6QIP

Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the albumin-biniding side chain of the human growth hormone derivative somapacitan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of Binding Sites on Human Serum Albumin for Somapacitan, a Long-Acting Growth Hormone Derivative.

Johansson, E.Nielsen, A.D.Demuth, H.Wiberg, C.Schjodt, C.B.Huang, T.Chen, J.Jensen, S.Petersen, J.Thygesen, P.

(2020) Biochemistry 59: 1410-1419

  • DOI: 10.1021/acs.biochem.0c00019
  • Primary Citation of Related Structures:  
    6QIO, 6QIP

  • PubMed Abstract: 
  • Somapacitan, a human growth hormone derivative that binds reversibly to albumin, was investigated for human serum albumin (HSA) and HSA domain binding. Isothermal titration calorimetry (ITC) binding profiles showed high-affinity binding (∼100-1000 nM ...

    Somapacitan, a human growth hormone derivative that binds reversibly to albumin, was investigated for human serum albumin (HSA) and HSA domain binding. Isothermal titration calorimetry (ITC) binding profiles showed high-affinity binding (∼100-1000 nM) of one somapacitan molecule and low-affinity binding (∼1000-10000 nM) of one to two somapacitan molecules to HSA. The high-affinity site was identified in HSA domain III using size exclusion chromatography (SEC) and ITC. SEC studies showed that the neonatal Fc receptor shields one binding site for somapacitan, indicating its position in domain III. A crystal structure of somapacitan in complex with HSA optimized for neonatal Fc receptor binding, having four amino acid residue replacements, identified a low-affinity site in fatty acid-binding site 6 (domain II). Surface plasmon resonance (SPR) showed these replacements affect the kinetics of the high-affinity binding site. Furthermore, small-angle X-ray scattering and SPR brace two somapacitan-binding sites on HSA.


    Organizational Affiliation

    Novo Nordisk A/S, Novo Nordisk Park 1, DK-2760 Måløv, Denmark.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serum albuminA585Homo sapiensMutation(s): 4 
Gene Names: ALBGIG20GIG42PRO0903PRO1708PRO2044PRO2619PRO2675UNQ696/PRO1341
Find proteins for P02768 (Homo sapiens)
Explore P02768 
Go to UniProtKB:  P02768
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PHAROS  P02768
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IgG receptor FcRn large subunit p51B274Homo sapiensMutation(s): 0 
Gene Names: FCGRTFCRN
Find proteins for P55899 (Homo sapiens)
Explore P55899 
Go to UniProtKB:  P55899
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PHAROS  P55899
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinC105Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
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PHAROS  P61769
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HDW
Query on HDW

Download Ideal Coordinates CCD File 
A
(2~{S})-6-[2-(2-hydroxyethylsulfanyl)ethanoylamino]-2-[2-[2-[2-[[(4~{R})-5-oxidanyl-5-oxidanylidene-4-[[(4~{S})-5-oxidanyl-5-oxidanylidene-4-[2-[2-[2-[4-[16-(2~{H}-1,2,3,4-tetrazol-5-yl)hexadecanoylsulfamoyl]butanoylamino]ethoxy]ethoxy]ethanoylamino]pentanoyl]amino]pentanoyl]amino]ethoxy]ethoxy]ethanoylamino]hexanoic acid
C53 H93 N11 O20 S2
ZNHGNAMZXIGHTQ-ZMWLRIRSSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
CYS
Query on CYS

Download Ideal Coordinates CCD File 
B
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.02α = 90
b = 114.45β = 90
c = 159.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2019-01-21 
  • Released Date: 2020-02-05 
  • Deposition Author(s): Johansson, E.

Revision History 

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references