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Engineered human interleukin-10 monomer complexed to 9D7 Fab fragment

Analyse Engineered human interleukin-10 monomer complexed to 9D7 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LK3
Type: protein
Length: 1,130 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-10; 9D7 light chain; 9D7 heavy chain
UniProt: P22301
Pockets: 18 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Interleukin-10	protein	136	72% helix, 0% strand	P22301
L, M	9D7 light chain	protein	210	6% helix, 50% strand	—
H, I	9D7 heavy chain	protein	219	10% helix, 53% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	574	0.63	0.75	54	empty
2	346	0.61	0.78	40	empty
3	276	0.58	0.78	44	empty
4	274	0.57	0.77	30	empty
5	201	0.54	0.78	26	empty

Interfaces

8 interfaces between chains.

M–I · 1838 Å² buried · 13 hydrogen bonds · protein-protein
L–H · 1756 Å² buried · 13 hydrogen bonds · protein-protein
B–I · 594 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 569 Å² buried · 14 hydrogen bonds · protein-protein
H–I · 495 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

1LK3 · Engineered human interleukin-10 monomer complexed to 9D7 Fab fragment · the same entry in another collection · chain H against H, TM-score 1.00
P22301 · AlphaFold monomer V2.0 prediction for interleukin-10 (P22301) · a predicted model of the same protein · chain A against A, TM-score 0.66

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 P22301
Elsewhere: RCSB PDB 1LK3 · PDBe 1LK3 · UniProt P22301

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