data_15443 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural Study of Ac-Phe-[Orn-Pro-dCha-Trp-Arg], a Potent C5a Receptor Antagonist, by NMR ; _BMRB_accession_number 15443 _BMRB_flat_file_name bmr15443.str _Entry_type original _Submission_date 2007-08-25 _Accession_date 2007-08-25 _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 Zhang Li . . 2 Mallik Buddhadeb . . 3 Morikis Dimitrios . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 62 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-02-11 update BMRB 'complete entry citation' 2008-10-21 update BMRB 'update entry citation' 2007-11-07 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural Study of Ac-Phe-[Orn-Pro-dCha-Trp-Arg], a Potent C5a Receptor Antagonist, by NMR ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18846567 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhang Li . . 2 Mallik Buddhadeb . . 3 Morikis Dimitrios . . stop_ _Journal_abbreviation Biopolymers _Journal_volume 90 _Journal_issue 6 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 803 _Page_last 815 _Year 2008 _Details . loop_ _Keyword 'Peptide structure' NMR C5a C5aR 'Complement system' Inflammation stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name cC5aR-pa _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label cC5aR-pa $cC5aR-pa stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_cC5aR-pa _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common cC5aR-pa _Molecular_mass 887.156 _Mol_thiol_state 'not present' loop_ _Biological_function 'Inhibitor of complement syetm' stop_ _Details 'There is an acetyl group, 5 L-amino acids, and 1 D-amino acid' ############################## # Polymer residue sequence # ############################## _Residue_count 6 _Mol_residue_sequence XXPXWR loop_ _Residue_seq_code _Residue_label 1 NFA 2 ORN 3 PRO 4 CHA 5 TRP 6 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_NFA _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 'PHENYLALANINE AMIDE' _BMRB_code . _PDB_code NFA _Standard_residue_derivative . _Molecular_mass 164.204 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Oct 12 12:50:04 2011 ; 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 . ? 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 . ? NXT NXT N . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA 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 . ? HXT1 HXT1 H . 0 . ? HXT2 HXT2 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 NXT ? ? 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 ? ? SING NXT HXT1 ? ? SING NXT HXT2 ? ? stop_ save_ save_chem_comp_ORN _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common L-ornithine _BMRB_code . _PDB_code ORN _Standard_residue_derivative . _Molecular_mass 132.161 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Oct 12 12:50:41 2011 ; 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 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? NE NE N . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 H . 0 . ? HXT HXT 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 CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD NE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING NE HE1 ? ? SING NE HE2 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_CHA _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 1-HYDROXY-2-AMINO-3-CYCLOHEXYLPROPANE _BMRB_code . _PDB_code CHA _Standard_residue_derivative . _Molecular_mass 157.253 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Oct 12 12:51:19 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C1' C1' C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4' C4' C . 0 . ? C5' C5' C . 0 . ? C6' C6' C . 0 . ? N2 N2 N . 0 . ? O1 O1 O . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H2 H2 H . 0 . ? H31 H31 H . 0 . ? H32 H32 H . 0 . ? H1' H1' H . 0 . ? H2'1 H2'1 H . 0 . ? H2'2 H2'2 H . 0 . ? H3'1 H3'1 H . 0 . ? H3'2 H3'2 H . 0 . ? H4'1 H4'1 H . 0 . ? H4'2 H4'2 H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? H6'1 H6'1 H . 0 . ? H6'2 H6'2 H . 0 . ? HN21 HN21 H . 0 . ? HN22 HN22 H . 0 . ? HO1 HO1 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 C1 C2 ? ? SING C1 O1 ? ? SING C1 H11 ? ? SING C1 H12 ? ? SING C2 C3 ? ? SING C2 N2 ? ? SING C2 H2 ? ? SING C3 C1' ? ? SING C3 H31 ? ? SING C3 H32 ? ? SING C1' C2' ? ? SING C1' C6' ? ? SING C1' H1' ? ? SING C2' C3' ? ? SING C2' H2'1 ? ? SING C2' H2'2 ? ? SING C3' C4' ? ? SING C3' H3'1 ? ? SING C3' H3'2 ? ? SING C4' C5' ? ? SING C4' H4'1 ? ? SING C4' H4'2 ? ? SING C5' C6' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING C6' H6'1 ? ? SING C6' H6'2 ? ? SING N2 HN21 ? ? SING N2 HN22 ? ? SING O1 HO1 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $cC5aR-pa . . . . . . 'Chemical synthesis peptide' 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 $cC5aR-pa 'chemical synthesis' . . . . N/A stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $cC5aR-pa . mM 2 3 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' 'data analysis' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 308 10 K pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DMSO-d6 H 1 protons ppm 2.50 internal direct . . . 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name cC5aR-pa _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 NFA H2 H 1.752 . 1 2 1 1 NFA H H 8.110 . 1 3 1 1 NFA HA H 4.515 . 1 4 1 1 NFA HB2 H 2.703 . 1 5 1 1 NFA HB3 H 2.973 . 1 6 1 1 NFA HD2 H 7.257 . 4 7 1 1 NFA HE1 H 7.240 . 4 8 1 1 NFA HZ H 7.185 . 4 9 2 2 ORN H H 7.970 . 1 10 2 2 ORN HA H 4.565 . 1 11 2 2 ORN HB2 H 1.653 . 2 12 2 2 ORN HB3 H 1.430 . 2 13 2 2 ORN HG2 H 1.482 . 2 14 2 2 ORN HG3 H 1.251 . 2 15 2 2 ORN HD2 H 3.395 . 2 16 2 2 ORN HD3 H 2.760 . 2 17 2 2 ORN HE1 H 7.057 . 1 18 3 3 PRO HA H 4.583 . 1 19 3 3 PRO HB2 H 1.884 . 1 20 3 3 PRO HB3 H 1.884 . 1 21 3 3 PRO HG2 H 1.999 . 1 22 3 3 PRO HG3 H 1.884 . 1 23 3 3 PRO HD2 H 3.624 . 1 24 3 3 PRO HD3 H 3.426 . 1 25 4 4 CHA H2 H 8.185 . 1 26 4 4 CHA H11 H 4.023 . 1 27 4 4 CHA H31 H 1.280 . 1 28 4 4 CHA H32 H 1.163 . 1 29 4 4 CHA H1' H 0.944 . 1 30 4 4 CHA H2'1 H 0.621 . 1 31 4 4 CHA H2'2 H 1.475 . 1 32 4 4 CHA H3'1 H 0.696 . 1 33 4 4 CHA H3'2 H 1.435 . 1 34 4 4 CHA H4'1 H 0.866 . 1 35 4 4 CHA H4'2 H 1.440 . 1 36 4 4 CHA H5'1 H 0.924 . 1 37 4 4 CHA H5'2 H 1.495 . 1 38 4 4 CHA H6'1 H 1.020 . 1 39 4 4 CHA H6'2 H 1.475 . 1 40 5 5 TRP H H 8.406 . 1 41 5 5 TRP HA H 4.137 . 1 42 5 5 TRP HB2 H 2.983 . 1 43 5 5 TRP HB3 H 3.283 . 1 44 5 5 TRP HD1 H 7.171 . 1 45 5 5 TRP HE1 H 10.872 . 1 46 5 5 TRP HE3 H 7.535 . 1 47 5 5 TRP HZ2 H 7.340 . 1 48 5 5 TRP HZ3 H 6.985 . 1 49 5 5 TRP HH2 H 7.067 . 1 50 6 6 ARG H H 7.820 . 1 51 6 6 ARG HA H 4.143 . 1 52 6 6 ARG HB2 H 1.646 . 1 53 6 6 ARG HB3 H 1.877 . 1 54 6 6 ARG HG2 H 1.527 . 1 55 6 6 ARG HG3 H 1.478 . 1 56 6 6 ARG HD2 H 3.108 . 1 57 6 6 ARG HD3 H 3.108 . 1 58 6 6 ARG HE H 7.512 . 1 59 6 6 ARG HH11 H 6.922 . 4 60 6 6 ARG HH12 H 6.497 . 4 61 6 6 ARG HH21 H 6.922 . 4 62 6 6 ARG HH22 H 6.497 . 4 stop_ save_