MolNFT v1 · #100937 · protein + DNA
Structure of thermus thermophilus argonaute bound to guide DNA 19-mer and target DNA in the presence of MN2+
4NCA: “Structure of thermus thermophilus argonaute bound to guide DNA 19-mer and target DNA in the presence of MN2+”. X-ray diffraction, 2 ligands (DT, MG), 15 pockets (best druggability 0.83). MolNFT v1 #100937 on GenesisL1: 3D structure…
- PDB
- 4NCA
- Type
- protein + DNA
- Length
- 1,425 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
- 15 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 683 | 28% helix, 31% strand | Q746M7 |
| B | Argonaute | protein | 678 | 30% helix, 31% 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 | — | — |
| D, F | 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3' | dna | 10 | — | — |
| G, H | 5'-D(*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, G, B, F, H, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.83 | 0.85 | 65 | empty |
| 2 | 994 | 0.83 | 0.85 | 62 | empty |
| 3 | 908 | 0.73 | 0.77 | 80 | empty |
| 4 | 782 | 0.70 | 0.77 | 73 | empty |
| 5 | 273 | 0.70 | 0.85 | 37 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2574 Ų buried · 42 hydrogen bonds · protein-protein
- B–E · 1703 Ų buried · 57 hydrogen bonds · protein-nucleic
- A–C · 1676 Ų buried · 51 hydrogen bonds · protein-nucleic
- A–D · 992 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–F · 968 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 4NCA · Structure of Thermus thermophilus Argonaute bound to guide DNA 19-mer and target DNA in… · 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 4NCA · PDBe 4NCA · UniProt Q746M7
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