2XDG: Crystal Structure Of The Extracellular Domain Of Human Growth ...

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247,287Structures from the PDB archive 1,068,577Computed Structure Models (CSM)

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Data API 2XDG | pdb_00002xdg

Crystal structure of the extracellular domain of human growth hormone releasing hormone receptor.

• PDB DOI: https://doi.org/10.2210/pdb2XDG/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Deposited: 2010-04-30 Released: 2010-06-16 
• Deposition Author(s): Pike, A.C.W., Quigley, A., Barr, A.J., Burgess Brown, N., Shrestha, L., Yang, J., Chaikuad, A., Vollmar, M., Muniz, J.R.C., von Delft, F., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Carpenter, E.P.

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.223 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Starting Model: experimentalView more details

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history. LiteratureDownload Primary Citation 

•  Download Mendeley

Crystal Structure of the Extracellular Domain of Human Growth Hormone Releasing Hormone Receptor.

Pike, A.C.W., Quigley, A., Barr, A.J., Burgess Brown, N., Shrestha, L., Yang, J., Chaikuad, A., Vollmar, M., Muniz, J.R.C., von Delft, F., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Carpenter, E.P.To be published.Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (EDO)

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (EDO)

Global Symmetry: Cyclic - C2 (Explore in 3D)Global Stoichiometry: Homo 2-mer - A2 LessFind Similar Assemblies

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (EDO)

Global Symmetry: Asymmetric - C1 Global Stoichiometry: Monomer - A1 LessFind Similar Assemblies

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (EDO)

Global Symmetry: Asymmetric - C1 Global Stoichiometry: Monomer - A1 LessFind Similar Assemblies

Biological assembly 3 assigned by authors.

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Macromolecule Content 

• Total Structure Weight: 20.25 kDa 
• Atom Count: 1,413 
• Modeled Residue Count: 178 
• Deposited Residue Count: 184 
• Unique protein chains: 1

MacromoleculesFind similar proteins by: Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GROWTH HORMONE-RELEASING HORMONE RECEPTOR	A, B	92	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q02643 (Homo sapiens)Explore Q02643 Go to UniProtKB:  Q02643
PHAROS:  Q02643GTEx:  ENSG00000106128
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02643
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDOQuery on EDODownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A],G [auth B]	1,2-ETHANEDIOLC2 H6 O2LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MGQuery on MGDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A],E [auth B],F [auth B]	MAGNESIUM IONMgJLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.223 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 61Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.648	α = 90
b = 31.648	β = 90
c = 287.138	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental dataEntry History 

Deposition Data

• Released Date: 2010-06-16 
Deposition Author(s): Pike, A.C.W., Quigley, A., Barr, A.J., Burgess Brown, N., Shrestha, L., Yang, J., Chaikuad, A., Vollmar, M., Muniz, J.R.C., von Delft, F., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Carpenter, E.P.

Revision History (Full details and data files)

• Version 1.0: 2010-06-16Type: Initial release
• Version 1.1: 2011-05-08Changes: Version format compliance
• Version 1.2: 2011-07-13Changes: Version format compliance
• Version 1.3: 2018-01-24Changes: Database references, Structure summary
• Version 1.4: 2023-12-20Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.5: 2024-10-23Changes: Structure summary

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