Research workbench
Crystal structure of MAGI2 and dendrin complex
Analyse Crystal structure of MAGI2 and dendrin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JJZ
- Type
- protein
- Length
- 210 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 2; Peptide…
- UniProt
- Q9WVQ1, Q80TS7
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 2 | protein | 88 | 17% helix, 32% strand | Q9WVQ1 |
| B | Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 2 | protein | 96 | 16% helix, 29% strand | Q9WVQ1 |
| C, D | Peptide from dendrin | protein | 13 | 0% helix, 0% strand | Q80TS7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.30 | 0.74 | 11 | empty |
Interfaces
4 interfaces between chains.
- A–C · 672 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 662 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 504 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 123 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6JJZ · Crystal Structure of MAGI2 and Dendrin complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WVQ1 · AlphaFold monomer V2.0 prediction for membrane-associated guanylate kinase, ww and PDZ… · a predicted model of the same protein · chain A against A, TM-score 0.70
- Q80TS7 · AlphaFold monomer V2.0 prediction for dendrin (Q80TS7) · a predicted model of the same protein · chain D against A, TM-score 0.33
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 Q9WVQ1
- Every structure of UniProt Q80TS7
- Elsewhere: RCSB PDB 6JJZ · PDBe 6JJZ · UniProt Q9WVQ1 · UniProt Q80TS7
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