MolNFT v1 · #139785 · protein + DNA
Crystal structure of T. thermophilus argonaute protein complexed with a bulge 5A6 on the guide strand
5XQ2 · Ttago (D546N): “Crystal structure of T. thermophilus argonaute protein complexed with a bulge 5A6 on the guide strand”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.81). MolNFT v1 #139785 on GenesisL1: 3D…
- PDB
- 5XQ2
- Type
- protein + DNA
- Length
- 1,430 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ttago (D546N); DNA (5'- D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3'); DNA…
- UniProt
- Q746M7
- Ligands
- MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ttago (D546N) | protein | 679 | 30% helix, 27% strand | Q746M7 |
| X, E | DNA (5'- D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3') | dna | 17 | — | — |
| Y, F | DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)- 3') | dna | 16 | — | — |
| C, D | DNA (5'-D(*AP*GP*T)-3') | dna | 3 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains X, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.81 | 0.84 | 55 | MG |
| 2 | 786 | 0.80 | 0.84 | 49 | MG |
| 3 | 929 | 0.76 | 0.79 | 99 | empty |
| 4 | 665 | 0.75 | 0.81 | 74 | empty |
| 5 | 204 | 0.67 | 0.86 | 34 | empty |
Interfaces
11 interfaces between chains.
- B–E · 1712 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–X · 1705 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–Y · 1545 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 1505 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1496 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 5XQ2 · Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 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 5XQ2 · PDBe 5XQ2 · UniProt Q746M7
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