Research workbench
Tax-interacting protein-1 (tip-1) PDZ domain bound to Y-ICAL36 (yptsii) peptide
Analyse Tax-interacting protein-1 (tip-1) PDZ domain bound to Y-ICAL36 (yptsii) peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NNM
- Type
- protein
- Length
- 235 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TAX1-binding protein 3; Tip-1 PDZ domain
- UniProt
- O14907
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TAX1-binding protein 3 | protein | 111 | 14% helix, 38% strand | O14907 |
| B | TAX1-binding protein 3 | protein | 112 | 14% helix, 39% strand | O14907 |
| C, D | Tip-1 PDZ domain | protein | 6 | 0% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.33 | 0.74 | 13 | empty |
| 2 | 60 | 0.32 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 538 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 535 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 359 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4NNM · Tax-Interacting Protein-1 (TIP-1) PDZ domain bound to Y-iCAL36 (YPTSII) peptide · the same entry in another collection · chain A against A, TM-score 1.00
- O14907 · AlphaFold monomer V2.0 prediction for TAX1-binding protein 3 (O14907) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 O14907
- Elsewhere: RCSB PDB 4NNM · PDBe 4NNM · UniProt O14907
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