Research workbench
Structure of the argonaute protein from methanocaldcoccus janaschii in complex with guide DNA
Analyse Structure of the argonaute protein from methanocaldcoccus janaschii in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G5T
- Type
- protein + DNA
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argonaute; Guide DNA
- UniProt
- Q58717
- Ligands
- MG, SO4
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 670 | 30% helix, 30% strand | Q58717 |
| D | Guide DNA | dna | 8 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.62 | 0.81 | 35 | SO4 |
| 2 | 505 | 0.61 | 0.75 | 56 | empty |
| 3 | 310 | 0.60 | 0.78 | 26 | empty |
| 4 | 111 | 0.51 | 0.81 | 18 | empty |
| 5 | 64 | 0.45 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–D · 1192 Ų buried · 35 hydrogen bonds · protein-nucleic
Compared structures
- 5G5T · Structure of the Argonaute protein from Methanocaldcoccus janaschii in complex with guide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58717 · AlphaFold monomer V2.0 prediction for protein argonaute (Q58717) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 Q58717
- Elsewhere: RCSB PDB 5G5T · PDBe 5G5T · UniProt Q58717
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