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- PDB-4d5m: Gonadotropin-releasing hormone agonist -

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Basic information

Entry
Database: PDB / ID: 4d5m
TitleGonadotropin-releasing hormone agonist
ComponentsTRIPTORELIN
KeywordsHORMONE / GNRH / LHRH / D-TRP / DECAPEPTIDE
Function / homology
Function and homology information


negative regulation of immature T cell proliferation / neurosecretory vesicle / regulation of ovarian follicle development / regulation of signaling / response to prolactin / gonadotropin hormone-releasing hormone activity / gonadotropin-releasing hormone receptor binding / Hormone ligand-binding receptors / negative regulation of neuron migration / response to potassium ion ...negative regulation of immature T cell proliferation / neurosecretory vesicle / regulation of ovarian follicle development / regulation of signaling / response to prolactin / gonadotropin hormone-releasing hormone activity / gonadotropin-releasing hormone receptor binding / Hormone ligand-binding receptors / negative regulation of neuron migration / response to potassium ion / male sex determination / response to steroid hormone / cytoplasmic side of rough endoplasmic reticulum membrane / Golgi-associated vesicle / response to testosterone / estrous cycle / response to prostaglandin E / axon terminus / female pregnancy / hormone activity / cell-cell signaling / regulation of gene expression / response to ethanol / response to lipopolysaccharide / perikaryon / G alpha (q) signalling events / dendrite / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular region
Similarity search - Function
Gonadoliberin I precursor / Gonadotropin-releasing hormone / Gonadoliberin / Gonadotropin-releasing hormone / Gonadotropin-releasing hormones signature.
Similarity search - Domain/homology
PHOSPHATE ION / Progonadoliberin-1
Similarity search - Component
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.85 Å
AuthorsLegrand, P. / Le Du, M.-H. / Valery, C. / Deville-Foillard, S. / Paternostre, M. / Artzner, F.
CitationJournal: Nat.Commun. / Year: 2015
Title: Atomic View of the Histidine Environment Stabilizing Higher- Ph Conformations of Ph-Dependent Proteins.
Authors: Valery, C. / Deville-Foillard, S. / Lefebvre, C. / Taberner, N. / Legrand, P. / Meneau, F. / Meriadec, C. / Delvaux, C. / Bizien, T. / Kasotakis, E. / Lopez-Iglesias, C. / Gall, A. / ...Authors: Valery, C. / Deville-Foillard, S. / Lefebvre, C. / Taberner, N. / Legrand, P. / Meneau, F. / Meriadec, C. / Delvaux, C. / Bizien, T. / Kasotakis, E. / Lopez-Iglesias, C. / Gall, A. / Bressanelli, S. / Le Du, M.-H. / Paternostre, M. / Artzner, F.
History
DepositionNov 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence / Category: entity_poly / pdbx_database_status / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIPTORELIN
B: TRIPTORELIN
C: TRIPTORELIN
D: TRIPTORELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5357
Polymers5,2504
Non-polymers2853
Water81145
1
A: TRIPTORELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4072
Polymers1,3121
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRIPTORELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4072
Polymers1,3121
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TRIPTORELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4072
Polymers1,3121
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TRIPTORELIN


Theoretical massNumber of molelcules
Total (without water)1,3121
Polymers1,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.900, 27.470, 13.150
Angle α, β, γ (deg.)90.00, 98.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1011-

PO4

21B-1011-

PO4

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1, 0.009, 0.005), (-0.009, 1, -0.002), (-0.005, 0.002, 1)-0.0577, -13.72572, 0.00171
2given(-1, -0.004, 0.016), (-0.004, 1, 0.016), (-0.016, 0.016, -1)17.07359, -7.05721, 25.86929
3given(-1, -0.011, -0.009), (-0.011, 1, -0.008), (0.009, -0.008, -1)17.52489, -20.43805, 26.04363

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Components

#1: Protein/peptide
TRIPTORELIN


Mass: 1312.458 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: TRIPTORELIN IS A MEDICINE AVAILABLE IN A NUMBER OF COUNTRIES WORLDWIDE.
Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: UniProt: P01148*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTRIPTORELIN IS RELATED TO GONADORELIN WITH THE G6W.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.42 Å3/Da / Density % sol: 14 % / Description: NONE
Crystal growpH: 6.2
Details: 300 MM POTASSIUM PHOSPHATE BUFFER, PH 6.2 MIXED WITH 80 MG/ML TRIPTORELIN IN WATER.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.78471
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2011 / Details: KB MIRRORS
RadiationMonochromator: CHANNEL-CUT MONOCHROMATOR SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78471 Å / Relative weight: 1
ReflectionResolution: 0.85→41.95 Å / Num. obs: 24802 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 26.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.6
Reflection shellResolution: 0.85→0.87 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.4 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: DIRECT METHODS
Starting model: NONE

Resolution: 0.85→41.95 Å / Cor.coef. Fo:Fc: 0.991 / Cor.coef. Fo:Fc free: 0.996 / SU B: 0.195 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.08739 1306 5 %RANDOM
Rwork0.08001 ---
obs0.08038 24802 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 1.746 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.08 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 0.85→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms380 0 15 45 440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.019472
X-RAY DIFFRACTIONr_bond_other_d0.0090.02379
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.809637
X-RAY DIFFRACTIONr_angle_other_deg0.8752.978826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.556538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.49218.18222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.811542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6154
X-RAY DIFFRACTIONr_chiral_restr0.0880.245
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.021532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02156
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.410.124184
X-RAY DIFFRACTIONr_mcbond_other0.4040.125182
X-RAY DIFFRACTIONr_mcangle_it0.50.188208
X-RAY DIFFRACTIONr_mcangle_other0.4990.187209
X-RAY DIFFRACTIONr_scbond_it0.5090.161288
X-RAY DIFFRACTIONr_scbond_other0.5080.161289
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6970.238430
X-RAY DIFFRACTIONr_long_range_B_refined1.2271.634685
X-RAY DIFFRACTIONr_long_range_B_other1.0921.472658
X-RAY DIFFRACTIONr_rigid_bond_restr5.5153851
X-RAY DIFFRACTIONr_sphericity_free5.40456
X-RAY DIFFRACTIONr_sphericity_bonded2.5285868
LS refinement shellResolution: 0.85→0.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.162 87 -
Rwork0.174 1658 -
obs--88.04 %

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