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Crystal structure of human cytomegalovirus il-10 bound to soluble human il-10R1

Analyse Crystal structure of human cytomegalovirus il-10 bound to soluble human il-10R1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LQS
Type: protein
Length: 697 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-10 receptor alpha chain; Interleukin-10-like protein
UniProt: Q13651, P17150
Ligands: NAG
Pockets: 6 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Interleukin-10 receptor alpha chain	protein	207	6% helix, 46% strand	Q13651
S	Interleukin-10 receptor alpha chain	protein	206	7% helix, 46% strand	Q13651
L, M	Interleukin-10-like protein	protein	142	73% helix, 0% strand	P17150

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L, M

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	258	0.65	0.83	30	empty
2	261	0.64	0.82	30	empty
3	130	0.48	0.79	26	empty
4	101	0.46	0.80	21	empty
5	121	0.46	0.78	23	empty

Interfaces

5 interfaces between chains.

L–M · 3987 Å² buried · 42 hydrogen bonds · protein-protein
R–L · 869 Å² buried · 16 hydrogen bonds · protein-protein
S–M · 843 Å² buried · 12 hydrogen bonds · protein-protein
R–M · 359 Å² buried · 9 hydrogen bonds · protein-protein
S–L · 352 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

1LQS · Crystal structure of human cytomegalovirus il-10 bound to soluble human il-10R1 · the same entry in another collection · chain R against R, TM-score 1.00
Q13651 · AlphaFold monomer V2.0 prediction for interleukin-10 receptor subunit alpha (Q13651) · a predicted model of the same protein · chain R against A, TM-score 0.98

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 Q13651
Every structure of UniProt P17150
Elsewhere: RCSB PDB 1LQS · PDBe 1LQS · UniProt Q13651 · UniProt P17150

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