data_17185 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Determination of the Binding Specificity of the Integral Membrane Protein by Saturation Transfer Difference NMR: RGD Peptide Ligands Binding to Integrin alphaIIbBeta3 ; _BMRB_accession_number 17185 _BMRB_flat_file_name bmr17185.str _Entry_type new _Submission_date 2010-09-10 _Accession_date 2010-09-10 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Meinecke Robert . . 2 Meyer Bernd . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count binding_constants 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-11-10 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Determination of the Binding Specificity of an Integral Membrane Protein by Saturation Transfer Difference NMR: RGD Peptide Ligands Binding to Integrin alphaIIbBeta3' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 11543674 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Meinecke Robert . . 2 Meyer Bernd . . stop_ _Journal_abbreviation 'J. Med. Chem.' _Journal_name_full 'Journal of Medicinal Chemistry' _Journal_volume 44 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3059 _Page_last 3065 _Year 2001 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'cyclo/integrin complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label cyclo $cyclo alphaIIb $alphaIIb beta3 $beta3 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'cyclo bound to alphaIIb-beta integrin liposome construct' save_ ######################## # Monomeric polymers # ######################## save_cyclo _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common cyclo _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 5 _Mol_residue_sequence RGDXV loop_ _Residue_seq_code _Residue_label 1 ARG 2 GLY 3 ASP 4 DPN 5 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_alphaIIb _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common alphaIIb _Molecular_mass . _Mol_thiol_state 'not reported' _Details . _Residue_count 42 _Mol_residue_sequence ; GALEERAIPIWWVLVGVLGG LLLLTILVLAMWKVGFFKRN RP ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 ALA 3 LEU 4 GLU 5 GLU 6 ARG 7 ALA 8 ILE 9 PRO 10 ILE 11 TRP 12 TRP 13 VAL 14 LEU 15 VAL 16 GLY 17 VAL 18 LEU 19 GLY 20 GLY 21 LEU 22 LEU 23 LEU 24 LEU 25 THR 26 ILE 27 LEU 28 VAL 29 LEU 30 ALA 31 MET 32 TRP 33 LYS 34 VAL 35 GLY 36 PHE 37 PHE 38 LYS 39 ARG 40 ASN 41 ARG 42 PRO stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 16496 AIIbTMCD 92.86 54 100.00 100.00 3.55e-05 BMRB 16497 Integrin_aIIb_transmembrane_segment,_b3_complexed 100.00 42 100.00 100.00 1.41e-18 PDB 2K1A "Bicelle-Embedded Integrin Alpha(Iib) Transmembrane Segment" 100.00 42 100.00 100.00 1.41e-18 PDB 2K9J "Integrin Alphaiib-Beta3 Transmembrane Complex" 100.00 42 100.00 100.00 1.41e-18 PDB 2KNC "Platelet Integrin Alfaiib-Beta3 Transmembrane-Cytoplasmic Heterocomplex" 92.86 54 100.00 100.00 3.55e-05 DBJ BAG37735 "unnamed protein product [Homo sapiens]" 97.62 1039 100.00 100.00 1.96e-18 DBJ BAI46167 "integrin, alpha 2b [synthetic construct]" 97.62 1039 100.00 100.00 1.96e-18 EMBL CAA29987 "platelet glycoprotein IIb (648 AA) [Homo sapiens]" 97.62 648 100.00 100.00 2.26e-19 GB AAA35926 "platelet glycoprotein IIb (GPIIb) [Homo sapiens]" 95.24 1039 100.00 100.00 5.44e-05 GB AAA52597 "glycoprotein IIb, partial [Homo sapiens]" 97.62 172 100.00 100.00 8.32e-18 GB AAA53150 "platelet Glycoprotein IIb (GPIIb), partial [Homo sapiens]" 97.62 1039 100.00 100.00 1.96e-18 GB AAA60114 "platelet membrane glycoprotein IIb [Homo sapiens]" 97.62 1039 100.00 100.00 1.96e-18 GB AAA65936 "glycoprotein IIb, partial [Papio cynocephalus]" 97.62 604 100.00 100.00 1.13e-19 PRF 1403305A "protein GPIIb" 97.62 649 100.00 100.00 2.60e-19 REF NP_000410 "integrin alpha-IIb preproprotein [Homo sapiens]" 97.62 1039 100.00 100.00 1.96e-18 REF XP_001114526 "PREDICTED: integrin alpha-IIb [Macaca mulatta]" 97.62 1039 100.00 100.00 7.03e-19 REF XP_001150497 "PREDICTED: integrin alpha-IIb isoform X2 [Pan troglodytes]" 97.62 1108 100.00 100.00 1.11e-18 REF XP_002827479 "PREDICTED: integrin alpha-IIb [Pongo abelii]" 97.62 1039 100.00 100.00 1.26e-18 REF XP_003282434 "PREDICTED: LOW QUALITY PROTEIN: integrin alpha-IIb [Nomascus leucogenys]" 97.62 1040 100.00 100.00 9.87e-19 SP P08514 "RecName: Full=Integrin alpha-IIb; AltName: Full=GPalpha IIb; Short=GPIIb; AltName: Full=Platelet membrane glycoprotein IIb; Alt" 97.62 1039 100.00 100.00 1.96e-18 SP P53711 "RecName: Full=Integrin alpha-IIb; AltName: Full=GPalpha IIb; Short=GPIIb; AltName: Full=Platelet membrane glycoprotein IIb; Alt" 97.62 604 100.00 100.00 1.13e-19 stop_ save_ save_beta3 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common beta3 _Molecular_mass . _Mol_thiol_state 'not reported' _Details . _Residue_count 43 _Mol_residue_sequence ; PESPKGPDILVVLLSVMGAI LLIGLAALLIWKLLITIHDR KEF ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 GLU 3 SER 4 PRO 5 LYS 6 GLY 7 PRO 8 ASP 9 ILE 10 LEU 11 VAL 12 VAL 13 LEU 14 LEU 15 SER 16 VAL 17 MET 18 GLY 19 ALA 20 ILE 21 LEU 22 LEU 23 ILE 24 GLY 25 LEU 26 ALA 27 ALA 28 LEU 29 LEU 30 ILE 31 TRP 32 LYS 33 LEU 34 LEU 35 ILE 36 THR 37 ILE 38 HIS 39 ASP 40 ARG 41 LYS 42 GLU 43 PHE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 16496 B3TMCD 90.70 79 100.00 100.00 6.87e-07 BMRB 16497 Integrin_b3_transmembrane_segment,_aIIb_complexed 100.00 43 100.00 100.00 2.90e-19 PDB 2K9J "Integrin Alphaiib-Beta3 Transmembrane Complex" 100.00 43 100.00 100.00 2.90e-19 PDB 2KNC "Platelet Integrin Alfaiib-Beta3 Transmembrane-Cytoplasmic Heterocomplex" 90.70 79 100.00 100.00 6.87e-07 PDB 2RMZ "Bicelle-Embedded Integrin Beta3 Transmembrane Segment" 100.00 43 100.00 100.00 2.90e-19 PDB 2RN0 "Micelle-Embedded Integrin Beta3 Transmembrane Segment" 100.00 43 100.00 100.00 2.90e-19 DBJ BAG62151 "unnamed protein product [Homo sapiens]" 100.00 751 97.67 97.67 8.70e-19 DBJ BAJ17755 "integrin, beta 3 [synthetic construct]" 100.00 788 97.67 97.67 9.15e-19 GB AAA35927 "plate glycoprotein IIIa (GPIIIa) [Homo sapiens]" 100.00 788 97.67 97.67 9.15e-19 GB AAA36121 "integrin beta-3, partial [Homo sapiens]" 100.00 74 97.67 97.67 9.82e-19 GB AAA52589 "glycoprotein IIIa precursor [Homo sapiens]" 100.00 788 97.67 97.67 9.15e-19 GB AAA52600 "platelet glycoprotein IIIa, partial [Homo sapiens]" 100.00 761 97.67 97.67 8.83e-19 GB AAA60122 "glycoprotein IIIa [Homo sapiens]" 100.00 788 97.67 97.67 9.15e-19 REF NP_000203 "integrin beta-3 precursor [Homo sapiens]" 100.00 788 97.67 97.67 9.15e-19 REF XP_002748172 "PREDICTED: integrin beta-3 [Callithrix jacchus]" 100.00 788 97.67 97.67 9.15e-19 REF XP_002834363 "PREDICTED: integrin beta-3 isoform X1 [Pongo abelii]" 100.00 788 97.67 97.67 9.15e-19 REF XP_003270746 "PREDICTED: integrin beta-3 [Nomascus leucogenys]" 100.00 788 97.67 97.67 9.15e-19 REF XP_004041501 "PREDICTED: integrin beta-3 [Gorilla gorilla gorilla]" 100.00 788 97.67 97.67 9.15e-19 SP P05106 "RecName: Full=Integrin beta-3; AltName: Full=Platelet membrane glycoprotein IIIa; Short=GPIIIa; AltName: CD_antigen=CD61; Flags" 100.00 788 97.67 97.67 9.15e-19 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_DPN _Saveframe_category polymer_residue _Mol_type 'D-peptide linking' _Name_common D-PHENYLALANINE _BMRB_code . _PDB_code DPN _Standard_residue_derivative . _Molecular_mass 165.189 _Mol_paramagnetic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 13:50:48 2009 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? CE1 CE1 C . 0 . ? CE2 CE2 C . 0 . ? CZ CZ C . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 H . 0 . ? HZ HZ H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N H2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 CE1 ? ? SING CD1 HD1 ? ? DOUB CD2 CE2 ? ? SING CD2 HD2 ? ? DOUB CE1 CZ ? ? SING CE1 HE1 ? ? SING CE2 CZ ? ? SING CE2 HE2 ? ? SING CZ HZ ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $cyclo . . . . . . $alphaIIb Human 9606 Eukaryota Metazoa . . $beta3 Human 9606 Eukaryota Metazoa . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $cyclo 'chemical synthesis' . . . . . $alphaIIb 'purified from the natural source' . . . . . $beta3 'purified from the natural source' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'cyclo titrated into integrin solution; two integrin parts were one unit; pD was adjusted with 100 mM DCl in D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $cyclo . uM 0 275 'natural abundance' $alphaIIb 5 uM . . 'natural abundance' $beta3 5 uM . . 'natural abundance' TRIS 10 mM . . 'natural abundance' 'sodium chloride' 10 mM . . 'natural abundance' 'sodium azide' 6 mM . . 'natural abundance' 'calcium chloride' 20.5 mM . . 'natural abundance' D2O 99.9 % . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling RGD 274 mM 'natural abundance' $cyclo 264 mM 'natural abundance' $alphaIIb 5 uM 'natural abundance' $beta3 5 uM 'natural abundance' TRIS 10 mM 'natural abundance' 'sodium chloride' 10 mM 'natural abundance' 'sodium azide' 6 mM 'natural abundance' 'calcium chloride' 20.5 mM 'natural abundance' D2O 99.9 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling RGD 274 mM 'natural abundance' $cyclo 264 mM 'natural abundance' $alphaIIb 5 uM 'natural abundance' $beta3 5 uM 'natural abundance' RGDS 264 mM 'natural abundance' TRIS 10 mM 'natural abundance' 'sodium azide' 6 mM 'natural abundance' 'sodium chloride' 10 mM 'natural abundance' 'calcium chloride' 20.5 mM 'natural abundance' D2O 99.9 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version 2.5 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_STD_NMR_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'STD NMR' _Sample_label $sample_1 save_ save_STD_NMR_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'STD NMR' _Sample_label $sample_2 save_ save_STD_NMR_3 _Saveframe_category NMR_applied_experiment _Experiment_name 'STD NMR' _Sample_label $sample_3 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 283 . K pD 7.4 . pH pressure ambient . atm stop_ save_