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- PDB-1yy2: NMR Conformational Analysis of LHRH and its analogues -

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Basic information

Entry
Database: PDB / ID: 1yy2
TitleNMR Conformational Analysis of LHRH and its analogues
ComponentsLeuprolide
KeywordsANTITUMOR PROTEIN / U-shape like peptide
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsSpyroulias, G.A. / Zompra, A. / Magafa, V. / Cordopatis, P.
CitationJournal: To be Published
Title: NMR Conformational Analysis of LHRH and its analogues
Authors: Spyroulias, G.A. / Zompra, A. / Magafa, V. / Cordopatis, P.
History
DepositionFeb 23, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Polymer sequence / Source and taxonomy
Category: entity_poly / pdbx_entity_src_syn ...entity_poly / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.details ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_software.name / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Mar 1, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.1Oct 23, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leuprolide


Theoretical massNumber of molelcules
Total (without water)1,2111
Polymers1,2111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area190 Å2
ΔGint-1 kcal/mol
Surface area1340 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 400target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Leuprolide


Mass: 1211.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: modified sequence of LHRH / Source: (synth.) synthetic construct (others)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1311H-13C HSQC
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2.0mM-3.0mM / Solvent system: DMSO
Sample conditionsPressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DPX / Manufacturer: Bruker / Model: DPX / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
XwinNMR3.1Brukerprocessing
XEASY1.3C.Eccles, P.Guntert, M.Billeter, K.Wuthrichdata analysis
DYANA1.5P.Guntert, C.Mumenthaler, K.Wuthrichstructure solution
Amber5D.A.PEARLMAN, D.A.CASE, W.CALDWELL, W.S.ROSS, T.E.CHEATHAM, D.M.FERGUSON, G.L.SEIBEL, U.C.SINGH, P.K.WEINER, P.A.KOLLMANrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The models have been determined using 135 NOE-derived distance constraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 21

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