3V6O

Leptin Receptor-antibody complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure of the human obesity receptor leptin-binding domain reveals the mechanism of leptin antagonism by a monoclonal antibody.

Carpenter, B., Hemsworth, G.R., Wu, Z., Maamra, M., Strasburger, C.J., Ross, R.J., Artymiuk, P.J.

(2012) Structure 20: 487-497

  • DOI: 10.1016/j.str.2012.01.019
  • Primary Citation of Related Structures:  
    3V6O, 3VG0

  • PubMed Abstract: 

    • Leptin regulates energy homeostasis, fertility, and the immune system, making it an important drug target. However, due to a complete lack of structural data for the obesity receptor (ObR), leptin's mechanism of receptor activation remains poorly understood ...

    Leptin regulates energy homeostasis, fertility, and the immune system, making it an important drug target. However, due to a complete lack of structural data for the obesity receptor (ObR), leptin's mechanism of receptor activation remains poorly understood. We have crystallized the Fab fragment of a leptin-blocking monoclonal antibody (9F8), both in its uncomplexed state and bound to the leptin-binding domain (LBD) of human ObR. We describe the structure of the LBD-9F8 Fab complex and the conformational changes in 9F8 associated with LBD binding. A molecular model of the putative leptin-LBD complex reveals that 9F8 Fab blocks leptin binding through only a small (10%) overlap in their binding sites, and that leptin binding is likely to involve an induced fit mechanism. This crystal structure of the leptin-binding domain of the obesity receptor will facilitate the design of therapeutics to modulate leptin signaling.

    Organizational Affiliation: 

    Academic Unit of Diabetes, Endocrinology and Reproduction, Department of Human Metabolism, University of Sheffield, Sheffield S10 2JF, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leptin receptorA, B206Homo sapiensMutation(s): 0 
Gene Names: DB, LEPR, OBR
UniProt & NIH Common Fund Data Resources
Find proteins for P48357 (Homo sapiens)
Explore P48357 
Go to UniProtKB:  P48357
PHAROS:  P48357
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48357
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody 9F8 fab fragment Heavy chainC, D221Mus musculusMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody 9F8 fab fragment Light chainE, F215Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
MA [auth F]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
CYS
Query on CYS
Download Ideal Coordinates CCD File 
G [auth A],
P [auth B]		CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N		 Ligand Interaction
EDO
Query on EDO
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BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
J [auth A],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
N [auth A],
O [auth A],
PA [auth F],
Q [auth B],
QA [auth F],
R [auth B],
RA [auth F],
S [auth B],
SA [auth F],
T [auth B],
TA [auth F],
U [auth B],
UA [auth F],
X [auth C],
Y [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
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AA [auth D],
IA [auth E],
NA [auth F],
OA [auth F],
V [auth C],
AA [auth D],
IA [auth E],
NA [auth F],
OA [auth F],
V [auth C],
W [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
Z [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.814α = 90
b = 118.829β = 90
c = 171.281γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary