Research workbench
Crystal structure of the PTPN4 PDZ domain complexed with the C- terminus of the GLUN2A NMDA receptor subunit
Analyse Crystal structure of the PTPN4 PDZ domain complexed with the C- terminus of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NFL
- Type
- protein
- Length
- 379 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 4; Glutamate [NMDA] receptor subunit…
- UniProt
- P29074, Q12879
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 4 | protein | 92 | 21% helix, 37% strand | P29074 |
| B | Tyrosine-protein phosphatase non-receptor type 4 | protein | 89 | 15% helix, 36% strand | P29074 |
| C | Tyrosine-protein phosphatase non-receptor type 4 | protein | 89 | 18% helix, 36% strand | P29074 |
| D | Tyrosine-protein phosphatase non-receptor type 4 | protein | 89 | 17% helix, 36% strand | P29074 |
| E, F, G, H | Glutamate [NMDA] receptor subunit epsilon-1 | protein | 5 | 0% helix, 60% strand | Q12879 |
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 | 104 | 0.38 | 0.75 | 21 | empty |
| 2 | 91 | 0.34 | 0.74 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–G · 445 Ų buried · 15 hydrogen bonds · protein-protein
- D–H · 436 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 419 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 416 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 407 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3NFL · Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A… · 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 0.98
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 Q12879
- Elsewhere: RCSB PDB 3NFL · PDBe 3NFL · UniProt P29074 · UniProt Q12879
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