Research workbench
Crystal structure of the complex between SLITRK2 LRR1 and ptp delta IG1-FN1
Analyse Crystal structure of the complex between SLITRK2 LRR1 and ptp delta IG1-FN1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y61
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase delta; Slit and ntrk-like protein 2
- EC
- 3.1.3.48
- UniProt
- Q64487, Q810C0
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 391 | 2% helix, 55% strand | Q64487 |
| B | Slit and ntrk-like protein 2 | protein | 235 | 13% helix, 20% strand | Q810C0 |
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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.65 | 0.76 | 44 | empty |
| 2 | 488 | 0.64 | 0.77 | 62 | empty |
| 3 | 157 | 0.51 | 0.79 | 26 | empty |
| 4 | 50 | 0.45 | 0.84 | 16 | empty |
| 5 | 118 | 0.40 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1134 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4Y61 · Crystal structure of the complex between Slitrk2 LRR1 and PTP delta Ig1-Fn1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q810C0 · AlphaFold monomer V2.0 prediction for slit and ntrk-like protein 2 (Q810C0) · a predicted model of the same protein · chain B against A, TM-score 0.96
- 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 0.62
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 Q810C0
- Elsewhere: RCSB PDB 4Y61 · PDBe 4Y61 · UniProt Q64487 · UniProt Q810C0
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