research workbench
Crystal structure of thermus thermophilus argonaute in complex with G1C sidna and DNA target
Analyse Crystal structure of thermus thermophilus argonaute in complex with G1C sidna… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GQ9
- Type
- protein + DNA
- Length
- 1,375 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermus thermophilus argonaute; DNA (5'- D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*…
- UniProt
- Q746M7
- Ligands
- MG
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermus thermophilus argonaute | protein | 638 | 29% helix, 30% strand | Q746M7 |
| C, E | DNA (5'- D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3') | dna | 16 | — | — |
| D, F | DNA (5'- D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3') | dna | 16 | — | — |
| B | Thermus thermophilus argonaute | protein | 673 | 29% helix, 30% strand | Q746M7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, D, C, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.83 | 0.84 | 65 | empty |
| 2 | 908 | 0.82 | 0.84 | 58 | empty |
| 3 | 843 | 0.71 | 0.77 | 77 | empty |
| 4 | 184 | 0.65 | 0.85 | 27 | empty |
| 5 | 119 | 0.64 | 0.88 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2297 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 1684 Ų buried · 49 hydrogen bonds · protein-nucleic
- B–E · 1644 Ų buried · 54 hydrogen bonds · protein-nucleic
- A–D · 1516 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–F · 1442 Ų buried · 28 hydrogen bonds · protein-nucleic
Compared structures
- 5GQ9 · Crystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA… · 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
- Every structure of UniProt Q746M7
- Elsewhere: RCSB PDB 5GQ9 · PDBe 5GQ9 · UniProt Q746M7
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