MolNFT v1 · #111057 · protein

Crystal structure ptp delta IG1-FN2 in complex with il-1RACP

4YFD · Interleukin-1 receptor accessory protein: “Crystal structure ptp delta IG1-FN2 in complex with il-1RACP”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.75). MolNFT v1 #111057 on GenesisL1: 3D structure, binding…

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.

Pocket	Volume (Å³)	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 Å² 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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