data_21010 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Binding Mechanism of a Peptidylic Cyclic Serine Protease Inhibitor - extended upain ; _BMRB_accession_number 21010 _BMRB_flat_file_name bmr21010.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. Here data on an extended upain variant (MGSADGACSWRGLENHAMCGAAG) is reported. ; 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" 111 "13C chemical shifts" 48 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 21009 upain-1 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 'extended upain' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'extended upain' $extended_upain 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_extended_upain _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common extended_upain _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; XMGSADGACSWRGLENHAMC GAAGX ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ACE 2 2 MET 3 3 GLY 4 4 SER 5 5 ALA 6 6 ASP 7 7 GLY 8 8 ALA 9 9 CYS 10 10 SER 11 11 TRP 12 12 ARG 13 13 GLY 14 14 LEU 15 15 GLU 16 16 ASN 17 17 HIS 18 18 ALA 19 19 MET 20 20 CYS 21 21 GLY 22 22 ALA 23 23 ALA 24 24 GLY 25 25 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-09 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 PDB 3OX7 "The Crystal Structure Of Upa Complex With Peptide Inhibitor Mh027 At Ph4.6" 92.00 23 100.00 100.00 3.72e-06 PDB 3OY5 "The Crystal Structure Of Upa Complex With Peptide Inhibitor Mh027 At Ph7.4" 92.00 23 100.00 100.00 3.72e-06 stop_ 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 $extended_upain . . . . . . 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 $extended_upain '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 $extended_upain 2 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 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_ ####################### # 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 _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 'extended upain' _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 24.230 0.05 1 2 1 1 ACE H1 H 2.048 0.01 1 3 1 1 ACE H2 H 2.048 0.01 1 4 1 1 ACE H3 H 2.048 0.01 1 5 2 2 MET H H 8.646 0.01 1 6 2 2 MET HA H 4.469 0.01 1 7 2 2 MET HB2 H 2.273 0.01 2 8 2 2 MET HB3 H 2.141 0.01 2 9 2 2 MET HG2 H 2.992 0.01 2 10 2 2 MET HG3 H 2.924 0.01 2 11 2 2 MET HE H 2.694 0.01 1 12 2 2 MET CA C 55.203 0.05 1 13 2 2 MET CB C 26.682 0.05 1 14 2 2 MET CG C 50.955 0.05 1 15 2 2 MET CE C 38.949 0.05 1 16 3 3 GLY H H 8.722 0.01 1 17 3 3 GLY HA2 H 3.989 0.01 2 18 3 3 GLY HA3 H 3.989 0.01 2 19 3 3 GLY CA C 44.971 0.05 1 20 4 4 SER H H 8.368 0.01 1 21 4 4 SER HA H 4.443 0.01 1 22 4 4 SER HB2 H 3.902 0.01 2 23 4 4 SER HB3 H 3.847 0.01 2 24 4 4 SER CA C 57.987 0.05 1 25 4 4 SER CB C 63.577 0.05 1 26 5 5 ALA H H 8.576 0.01 1 27 5 5 ALA HA H 4.340 0.01 1 28 5 5 ALA HB H 1.397 0.01 1 29 5 5 ALA CA C 52.528 0.05 1 30 6 6 ASP H H 8.428 0.01 1 31 6 6 ASP HA H 4.661 0.01 1 32 6 6 ASP HB2 H 2.874 0.01 2 33 6 6 ASP HB3 H 2.788 0.01 2 34 6 6 ASP CA C 53.101 0.05 1 35 6 6 ASP CB C 38.566 0.05 1 36 7 7 GLY H H 8.385 0.01 1 37 7 7 GLY HA2 H 3.930 0.01 2 38 7 7 GLY HA3 H 3.930 0.01 2 39 8 8 ALA H H 8.236 0.01 1 40 8 8 ALA HA H 4.249 0.01 1 41 8 8 ALA HB H 1.385 0.01 1 42 9 9 CYS H H 8.482 0.01 1 43 9 9 CYS HA H 4.630 0.01 1 44 9 9 CYS HB2 H 3.105 0.01 2 45 9 9 CYS HB3 H 2.972 0.01 2 46 9 9 CYS CA C 55.274 0.05 1 47 9 9 CYS CB C 40.935 0.05 1 48 10 10 SER H H 8.388 0.01 1 49 10 10 SER HA H 4.467 0.01 1 50 10 10 SER HB2 H 3.844 0.01 2 51 10 10 SER HB3 H 3.785 0.01 2 52 10 10 SER CA C 58.099 0.05 1 53 10 10 SER CB C 63.599 0.05 1 54 11 11 TRP H H 8.231 0.01 1 55 11 11 TRP HA H 4.682 0.01 1 56 11 11 TRP HB2 H 3.273 0.01 2 57 11 11 TRP HB3 H 3.273 0.01 2 58 11 11 TRP HD1 H 7.249 0.01 1 59 11 11 TRP HE1 H 10.188 0.01 1 60 11 11 TRP HE3 H 7.544 0.01 1 61 11 11 TRP HZ2 H 7.455 0.01 1 62 11 11 TRP HZ3 H 7.108 0.01 1 63 11 11 TRP HH2 H 7.202 0.01 1 64 11 11 TRP CA C 57.279 0.05 1 65 11 11 TRP CB C 29.078 0.05 1 66 11 11 TRP CD1 C 126.874 0.05 1 67 11 11 TRP CE3 C 120.474 0.05 1 68 11 11 TRP CZ2 C 114.223 0.05 1 69 11 11 TRP CZ3 C 121.698 0.05 1 70 11 11 TRP CH2 C 124.342 0.05 1 71 12 12 ARG H H 8.200 0.01 1 72 12 12 ARG HA H 4.160 0.01 1 73 12 12 ARG HB2 H 1.736 0.01 2 74 12 12 ARG HB3 H 1.542 0.01 2 75 12 12 ARG HG2 H 1.289 0.01 2 76 12 12 ARG HG3 H 1.289 0.01 2 77 12 12 ARG HD2 H 3.050 0.01 2 78 12 12 ARG HD3 H 3.050 0.01 2 79 12 12 ARG HE H 7.133 0.01 1 80 12 12 ARG CA C 56.051 0.05 1 81 12 12 ARG CB C 30.109 0.05 1 82 12 12 ARG CG C 26.535 0.05 1 83 12 12 ARG CD C 42.873 0.05 1 84 13 13 GLY H H 7.986 0.01 1 85 13 13 GLY HA2 H 3.929 0.01 2 86 13 13 GLY HA3 H 3.813 0.01 2 87 13 13 GLY CA C 45.134 0.05 1 88 14 14 LEU H H 8.213 0.01 1 89 14 14 LEU HA H 4.319 0.01 1 90 14 14 LEU HB2 H 1.685 0.01 2 91 14 14 LEU HB3 H 1.588 0.01 2 92 14 14 LEU HG H 1.619 0.01 1 93 14 14 LEU HD1 H 0.923 0.01 2 94 14 14 LEU HD2 H 0.871 0.01 2 95 14 14 LEU CA C 55.229 0.05 1 96 14 14 LEU CB C 42.035 0.05 1 97 14 14 LEU CG C 26.607 0.05 1 98 14 14 LEU CD1 C 24.759 0.05 2 99 14 14 LEU CD2 C 22.987 0.05 2 100 15 15 GLU H H 8.479 0.01 1 101 15 15 GLU HA H 4.238 0.01 1 102 15 15 GLU HB2 H 2.063 0.01 2 103 15 15 GLU HB3 H 1.961 0.01 2 104 15 15 GLU HG2 H 2.392 0.01 2 105 15 15 GLU HG3 H 2.392 0.01 2 106 15 15 GLU CA C 55.978 0.05 1 107 15 15 GLU CB C 28.154 0.05 1 108 15 15 GLU CG C 32.930 0.05 1 109 16 16 ASN H H 8.344 0.01 1 110 16 16 ASN HA H 4.546 0.01 1 111 16 16 ASN HB2 H 2.801 0.01 2 112 16 16 ASN HB3 H 2.704 0.01 2 113 16 16 ASN HD21 H 7.634 0.01 2 114 16 16 ASN HD22 H 6.984 0.01 2 115 16 16 ASN CA C 53.061 0.05 1 116 16 16 ASN CB C 38.083 0.05 1 117 17 17 HIS H H 8.423 0.01 1 118 17 17 HIS HA H 4.533 0.01 1 119 17 17 HIS HB2 H 3.251 0.01 2 120 17 17 HIS HB3 H 3.131 0.01 2 121 17 17 HIS HD2 H 7.210 0.01 1 122 17 17 HIS HE1 H 8.529 0.01 1 123 17 17 HIS CB C 28.107 0.05 1 124 17 17 HIS CD2 C 119.536 0.05 1 125 17 17 HIS CE1 C 135.765 0.05 1 126 18 18 ALA H H 8.308 0.01 1 127 18 18 ALA HA H 4.251 0.01 1 128 18 18 ALA HB H 1.375 0.01 1 129 19 19 MET H H 8.507 0.01 1 130 19 19 MET HA H 4.529 0.01 1 131 19 19 MET HB2 H 2.258 0.01 2 132 19 19 MET HB3 H 2.150 0.01 2 133 19 19 MET HG2 H 2.928 0.01 2 134 19 19 MET HG3 H 2.884 0.01 2 135 19 19 MET HE H 2.681 0.01 1 136 19 19 MET CB C 26.415 0.05 1 137 19 19 MET CG C 50.955 0.05 1 138 19 19 MET CE C 38.949 0.05 1 139 20 20 CYS H H 8.561 0.01 1 140 20 20 CYS HA H 4.679 0.01 1 141 20 20 CYS HB2 H 3.165 0.01 2 142 20 20 CYS HB3 H 2.891 0.01 2 143 20 20 CYS CA C 55.298 0.05 1 144 20 20 CYS CB C 40.880 0.05 1 145 21 21 GLY H H 8.612 0.01 1 146 21 21 GLY HA2 H 3.956 0.01 2 147 21 21 GLY HA3 H 3.956 0.01 2 148 21 21 GLY CA C 44.962 0.05 1 149 22 22 ALA H H 8.302 0.01 1 150 22 22 ALA HA H 4.296 0.01 1 151 22 22 ALA HB H 1.386 0.01 1 152 22 22 ALA CA C 52.091 0.05 1 153 23 23 ALA H H 8.519 0.01 1 154 23 23 ALA HA H 4.266 0.01 1 155 23 23 ALA HB H 1.393 0.01 1 156 24 24 GLY H H 8.433 0.01 1 157 24 24 GLY HA2 H 3.915 0.01 2 158 24 24 GLY HA3 H 3.862 0.01 2 159 24 24 GLY CA C 44.616 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_