MolNFT v1 · #78443 · protein
Ptprz CNTN1 complex
3S97 · Receptor-type tyrosine-protein phosphatase zeta: “Ptprz CNTN1 complex”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.61). MolNFT v1 #78443 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3S97
- Type
- protein
- Length
- 925 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase zeta; Contactin-1
- EC
- 3.1.3.48
- UniProt
- P23471, Q12860
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase zeta (EC 3.1.3.48) | protein | 266 | 15% helix, 36% strand | P23471 |
| B | Receptor-type tyrosine-protein phosphatase zeta (EC 3.1.3.48) | protein | 265 | 16% helix, 33% strand | P23471 |
| C, D | Contactin-1 | protein | 197 | 5% helix, 51% strand | Q12860 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.61 | 0.80 | 20 | empty |
| 2 | 371 | 0.59 | 0.76 | 50 | empty |
| 3 | 193 | 0.57 | 0.80 | 20 | empty |
| 4 | 272 | 0.52 | 0.75 | 37 | empty |
| 5 | 58 | 0.28 | 0.74 | 12 | empty |
Interfaces
4 interfaces between chains.
- B–D · 903 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 868 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 419 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 369 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3S97 · PTPRZ CNTN1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- P23471 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase zeta… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q12860 · AlphaFold monomer V2.0 prediction for contactin-1 (Q12860) · a predicted model of the same protein · chain C 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 P23471
- Every structure of UniProt Q12860
- Elsewhere: RCSB PDB 3S97 · PDBe 3S97 · UniProt P23471 · UniProt Q12860
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