MolNFT v1 · #111120 · protein
Crystal structure of ptpdelta ectodomain in complex with IL1RAPL1
4YH7 · Receptor-type tyrosine-protein phosphatase delta: “Crystal structure of ptpdelta ectodomain in complex with IL1RAPL1”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 9 pockets (best druggability 0.71). MolNFT v1 #111120 on GenesisL1…
- PDB
- 4YH7
- Type
- protein
- Length
- 909 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
- Q64487, P59823
- Ligands
- NAG, MAN, BMA
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 585 | 2% helix, 49% strand | Q64487 |
| B | Interleukin-1 receptor accessory protein-like 1 | protein | 324 | 6% helix, 45% strand | P59823 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar
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 | 504 | 0.71 | 0.80 | 48 | empty |
| 2 | 158 | 0.59 | 0.83 | 24 | empty |
| 3 | 243 | 0.53 | 0.76 | 27 | empty |
| 4 | 209 | 0.51 | 0.76 | 27 | empty |
| 5 | 164 | 0.50 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1626 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4YH7 · Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1 · the same entry in another collection · chain A against A, TM-score 1.00
- P59823 · 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 0.97
- 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 0.51
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 P59823
- Elsewhere: RCSB PDB 4YH7 · PDBe 4YH7 · UniProt Q64487 · UniProt P59823
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.