MolNFT v1 · #127799 · protein
Magi-1 complexed with a PRSK1 peptide
5N7F · Membrane-associated guanylate kinase, ww and PDZ domain…: “Magi-1 complexed with a PRSK1 peptide”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.75). MolNFT v1 #127799 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5N7F
- Type
- protein
- Length
- 845 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 0.75
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 8% 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 | 57% helix, 9% strand | Q96QZ7, P07355 |
| B | Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 1,ANNEXIN A2 | protein | 416 | 56% helix, 6% strand | Q96QZ7, P07355 |
| C | Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) | protein | 6 | 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.75 | 0.80 | 75 | GOL |
| 2 | 405 | 0.63 | 0.77 | 47 | GOL |
| 3 | 244 | 0.54 | 0.77 | 35 | GOL |
| 4 | 142 | 0.50 | 0.79 | 23 | GOL |
| 5 | 92 | 0.45 | 0.80 | 28 | GOL |
Interfaces
2 interfaces between chains.
- A–C · 451 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 236 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5N7F · MAGI-1 complexed with a pRSK1 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
- 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 0.62
- 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 5N7F · PDBe 5N7F · UniProt Q96QZ7 · UniProt P07355 · UniProt Q15418
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