Research workbench
Crystal structure of the PTPN4 PDZ domain complexed with the tailored peptide CYTO8-retev
Analyse Crystal structure of the PTPN4 PDZ domain complexed with the tailored peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EYZ
- Type
- protein
- Length
- 396 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 4; CYTO8-retev
- EC
- 3.1.3.48
- UniProt
- P29074
- Ligands
- CL
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tyrosine-protein phosphatase non-receptor type 4 (EC 3.1.3.48) | protein | 93 | 17% helix, 35% strand | P29074 |
| B | Tyrosine-protein phosphatase non-receptor type 4 (EC 3.1.3.48) | protein | 94 | 14% helix, 34% strand | P29074 |
| D | Tyrosine-protein phosphatase non-receptor type 4 (EC 3.1.3.48) | protein | 92 | 14% helix, 36% strand | P29074 |
| E, F, G, H | CYTO8-retev | protein | 6 | 0% helix, 50% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.70 | 0.75 | 69 | empty |
| 2 | 57 | 0.44 | 0.83 | 13 | empty |
| 3 | 66 | 0.39 | 0.79 | 14 | empty |
Interfaces
11 interfaces between chains.
- D–H · 557 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 552 Ų buried · 16 hydrogen bonds · protein-protein
- C–G · 532 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 517 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 459 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5EYZ · Crystal structure of the PTPN4 PDZ domain complexed with the tailored peptide CYTO8-retev · the same entry in another collection · chain H against H, TM-score 1.00
- P29074 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 4… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P29074
- Elsewhere: RCSB PDB 5EYZ · PDBe 5EYZ · UniProt P29074
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