MolNFT v1 · #58892 · protein
Crystal structure of the RP2-ARL3 complex bound to GDP-ALF4
3BH7 · ADP-ribosylation factor-like protein 3: “Crystal structure of the RP2-ARL3 complex bound to GDP-ALF4”. X-ray diffraction, 3 ligands (GDP, ALF, MG), 5 pockets (best druggability 0.76). MolNFT v1 #58892 on GenesisL1: 3D structure…
- PDB
- 3BH7
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-like protein 3; Protein XRP2
- UniProt
- Q9WUL7, O75695
- Ligands
- GDP, ALF, MG
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor-like protein 3 | protein | 161 | 35% helix, 25% strand | Q9WUL7 |
| B | Protein XRP2 | protein | 314 | 25% helix, 33% strand | O75695 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A, B
- ALF · Tetrafluoroaluminate ion · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.76 | 0.92 | 40 | MG, GDP, ALF |
| 2 | 177 | 0.53 | 0.79 | 29 | empty |
| 3 | 158 | 0.46 | 0.76 | 30 | empty |
| 4 | 114 | 0.44 | 0.78 | 25 | empty |
| 5 | 85 | 0.32 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1418 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3BH7 · Crystal structure of the RP2-Arl3 complex bound to GDP-AlF4 · the same entry in another collection · chain A against A, TM-score 1.00
- O75695 · AlphaFold monomer V2.0 prediction for protein XRP2 (O75695) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9WUL7 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 3 (Q9WUL7) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O75695
- Elsewhere: RCSB PDB 3BH7 · PDBe 3BH7 · UniProt Q9WUL7 · UniProt O75695
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