Research workbench
Crystal structure analysis of the ARFAPTIN2 bar domain in complex with ARL1
Analyse Crystal structure analysis of the ARFAPTIN2 bar domain in complex with ARL1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DCN
- Type
- protein
- Length
- 719 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-like protein 1; Arfaptin-2
- UniProt
- P40616, P53365
- Ligands
- GNP, MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosylation factor-like protein 1 | protein | 165 | 30% helix, 26% strand | P40616 |
| C | Arfaptin-2 | protein | 193 | 92% helix, 0% strand | P53365 |
| D | Arfaptin-2 | protein | 196 | 93% helix, 0% strand | P53365 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.81 | 0.96 | 24 | empty |
| 2 | 121 | 0.55 | 0.82 | 19 | empty |
| 3 | 127 | 0.49 | 0.79 | 24 | empty |
| 4 | 102 | 0.43 | 0.78 | 15 | empty |
| 5 | 142 | 0.43 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2049 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 816 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 781 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4DCN · Crystal Structure Analysis of the Arfaptin2 BAR domain in Complex with ARL1 · the same entry in another collection · chain D against D, TM-score 1.00
- P40616 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 1 (P40616) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P53365 · AlphaFold monomer V2.0 prediction for arfaptin-2 (P53365) · a predicted model of the same protein · chain D 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 P40616
- Every structure of UniProt P53365
- Elsewhere: RCSB PDB 4DCN · PDBe 4DCN · UniProt P40616 · UniProt P53365
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