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Crystal structure of the PTPN4 PDZ domain complexed with the PDZ binding motif of the mitogen activated protein kinase P38GAMMA.
Analyse Crystal structure of the PTPN4 PDZ domain complexed with the PDZ binding motif… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EZ0
- Type
- protein
- Length
- 405 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 4; Mitogen-activated protein kinase 12
- EC
- 3.1.3.48
- UniProt
- P29074, B5MDL5
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 14% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 4 (EC 3.1.3.48) | protein | 90 | 13% helix, 36% strand | P29074 |
| B | Tyrosine-protein phosphatase non-receptor type 4 (EC 3.1.3.48) | protein | 92 | 13% helix, 30% strand | P29074 |
| C | Tyrosine-protein phosphatase non-receptor type 4 (EC 3.1.3.48) | protein | 94 | 17% helix, 31% strand | P29074 |
| D | Tyrosine-protein phosphatase non-receptor type 4 (EC 3.1.3.48) | protein | 95 | 17% helix, 32% strand | P29074 |
| E, F | Mitogen-activated protein kinase 12 | protein | 6 | 0% helix, 50% strand | B5MDL5 |
| G, H | Mitogen-activated protein kinase 12 | protein | 11 | 0% helix, 27% strand | B5MDL5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains D, H, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.72 | 0.76 | 83 | empty |
| 2 | 61 | 0.38 | 0.80 | 15 | empty |
Interfaces
10 interfaces between chains.
- B–D · 619 Ų buried · 9 hydrogen bonds · protein-protein
- D–H · 580 Ų buried · 16 hydrogen bonds · protein-protein
- C–G · 553 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 547 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 523 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5EZ0 · Crystal structure of the PTPN4 PDZ domain complexed with the PDZ binding motif of the… · 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 A against A, TM-score 0.96
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
- Every structure of UniProt B5MDL5
- Elsewhere: RCSB PDB 5EZ0 · PDBe 5EZ0 · UniProt P29074 · UniProt B5MDL5
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