Research workbench
Magi-1 complexed with a RSK1 peptide
Analyse Magi-1 complexed with a RSK1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N7D
- Type
- protein
- Length
- 847 residues
- Chains
- 3
- 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…
- EC
- 2.7.11.1
- UniProt
- Q96QZ7, P07355, Q15418
- Ligands
- CA
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 1,ANNEXIN A2 | protein | 423 | 58% helix, 8% strand | Q96QZ7, P07355 |
| B | Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 1,ANNEXIN A2 | protein | 420 | 56% helix, 5% strand | Q96QZ7, P07355 |
| C | Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) | protein | 4 | 0% helix, 50% strand | Q15418 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.74 | 0.77 | 97 | GOL |
| 2 | 63 | 0.69 | 0.95 | 22 | empty |
| 3 | 543 | 0.65 | 0.77 | 73 | GOL |
| 4 | 369 | 0.62 | 0.78 | 51 | GOL |
| 5 | 148 | 0.60 | 0.84 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–B · 385 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 344 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5N7D · MAGI-1 complexed with a RSK1 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q15418 · AlphaFold monomer V2.0 prediction for ribosomal protein S6 kinase alpha-1 (Q15418) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P07355 · AlphaFold monomer V2.0 prediction for annexin A2 (P07355) · a predicted model of the same protein · chain B against A, TM-score 0.76
- 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 0.33
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 Q96QZ7
- Every structure of UniProt P07355
- Every structure of UniProt Q15418
- Elsewhere: RCSB PDB 5N7D · PDBe 5N7D · UniProt Q96QZ7 · UniProt P07355 · UniProt Q15418
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.