Research workbench
Crystal structure of ARFGAP1-ARF1 fusion protein
Analyse Crystal structure of ARFGAP1-ARF1 fusion protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O47
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor GTPase-activating protein 1, ADP- ribosylation factor 1
- UniProt
- Q8N6T3, P84077
- Ligands
- GDP, ZN
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor GTPase-activating protein 1, ADP- ribosylation factor 1 | protein | 289 | 37% helix, 21% strand | Q8N6T3, P84077 |
| B | ADP-ribosylation factor GTPase-activating protein 1, ADP- ribosylation factor 1 | protein | 289 | 38% helix, 21% strand | Q8N6T3, P84077 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.67 | 0.79 | 48 | empty |
| 2 | 290 | 0.66 | 0.82 | 36 | empty |
| 3 | 76 | 0.35 | 0.75 | 17 | empty |
| 4 | 61 | 0.31 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 151 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3O47 · Crystal structure of ARFGAP1-ARF1 fusion protein · the same entry in another collection · chain A against A, TM-score 1.00
- P84077 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 1 (P84077) · a predicted model of the same protein · chain A against A, TM-score 0.49
- Q8N6T3 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor GTPase- activating protein… · a predicted model of the same protein · chain B against A, TM-score 0.48
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 Q8N6T3
- Every structure of UniProt P84077
- Elsewhere: RCSB PDB 3O47 · PDBe 3O47 · UniProt Q8N6T3 · UniProt P84077
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