6KO5

Complex structure of Ghrelin receptor with Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

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This is version 1.3 of the entry. See complete history


Literature

Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode.

Shiimura, Y.Horita, S.Hamamoto, A.Asada, H.Hirata, K.Tanaka, M.Mori, K.Uemura, T.Kobayashi, T.Iwata, S.Kojima, M.

(2020) Nat Commun 11: 4160-4160

  • DOI: https://doi.org/10.1038/s41467-020-17554-1
  • Primary Citation of Related Structures:  
    6KO5, 6KS2

  • PubMed Abstract: 

    Ghrelin is a gastric peptide hormone with important physiological functions. The unique feature of ghrelin is its Serine 3 acyl-modification, which is essential for ghrelin's activity. However, it remains to be elucidated why the acyl-modification of ghrelin is necessary for activity. To address these questions, we solved the crystal structure of the ghrelin receptor bound to antagonist. The ligand-binding pocket of the ghrelin receptor is bifurcated by a salt bridge between E124 and R283. A striking feature of the ligand-binding pocket of the ghrelin receptor is a wide gap (crevasse) between the TM6 and TM7 bundles that is rich in hydrophobic amino acids, including a cluster of phenylalanine residues. Mutagenesis analyses suggest that the interaction between the gap structure and the acyl acid moiety of ghrelin may participate in transforming the ghrelin receptor into an active conformation.


  • Organizational Affiliation

    Division of Molecular Genetics, Institute of Life Science, Kurume University, Fukuoka, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1424Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 5 
Gene Names: cybCGHSR
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92847 (Homo sapiens)
Explore Q92847 
Go to UniProtKB:  Q92847
PHAROS:  Q92847
GTEx:  ENSG00000121853 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7Q92847
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab7881 Heavy ChainB [auth H]218Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab7881 Light ChainC [auth L]219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8QX (Subject of Investigation/LOI)
Query on 8QX

Download Ideal Coordinates CCD File 
D [auth A]6-(4-bromanyl-2-fluoranyl-phenoxy)-2-methyl-3-[[(3~{S})-1-propan-2-ylpiperidin-3-yl]methyl]pyrido[3,2-d]pyrimidin-4-one
C23 H26 Br F N4 O2
LMBFVVBQYYWDKN-INIZCTEOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 253.76α = 90
b = 44.75β = 97.26
c = 94.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references
  • Version 1.2: 2020-09-02
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description