MolNFT v1 · #100938 · protein + DNA
Structure of thermus thermophilus argonaute bound to guide DNA and 19- mer target DNA with MG2+
4NCB: “Structure of thermus thermophilus argonaute bound to guide DNA and 19- mer target DNA with MG2+”. X-ray diffraction, 2 ligands (DT, MG), 17 pockets (best druggability 0.83). MolNFT v1 #100938 on GenesisL1: 3D structure, binding…
- PDB
- 4NCB
- Type
- protein + DNA
- Length
- 1,417 residues
- Chains
- 8
- 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
- DT, MG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 676 | 28% helix, 31% strand | Q746M7 |
| B | Argonaute | protein | 672 | 29% helix, 32% strand | Q746M7 |
| C | 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 | — | — |
| P | 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3' | dna | 5 | — | — |
| D | 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP *G)-3' | dna | 15 | — | — |
| 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 | 17 | — | — |
| F | 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3' | dna | 10 | — | — |
| H | 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3' | dna | 6 | — | — |
Ligands and binding sites
- DT · Thymidine-5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, D, B, F, H, P, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.83 | 0.85 | 56 | empty |
| 2 | 905 | 0.82 | 0.85 | 61 | empty |
| 3 | 682 | 0.71 | 0.79 | 78 | empty |
| 4 | 326 | 0.68 | 0.82 | 43 | DT |
| 5 | 456 | 0.68 | 0.79 | 48 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2648 Ų buried · 43 hydrogen bonds · protein-protein
- B–E · 1787 Ų buried · 50 hydrogen bonds · protein-nucleic
- A–C · 1745 Ų buried · 54 hydrogen bonds · protein-nucleic
- A–D · 1403 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–F · 1011 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 4NCB · Structure of Thermus thermophilus Argonaute bound to guide DNA and 19-mer target DNA with… · 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 4NCB · PDBe 4NCB · UniProt Q746M7
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