Research workbench
The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1
Analyse The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PC9
- Type
- protein
- Length
- 812 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptojanin-2-binding PROTEIN,ANNEXIN A2; Protein tax-1
- UniProt
- P57105, P07355, P03409
- Ligands
- CA
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Synaptojanin-2-binding PROTEIN,ANNEXIN A2 | protein | 397 | 61% helix, 8% strand | P57105, P07355 |
| A | Synaptojanin-2-binding PROTEIN,ANNEXIN A2 | protein | 407 | 60% helix, 8% strand | P57105, P07355 |
| C | Protein tax-1 | protein | 8 | 0% helix, 25% strand | P03409 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.74 | 0.77 | 91 | empty |
| 2 | 134 | 0.53 | 0.81 | 29 | empty |
| 3 | 130 | 0.52 | 0.81 | 29 | empty |
| 4 | 151 | 0.48 | 0.78 | 28 | empty |
| 5 | 65 | 0.48 | 0.84 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–A · 792 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 613 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7PC9 · The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1 · the same entry in another collection · chain C against C, 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
- P57105 · AlphaFold monomer V2.0 prediction for synaptojanin-2-binding protein (P57105) · a predicted model of the same protein · chain A against A, TM-score 0.24
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 P57105
- Every structure of UniProt P07355
- Every structure of UniProt P03409
- Elsewhere: RCSB PDB 7PC9 · PDBe 7PC9 · UniProt P57105 · UniProt P07355 · UniProt P03409
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