MolNFT v1 · #139757 · protein + DNA
Crystal structure of T. thermophilus argonaute protein complexed with a bulge 4A5 on the guide strand
5XP8 · Ttago: “Crystal structure of T. thermophilus argonaute protein complexed with a bulge 4A5 on the guide strand”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.82). MolNFT v1 #139757 on GenesisL1: 3D structure…
- PDB
- 5XP8
- Type
- protein + DNA
- Length
- 713 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ttago; DNA (5'- D(P*TP*GP*AP*GP*AP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3'); DNA…
- UniProt
- Q746M7
- Ligands
- MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ttago | protein | 678 | 29% helix, 31% strand | Q746M7 |
| E | DNA (5'- D(P*TP*GP*AP*GP*AP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3') | dna | 17 | — | — |
| F | DNA (5'-D(*CP*AP*AP*CP*C*AP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)- 3') | dna | 15 | — | — |
| C | DNA (5'-D(*AP*GP*T)-3') | dna | 3 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.82 | 0.84 | 56 | empty |
| 2 | 504 | 0.74 | 0.83 | 39 | empty |
| 3 | 82 | 0.65 | 0.91 | 26 | empty |
| 4 | 254 | 0.56 | 0.78 | 28 | empty |
| 5 | 337 | 0.55 | 0.75 | 36 | empty |
Interfaces
4 interfaces between chains.
- A–E · 1748 Ų buried · 44 hydrogen bonds · protein-nucleic
- A–F · 1182 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 656 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–C · 317 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 5XP8 · Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 4A5 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 5XP8 · PDBe 5XP8 · UniProt Q746M7
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