Research workbench
Concomitant binding of Afadin to LGN and F-actin directs planar spindle orientation
Analyse Concomitant binding of Afadin to LGN and F-actin directs planar spindle… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A6C
- Type
- protein
- Length
- 732 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.901
- Source
- HOMO SAPIENS
- Molecule
- G-protein-signaling modulator 2, afadin
- UniProt
- P81274, P55196
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.901 · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G-protein-signaling modulator 2, afadin | protein | 363 | 77% helix, 0% strand | P81274, P55196 |
| B | G-protein-signaling modulator 2, afadin | protein | 369 | 74% helix, 0% strand | P81274, P55196 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.77 | 0.81 | 72 | empty |
| 2 | 569 | 0.68 | 0.78 | 59 | empty |
| 3 | 575 | 0.65 | 0.76 | 60 | empty |
| 4 | 196 | 0.60 | 0.82 | 35 | empty |
| 5 | 307 | 0.56 | 0.76 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 677 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5A6C · Concomitant binding of afadin to lgn and F-actin directs planar spindle orientation · the same entry in another collection · chain A against A, TM-score 1.00
- P81274 · AlphaFold monomer V2.0 prediction for G-protein-signaling modulator 2 (P81274) · a predicted model of the same protein · chain A against A, TM-score 0.88
- P55196 · AlphaFold monomer V2.0 prediction for afadin (P55196) · a predicted model of the same protein · chain A against A, TM-score 0.36
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 P81274
- Every structure of UniProt P55196
- Elsewhere: RCSB PDB 5A6C · PDBe 5A6C · UniProt P81274 · UniProt P55196
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