MolNFT v1 · #66224 · protein + DNA + RNA
Crystal structure of T. thermophilus argonaute N478 mutant protein complexed with DNA guide strand and 19-nt RNA target strand
3HK2: “Crystal structure of T. thermophilus argonaute N478 mutant protein complexed with DNA guide strand and 19-nt…”. X-ray diffraction, 1 ligand (MG), 18 pockets (best druggability 0.81). MolNFT v1 #66224 on GenesisL1: 3D structure…
- PDB
- 3HK2
- Type
- protein + DNA + RNA
- Length
- 1,392 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argonaute; 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T P*AP*GP*T)-3'…
- UniProt
- Q746M7
- Ligands
- MG
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 664 | 27% helix, 27% strand | Q746M7 |
| B | Argonaute | protein | 666 | 28% helix, 27% strand | Q746M7 |
| C, E | 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T P*AP*GP*T)-3' | dna | 16 | — | — |
| F, D | 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP *G)-3' | rna | 15 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.81 | 0.84 | 60 | empty |
| 2 | 867 | 0.80 | 0.83 | 58 | empty |
| 3 | 1180 | 0.73 | 0.76 | 116 | empty |
| 4 | 252 | 0.66 | 0.83 | 24 | empty |
| 5 | 391 | 0.65 | 0.79 | 46 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2245 Ų buried · 46 hydrogen bonds · protein-protein
- B–E · 1536 Ų buried · 39 hydrogen bonds · protein-nucleic
- A–C · 1519 Ų buried · 39 hydrogen bonds · protein-nucleic
- B–F · 812 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 809 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 3HK2 · Crystal structure of T. thermophilus Argonaute N478 mutant protein complexed with 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 3HK2 · PDBe 3HK2 · UniProt Q746M7
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