MolNFT v1 · #72673 · protein
Crystal structure of the PTPN4 PDZ domain complexed with the C- terminus of a rabies virus G protein
3NFK · Tyrosine-protein phosphatase non-receptor type 4: “Crystal structure of the PTPN4 PDZ domain complexed with the C- terminus of a rabies virus G protein”. X-ray diffraction, 2 pockets (best druggability 0.43). MolNFT v1 #72673 on…
- PDB
- 3NFK
- Type
- protein
- Length
- 201 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 4; Glycoprotein G
- UniProt
- P29074, P03524
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 4 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 | 91 | 18% helix, 35% strand | P29074 |
| C | Glycoprotein G | protein | 13 | 0% helix, 38% strand | P03524 |
| D | Glycoprotein G | protein | 5 | 0% helix, 60% strand | P03524 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A
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 | 146 | 0.43 | 0.75 | 22 | empty |
| 2 | 115 | 0.36 | 0.73 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 601 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 406 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 390 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 170 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3NFK · Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of a rabies virus… · the same entry in another collection · chain A against A, 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 B 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
- Every structure of UniProt P03524
- Elsewhere: RCSB PDB 3NFK · PDBe 3NFK · UniProt P29074 · UniProt P03524
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