Research workbench
Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4
Analyse Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W83
- Type
- protein
- Length
- 613 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor 6; C-jun-amino-terminal kinase-interacting protein 4
- UniProt
- P62330, O60271
- Ligands
- GTP, MG
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosylation factor 6 | protein | 161 | 34% helix, 27% strand | P62330 |
| C | C-jun-amino-terminal kinase-interacting protein 4 | protein | 67 | 94% helix, 0% strand | O60271 |
| D | C-jun-amino-terminal kinase-interacting protein 4 | protein | 62 | 97% helix, 0% strand | O60271 |
| E | ADP-ribosylation factor 6 | protein | 162 | 36% helix, 28% strand | P62330 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, E
- MG · Magnesium ion · metal · 3 copies · chains A, B, E
- DIO · 1,4-diethylene dioxide · additive · 6 copies · chains A, E, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.45 | 0.79 | 23 | GTP, MG |
| 2 | 89 | 0.43 | 0.79 | 22 | GTP, MG |
| 3 | 66 | 0.39 | 0.80 | 17 | GTP, MG |
Interfaces
6 interfaces between chains.
- C–D · 1696 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 789 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 534 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 504 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 432 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2W83 · Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4 · the same entry in another collection · chain E against E, TM-score 1.00
- P62330 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 6 (P62330) · a predicted model of the same protein · chain E against A, TM-score 0.99
- O60271 · AlphaFold monomer V2.0 prediction for C-jun-amino-terminal kinase- interacting protein 4… · a predicted model of the same protein · chain D against A, TM-score 0.88
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 P62330
- Every structure of UniProt O60271
- Elsewhere: RCSB PDB 2W83 · PDBe 2W83 · UniProt P62330 · UniProt O60271
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