Research workbench
The crystal structure of full length ARL3GPPNHP in complex with UNC119A
Analyse The crystal structure of full length ARL3GPPNHP 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
- 4GOJ
- Type
- protein
- Length
- 673 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-like protein 3; Protein unc-119 homolog a
- UniProt
- Q9WUL7, Q13432
- Ligands
- GNP, MG
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor-like protein 3 | protein | 175 | 34% helix, 23% strand | Q9WUL7 |
| B | ADP-ribosylation factor-like protein 3 | protein | 176 | 35% helix, 23% strand | Q9WUL7 |
| C, D | Protein unc-119 homolog a | protein | 161 | 12% helix, 53% strand | Q13432 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.80 | 0.91 | 49 | empty |
| 2 | 359 | 0.80 | 0.89 | 54 | empty |
| 3 | 99 | 0.54 | 0.84 | 20 | empty |
| 4 | 131 | 0.52 | 0.81 | 22 | empty |
| 5 | 121 | 0.47 | 0.79 | 24 | GNP, MG |
Interfaces
2 interfaces between chains.
- B–D · 1000 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 989 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4GOJ · The Crystal Structure of full length Arl3GppNHp in complex with UNC119a · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WUL7 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 3 (Q9WUL7) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q13432 · AlphaFold monomer V2.0 prediction for protein unc-119 homolog a (Q13432) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q9WUL7
- Every structure of UniProt Q13432
- Elsewhere: RCSB PDB 4GOJ · PDBe 4GOJ · UniProt Q9WUL7 · UniProt Q13432
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