Research workbench
MAGI1_2 complexed with a phosphorylated 16E6 peptide
Analyse MAGI1_2 complexed with a phosphorylated 16E6 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TWX
- Type
- protein
- Length
- 849 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 1,ANNEXIN A2…
- UniProt
- Q96QZ7, P07355
- Ligands
- CA
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 1,ANNEXIN A2 | protein | 421 | 57% helix, 8% strand | Q96QZ7, P07355 |
| C | 16E6 peptide | protein | 4 | 0% helix, 25% strand | — |
| D | 16E6 peptide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 11 copies · chains A, B
- CIT · Citric acid · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.76 | 0.78 | 88 | CA |
| 2 | 672 | 0.68 | 0.77 | 75 | GOL |
| 3 | 486 | 0.66 | 0.78 | 53 | empty |
| 4 | 184 | 0.51 | 0.78 | 35 | GOL |
| 5 | 78 | 0.33 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 376 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 355 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 295 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6TWX · MAGI1_2 complexed with a phosphorylated 16E6 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P07355 · AlphaFold monomer V2.0 prediction for annexin A2 (P07355) · a predicted model of the same protein · chain B against A, TM-score 0.77
- Q96QZ7 · 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 0.31
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 Q96QZ7
- Every structure of UniProt P07355
- Elsewhere: RCSB PDB 6TWX · PDBe 6TWX · UniProt Q96QZ7 · UniProt P07355
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