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- PDB-1hgu: HUMAN GROWTH HORMONE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1hgu
TitleHUMAN GROWTH HORMONE
ComponentsHUMAN GROWTH HORMONE
KeywordsHORMONE
Function / homology
Function and homology information


growth hormone activity / growth hormone receptor complex / prolactin receptor binding / bone maturation / animal organ development / positive regulation of multicellular organism growth / positive regulation of D-glucose transmembrane transport / cell surface receptor signaling pathway via STAT / growth hormone receptor binding / positive regulation of insulin-like growth factor receptor signaling pathway ...growth hormone activity / growth hormone receptor complex / prolactin receptor binding / bone maturation / animal organ development / positive regulation of multicellular organism growth / positive regulation of D-glucose transmembrane transport / cell surface receptor signaling pathway via STAT / growth hormone receptor binding / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor signaling pathway / Prolactin receptor signaling / positive regulation of MAP kinase activity / growth hormone receptor signaling pathway via JAK-STAT / Synthesis, secretion, and deacylation of Ghrelin / cell surface receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / endosome lumen / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / response to nutrient levels / hormone activity / cytokine-mediated signaling pathway / response to estradiol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Somatotropin / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsChantalat, L. / Jones, N. / Korber, F. / Navaza, J. / Pavlovsky, A.G.
CitationJournal: Protein Pept.Lett. / Year: 1995
Title: THE CRYSTAL-STRUCTURE OF WILD-TYPE GROWTH-HORMONE AT 2.5 ANGSTROM RESOLUTION.
Authors: Chantalat, L. / Jones, N.D. / Korber, F. / Navaza, J. / Pavlovsky, A.G.
History
DepositionMay 11, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_database_status.process_site / _software.classification / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN GROWTH HORMONE


Theoretical massNumber of molelcules
Total (without water)21,9031
Polymers21,9031
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.020, 57.020, 130.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: CIS PROLINE - PRO 37
2: ALA 67 - GLN 68 OMEGA = 215.88 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: GLN 68 - GLN 69 OMEGA = 226.17 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ASP 107 - SER 108 OMEGA = 238.99 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: SER 108 - ASP 109 OMEGA = 269.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: ASN 149 - SER 150 OMEGA = 137.02 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: ASP 153 - ASP 154 OMEGA = 141.53 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein HUMAN GROWTH HORMONE / HUMAN SOMATOTROPIN


Mass: 21902.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01241
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein dimer1drop
20.1 MBES1drop
325-28 %ethanol1reservoir
40.1 MBES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRmerge(I) obs: 0.0747
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / Num. obs: 5364 / % possible obs: 66.6 % / Num. measured all: 13055 / Rmerge(I) obs: 0.0747
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.75 Å / % possible obs: 37.1 %

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Processing

Software
NameClassification
XENGENdata collection
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementRfactor Rwork: 0.212 / Rfactor obs: 0.212 / Highest resolution: 2.5 Å
Displacement parametersBiso mean: 34 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 0 81 1576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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