8SVE

Structure of Monomeric Interleukin-10 Grafted into and Antibody CDR

• PDB DOI: https://doi.org/10.2210/pdb8SVE/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-05-16 Released: 2024-05-22 
• Deposition Author(s): DiDonato, M., Spraggon, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.232 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Starting Models: experimental, in silico

Literature

A Novel Interleukin-10 Antibody Graft to Treat Inflammatory Bowel Disease.

DiDonato, M., Spraggon, G., Simpson, C.T., Vo, M.T., Knuth, M., Geierstanger, B., Jamontt, J., Fathman, J.J., DeLarosa, D., Junt, T., Picard, D., Sommer, U., Vogel, B., Bagger, M., Peters, E., Meeusen, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 133.41 kDa 
• Atom Count: 9,252 
• Modelled Residue Count: 1,156 
• Deposited Residue Count: 1,212 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Heavy chain	A [auth H], B [auth I]	227	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-10,Fab light chain	C [auth L], D [auth M]	379	Homo sapiens	Mutation(s): 0  Gene Names: IL10
UniProt & NIH Common Fund Data Resources
Find proteins for P22301 (Homo sapiens) Explore P22301  Go to UniProtKB:  P22301
GTEx:  ENSG00000136634

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth I], G [auth L], H [auth M], I [auth M], J [auth M]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	E [auth H]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth H], B [auth I]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.232 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.641	α = 90
b = 104.662	β = 115.29
c = 82.826	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): DiDonato, M., Spraggon, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release