Research workbench
Arf1(Delta1-17)in complex with BRAG2 Sec7-PH domain
Analyse Arf1(Delta1-17)in complex with BRAG2 Sec7-PH domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C0A
- Type
- protein
- Length
- 2,057 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- BOS TAURUS; HOMO SAPIENS
- Molecule
- Iq motif and SEC7 domain-containing protein 1; ADP-ribosylation factor 1
- UniProt
- Q6DN90, P84080
- Ligands
- G3D
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 3.3 · 8 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iq motif and SEC7 domain-containing protein 1 | protein | 352 | 49% helix, 14% strand | Q6DN90 |
| B | Iq motif and SEC7 domain-containing protein 1 | protein | 357 | 47% helix, 14% strand | Q6DN90 |
| C | ADP-ribosylation factor 1 | protein | 161 | 32% helix, 24% strand | P84080 |
| D | ADP-ribosylation factor 1 | protein | 164 | 28% helix, 23% strand | P84080 |
| E | Iq motif and SEC7 domain-containing protein 1 | protein | 351 | 51% helix, 15% strand | Q6DN90 |
| F | Iq motif and SEC7 domain-containing protein 1 | protein | 351 | 49% helix, 15% strand | Q6DN90 |
| G | ADP-ribosylation factor 1 | protein | 162 | 31% helix, 25% strand | P84080 |
| H | ADP-ribosylation factor 1 | protein | 159 | 29% helix, 22% strand | P84080 |
Ligands and binding sites
- G3D · Guanosine-3'-monophosphate-5'-diphosphate · ligand · 4 copies · chains C, F, D, E, B, G, A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.81 | 0.83 | 93 | empty |
| 2 | 847 | 0.77 | 0.80 | 72 | empty |
| 3 | 498 | 0.74 | 0.83 | 59 | empty |
| 4 | 615 | 0.72 | 0.80 | 56 | empty |
| 5 | 709 | 0.70 | 0.77 | 69 | empty |
Interfaces
12 interfaces between chains.
- C–F · 1704 Ų buried · 21 hydrogen bonds · protein-protein
- B–G · 1576 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 1564 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1562 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 594 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4C0A · ARF1(DELTA1-17)IN complex with BRAG2 SEC7-pH domain · the same entry in another collection · chain H against H, TM-score 1.00
- Q6DN90 · AlphaFold monomer V2.0 prediction for iq motif and SEC7 domain- containing protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6DN90
- Every structure of UniProt P84080
- Elsewhere: RCSB PDB 4C0A · PDBe 4C0A · UniProt Q6DN90 · UniProt P84080
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