Research workbench
The third PDZ domain of PDZD7 complexed with the PDZ-binding motif of EXOC4
Analyse The third PDZ domain of PDZD7 complexed with the PDZ-binding motif of EXOC4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PC5
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PDZ domain-containing protein 7,ANNEXIN A2; Exocyst complex component 4
- UniProt
- Q9H5P4, P07355, Q96A65
- Ligands
- CA
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PDZ domain-containing protein 7,ANNEXIN A2 | protein | 405 | 61% helix, 7% strand | Q9H5P4, P07355 |
| B | Exocyst complex component 4 | protein | 6 | 0% helix, 50% strand | Q96A65 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.62 | 0.82 | 41 | empty |
| 2 | 121 | 0.51 | 0.81 | 27 | GOL |
| 3 | 89 | 0.34 | 0.74 | 16 | empty |
| 4 | 59 | 0.33 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 481 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7PC5 · The third PDZ domain of PDZD7 complexed with the PDZ-binding motif of EXOC4 · 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 A against A, TM-score 0.78
- Q96A65 · AlphaFold monomer V2.0 prediction for exocyst complex component 4 (Q96A65) · a predicted model of the same protein · chain B against A, TM-score 0.66
- Q9H5P4 · AlphaFold monomer V2.0 prediction for PDZ domain-containing protein 7 (Q9H5P4) · a predicted model of the same protein · chain A against A, TM-score 0.26
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 Q9H5P4
- Every structure of UniProt P07355
- Every structure of UniProt Q96A65
- Elsewhere: RCSB PDB 7PC5 · PDBe 7PC5 · UniProt Q9H5P4 · UniProt P07355 · UniProt Q96A65
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.