Research workbench
Crystal structure of mid domain from HAGO2 in complex with gmp
Analyse Crystal structure of mid domain from HAGO2 in complex with gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LUH
- Type
- protein
- Length
- 399 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein argonaute-2
- UniProt
- Q9UKV8
- Ligands
- 5GP, PO4
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein argonaute-2 | protein | 133 | 49% helix, 17% strand | Q9UKV8 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.42 | 0.78 | 18 | empty |
| 2 | 93 | 0.37 | 0.76 | 24 | empty |
| 3 | 50 | 0.30 | 0.76 | 13 | empty |
Interfaces
2 interfaces between chains.
- B–C · 742 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 710 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 Q9UKV8
- Elsewhere: RCSB PDB 3LUH · PDBe 3LUH · UniProt Q9UKV8
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