MolNFT v1 · #118343 · protein
Crystal structure of the PTPN4 PDZ domain complexed with the PDZ binding motif of the mitogen activated protein kinase P38GAMMA.
5EZ0 · Tyrosine-protein phosphatase non-receptor type 4: “Crystal structure of the PTPN4 PDZ domain complexed with the PDZ binding motif of the mitogen activated…”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.72).…
- 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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