MolNFT v1 · #184910 · protein
The PDZ domain of MAGI1_2 complexed with the PDZ-binding motif of HPV35-E6
7P71 · Membrane-associated guanylate kinase, ww and PDZ domain…: “The PDZ domain of MAGI1_2 complexed with the PDZ-binding motif of HPV35-E6”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.76). MolNFT v1 #184910 on…
- PDB
- 7P71
- Type
- protein
- Length
- 854 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, P27228
- Ligands
- CA
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 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, 8% strand | Q96QZ7, P07355 |
| B | Membrane-associated guanylate kinase, ww and PDZ domain- containing protein 1,ANNEXIN A2 | protein | 420 | 58% helix, 8% strand | Q96QZ7, P07355 |
| C | Protein E6 | protein | 7 | 0% helix, 43% strand | P27228 |
| D | Protein E6 | protein | 4 | 0% helix, 50% strand | P27228 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.76 | 0.78 | 76 | GOL |
| 2 | 616 | 0.66 | 0.76 | 74 | GOL |
| 3 | 424 | 0.63 | 0.77 | 59 | GOL |
| 4 | 123 | 0.56 | 0.83 | 22 | empty |
| 5 | 102 | 0.47 | 0.80 | 24 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 542 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 412 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 347 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7P71 · The PDZ domain of MAGI1_2 complexed with the PDZ-binding motif of HPV35-E6 · the same entry in another collection · chain D against D, TM-score 1.00
- P07355 · AlphaFold monomer V2.0 prediction for annexin A2 (P07355) · a predicted model of the same protein · chain A 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 P27228
- Elsewhere: RCSB PDB 7P71 · PDBe 7P71 · UniProt Q96QZ7 · UniProt P07355 · UniProt P27228
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