Research workbench
Crystal structure ptp delta IG1-FN2 in complex with il-1RACP
Analyse Crystal structure ptp delta IG1-FN2 in complex with il-1RACP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YFD
- Type
- protein
- Length
- 813 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-1 receptor accessory protein; Receptor-type tyrosine-protein phosphatase delta
- EC
- 3.1.3.48
- UniProt
- Q61730, Q64487
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Interleukin-1 receptor accessory protein | protein | 322 | 6% helix, 42% strand | Q61730 |
| A | Receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 491 | 2% helix, 53% strand | Q64487 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.75 | 0.88 | 33 | empty |
| 2 | 535 | 0.69 | 0.79 | 48 | empty |
| 3 | 227 | 0.55 | 0.78 | 28 | empty |
| 4 | 275 | 0.55 | 0.76 | 38 | empty |
| 5 | 68 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 1627 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 4YFD · Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP · the same entry in another collection · chain B against B, TM-score 1.00
- Q61730 · AlphaFold monomer V2.0 prediction for interleukin-1 receptor accessory protein (Q61730) · a predicted model of the same protein · chain B against A, TM-score 0.83
- 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 0.48
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 Q61730
- Every structure of UniProt Q64487
- Elsewhere: RCSB PDB 4YFD · PDBe 4YFD · UniProt Q61730 · UniProt Q64487
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