Research workbench
The Crystal structure of Arl2GppNHp in complex with UNC119a
Analyse The Crystal structure of Arl2GppNHp in complex with UNC119a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GOK
- Type
- protein
- Length
- 637 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens; Mus musculus
- Molecule
- ADP-ribosylation factor-like protein 2; Protein unc-119 homolog A
- UniProt
- Q9D0J4, Q13432
- Ligands
- GNP, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.6 · 3 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | ADP-ribosylation factor-like protein 2 | protein | 157 | 35% helix, 27% strand | Q9D0J4 |
| G, C | Protein unc-119 homolog A | protein | 161 | 14% helix, 50% strand | Q13432 |
| A | ADP-ribosylation factor-like protein 2 | protein | 158 | 35% helix, 27% strand | Q9D0J4 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.79 | 0.84 | 56 | empty |
| 2 | 632 | 0.79 | 0.84 | 56 | empty |
| 3 | 196 | 0.53 | 0.78 | 28 | empty |
| 4 | 179 | 0.52 | 0.78 | 25 | empty |
| 5 | 101 | 0.42 | 0.78 | 22 | GNP, MG |
Interfaces
2 interfaces between chains.
- A–C · 724 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 712 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4GOK · The crystal structure of ARL2GPPNHP in complex with UNC119A · the same entry in another collection · chain A against A, TM-score 1.00
- Q9D0J4 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 2 (Q9D0J4) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q13432 · AlphaFold monomer V2.0 prediction for protein unc-119 homolog a (Q13432) · a predicted model of the same protein · chain G against A, TM-score 0.94
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 Q9D0J4
- Every structure of UniProt Q13432
- Elsewhere: RCSB PDB 4GOK · PDBe 4GOK · UniProt Q9D0J4 · UniProt Q13432
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