MolNFT v1 · #92967 · protein
The crystal structure of ARL2GPPNHP in complex with UNC119A
4GOK · ADP-ribosylation factor-like protein 2: “The crystal structure of ARL2GPPNHP in complex with UNC119A”. X-ray diffraction, 2 ligands (GNP, MG), 6 pockets (best druggability 0.79). MolNFT v1 #92967 on GenesisL1: 3D structure, binding…
- PDB
- 4GOK
- Type
- protein
- Length
- 637 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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 B against B, 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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