Research workbench
Crystal structure of T. thermophilus argonaute protein complexed with a bulge 7T8 on the guide strand
Analyse Crystal structure of T. thermophilus argonaute protein complexed with a bulge… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XOU
- Type
- protein + DNA
- Length
- 1,200 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ttago (D546N); DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*TP*GP*GP*TP*TP*GP*T)-3'); DNA…
- UniProt
- Q746M7
- Ligands
- MG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ttago (D546N) | protein | 564 | 32% helix, 30% strand | Q746M7 |
| B | Ttago (D546N) | protein | 574 | 30% helix, 31% strand | Q746M7 |
| C | DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*TP*GP*GP*TP*TP*GP*T)-3') | dna | 14 | — | — |
| D, F | DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)- 3') | dna | 16 | — | — |
| E | DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*TP*GP*GP*TP*TP*GP*T)-3') | dna | 16 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.81 | 0.83 | 65 | empty |
| 2 | 1120 | 0.81 | 0.83 | 80 | empty |
| 3 | 55 | 0.66 | 0.96 | 17 | empty |
| 4 | 53 | 0.65 | 0.96 | 17 | empty |
| 5 | 346 | 0.63 | 0.79 | 45 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1887 Ų buried · 44 hydrogen bonds · protein-protein
- B–E · 1360 Ų buried · 44 hydrogen bonds · protein-nucleic
- A–C · 1306 Ų buried · 41 hydrogen bonds · protein-nucleic
- B–F · 1264 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–D · 1259 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 5XOU · Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 7T8 on the… · 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 5XOU · PDBe 5XOU · UniProt Q746M7
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