data_21009 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Binding Mechanism of a Peptidylic Cyclic Serine Protease Inhibitor - upain-1 ; _BMRB_accession_number 21009 _BMRB_flat_file_name bmr21009.str _Entry_type new _Submission_date 2011-04-29 _Accession_date 2011-04-29 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; Our model is upain-1 (CSWRGLENHRMC), a disulphide bond-constrained competitive inhibitor of human urokinase-type plasminogen activator with a non-canonical inhibitory mechanism and an unusually high specificity. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Svane Anna S.P. . 2 Jensen Jan K. . 3 Nielsen Jakob T. . 4 Nielsen Niels Chr . 5 Malmendal Anders . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 76 "13C chemical shifts" 37 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-08-07 original author 'coordinate file not annotated' stop_ loop_ _Related_BMRB_accession_number _Relationship 21010 'extended upain' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'The binding mechanism of a peptidic cyclic serine protease inhibitor' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21802428 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Jiang Longguang . . 2 Svane Anna S.P. . 3 Sorensen 'Hans Peter' . . 4 Jensen Jan K. . 5 Hosseini Masood . . 6 Chen Zhuo . . 7 Weydert Caroline . . 8 Nielsen Jakob T. . 9 Christensen Anni . . 10 Yuan Cai . . 11 Jensen Knud J. . 12 Nielsen Niels Chr . 13 Malmendal Anders . . 14 Huang Mingdong . . 15 Andreasen Peter A. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 412 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 235 _Page_last 250 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name upain-1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label upain-1 $upain-1 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_upain-1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common upain-1 _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence XCSWRGLENHRMCX loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ACE 2 2 CYS 3 3 SER 4 4 TRP 5 5 ARG 6 6 GLY 7 7 LEU 8 8 GLU 9 9 ASN 10 10 HIS 11 11 ARG 12 12 MET 13 13 CYS 14 14 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ACE _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'ACETYL GROUP' _BMRB_code . _PDB_code ACE _Standard_residue_derivative . _Molecular_mass 44.053 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Jun 8 10:18:58 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? O O O . 0 . ? CH3 CH3 C . 0 . ? H H H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 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 DOUB C O ? ? SING C CH3 ? ? SING C H ? ? SING CH3 H1 ? ? SING CH3 H2 ? ? SING CH3 H3 ? ? stop_ save_ save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'AMINO GROUP' _BMRB_code . _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Jun 8 12:26:36 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $upain-1 . . . . . . 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 $upain-1 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details '278 K' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $upain-1 4 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details 'Cryogenic probe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample save_ save_2D_1H-1H_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample save_ ####################### # Sample conditions # ####################### save_sample_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.4 . pH temperature 278 . K 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 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' '2D 1H-13C HSQC' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name upain-1 _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 ACE C C 24.123 0.05 1 2 1 1 ACE H1 H 2.032 0.01 1 3 1 1 ACE H2 H 2.032 0.01 1 4 1 1 ACE H3 H 2.032 0.01 1 5 2 2 CYS H H 8.514 0.01 1 6 2 2 CYS HA H 4.628 0.01 1 7 2 2 CYS HB2 H 2.977 0.01 2 8 2 2 CYS HB3 H 2.977 0.01 2 9 2 2 CYS CA C 55.327 0.05 1 10 2 2 CYS CB C 41.792 0.05 1 11 3 3 SER H H 8.658 0.01 1 12 3 3 SER HA H 4.521 0.01 1 13 3 3 SER HB2 H 3.780 0.01 2 14 3 3 SER HB3 H 3.780 0.01 2 15 3 3 SER CA C 57.836 0.05 1 16 3 3 SER CB C 63.599 0.05 1 17 4 4 TRP H H 8.276 0.01 1 18 4 4 TRP HA H 4.719 0.01 1 19 4 4 TRP HB2 H 3.229 0.01 2 20 4 4 TRP HB3 H 3.229 0.01 2 21 4 4 TRP HD1 H 7.232 0.01 1 22 4 4 TRP HE1 H 10.206 0.01 1 23 4 4 TRP HE3 H 7.522 0.01 1 24 4 4 TRP HZ2 H 7.463 0.01 1 25 4 4 TRP HZ3 H 7.091 0.01 1 26 4 4 TRP HH2 H 7.207 0.01 1 27 4 4 TRP CA C 57.222 0.05 1 28 4 4 TRP CB C 29.325 0.05 1 29 4 4 TRP CD1 C 127.046 0.05 1 30 4 4 TRP CE3 C 120.504 0.05 1 31 4 4 TRP CZ2 C 114.325 0.05 1 32 4 4 TRP CZ3 C 121.775 0.05 1 33 4 4 TRP CH2 C 124.404 0.05 1 34 5 5 ARG H H 8.411 0.01 1 35 5 5 ARG HA H 4.280 0.01 1 36 5 5 ARG HB2 H 1.778 0.01 2 37 5 5 ARG HB3 H 1.591 0.01 2 38 5 5 ARG HG2 H 1.332 0.01 2 39 5 5 ARG HG3 H 1.332 0.01 2 40 5 5 ARG HD2 H 3.063 0.01 2 41 5 5 ARG HD3 H 3.063 0.01 2 42 5 5 ARG HE H 7.162 0.01 1 43 5 5 ARG CA C 55.685 0.05 1 44 5 5 ARG CB C 30.457 0.05 1 45 5 5 ARG CG C 26.454 0.05 1 46 6 6 GLY H H 8.124 0.01 1 47 6 6 GLY HA2 H 4.045 0.01 2 48 6 6 GLY HA3 H 3.800 0.01 2 49 6 6 GLY CA C 44.976 0.05 1 50 7 7 LEU H H 8.275 0.01 1 51 7 7 LEU HA H 4.345 0.01 1 52 7 7 LEU HB2 H 1.682 0.01 2 53 7 7 LEU HB3 H 1.617 0.01 2 54 7 7 LEU HG H 1.624 0.01 1 55 7 7 LEU HD1 H 0.923 0.01 2 56 7 7 LEU HD2 H 0.872 0.01 2 57 7 7 LEU CA C 55.078 0.05 1 58 7 7 LEU CB C 42.151 0.05 1 59 7 7 LEU CG C 26.661 0.05 1 60 7 7 LEU CD1 C 24.679 0.05 2 61 7 7 LEU CD2 C 22.892 0.05 2 62 8 8 GLU H H 8.685 0.01 1 63 8 8 GLU HA H 4.141 0.01 1 64 8 8 GLU HB2 H 1.966 0.01 2 65 8 8 GLU HB3 H 1.966 0.01 2 66 8 8 GLU HG2 H 2.243 0.01 2 67 8 8 GLU HG3 H 2.243 0.01 2 68 8 8 GLU CA C 56.984 0.05 1 69 8 8 GLU CB C 29.259 0.05 1 70 8 8 GLU CG C 35.847 0.05 1 71 9 9 ASN H H 8.439 0.01 1 72 9 9 ASN HA H 4.518 0.01 1 73 9 9 ASN HB2 H 2.768 0.01 2 74 9 9 ASN HB3 H 2.768 0.01 2 75 9 9 ASN CA C 53.448 0.05 1 76 9 9 ASN CB C 37.927 0.05 1 77 10 10 HIS H H 8.330 0.01 1 78 10 10 HIS HA H 4.528 0.01 1 79 10 10 HIS HB2 H 3.213 0.01 2 80 10 10 HIS HB3 H 3.101 0.01 2 81 10 10 HIS HD2 H 7.121 0.01 1 82 10 10 HIS HE1 H 8.264 0.01 1 83 10 10 HIS CA C 55.884 0.05 1 84 10 10 HIS CB C 28.985 0.05 1 85 10 10 HIS CD2 C 119.504 0.05 1 86 10 10 HIS CE1 C 136.646 0.05 1 87 11 11 ARG H H 8.266 0.01 1 88 11 11 ARG HA H 4.264 0.01 1 89 11 11 ARG HB2 H 1.780 0.01 2 90 11 11 ARG HB3 H 1.712 0.01 2 91 11 11 ARG HG2 H 1.513 0.01 2 92 11 11 ARG HG3 H 1.513 0.01 2 93 11 11 ARG HD2 H 3.075 0.01 2 94 11 11 ARG HD3 H 3.075 0.01 2 95 11 11 ARG HE H 7.181 0.01 1 96 11 11 ARG CA C 56.377 0.05 1 97 11 11 ARG CB C 30.230 0.05 1 98 11 11 ARG CG C 26.801 0.05 1 99 12 12 MET H H 8.580 0.01 1 100 12 12 MET HA H 4.553 0.01 1 101 12 12 MET HB2 H 2.031 0.01 2 102 12 12 MET HB3 H 1.945 0.01 2 103 12 12 MET HG2 H 2.474 0.01 2 104 12 12 MET HG3 H 2.474 0.01 2 105 12 12 MET HE H 2.022 0.01 1 106 12 12 MET CB C 32.431 0.05 1 107 12 12 MET CG C 31.576 0.05 1 108 12 12 MET CE C 16.447 0.05 1 109 13 13 CYS H H 8.406 0.01 1 110 13 13 CYS HA H 4.556 0.01 1 111 13 13 CYS HB2 H 3.080 0.01 2 112 13 13 CYS HB3 H 2.634 0.01 2 113 13 13 CYS CB C 41.172 0.05 1 stop_ save_ save_constraint_statistics _Saveframe_category constraint_statistics _Text_data_format . _Text_data . _NOE_interproton_distance_evaluation . _NOE_pseudoatom_corrections . _Details . save_