MolNFT v1 · #175048 · protein
Crystal structure of the complex between mouse ptp delta and neuroligin-3
7CEG · Isoform C of receptor-type tyrosine-protein phosphatase…: “Crystal structure of the complex between mouse ptp delta and neuroligin-3”. X-ray diffraction, 1 ligand (NAG), 14 pockets (best druggability 0.75). MolNFT v1 #175048 on…
- PDB
- 7CEG
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform C of receptor-type tyrosine-protein phosphatase delta; Neuroligin-3
- EC
- 3.1.3.48
- UniProt
- Q64487, Q8BYM5
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform C of receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 386 | 1% helix, 48% strand | Q64487 |
| B | Neuroligin-3 | protein | 540 | 37% helix, 16% strand | Q8BYM5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.75 | 0.78 | 63 | empty |
| 2 | 98 | 0.75 | 0.96 | 28 | empty |
| 3 | 220 | 0.63 | 0.82 | 30 | empty |
| 4 | 100 | 0.55 | 0.84 | 18 | empty |
| 5 | 184 | 0.52 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1614 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7CEG · Crystal structure of the complex between mouse PTP delta and neuroligin-3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8BYM5 · AlphaFold monomer V2.0 prediction for neuroligin-3 (Q8BYM5) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q64487 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase delta… · a predicted model of the same protein · chain A against A, TM-score 0.58
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 Q64487
- Every structure of UniProt Q8BYM5
- Elsewhere: RCSB PDB 7CEG · PDBe 7CEG · UniProt Q64487 · UniProt Q8BYM5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.