Research workbench
Crystal structure of ptp delta IG1-IG3 in complex with IL1RAPL1 IG1- IG3
Analyse Crystal structure of ptp delta IG1-IG3 in complex with IL1RAPL1 IG1- IG3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WY8
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase delta; Interleukin-1 receptor accessory…
- EC
- 3.1.3.48
- UniProt
- P23468, Q9NZN1
- Ligands
- NAG, FUC, BMA, MAN, ZN
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 298 | 1% helix, 52% strand | P23468 |
| B | Interleukin-1 receptor accessory protein-like 1 | protein | 323 | 7% helix, 46% strand | Q9NZN1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.73 | 0.79 | 67 | empty |
| 2 | 145 | 0.61 | 0.85 | 25 | empty |
| 3 | 179 | 0.54 | 0.80 | 36 | empty |
| 4 | 191 | 0.51 | 0.77 | 26 | empty |
| 5 | 104 | 0.50 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2033 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 5WY8 · Crystal structure of PTP delta Ig1-Ig3 in complex with IL1RAPL1 Ig1-Ig3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZN1 · AlphaFold monomer V2.0 prediction for interleukin-1 receptor accessory protein-like 1… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P23468 · 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 0.81
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 P23468
- Every structure of UniProt Q9NZN1
- Elsewhere: RCSB PDB 5WY8 · PDBe 5WY8 · UniProt P23468 · UniProt Q9NZN1
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