data_17340 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; An Antibody Binding Site on Cytochrome c Defined by Hydrogen Exchange and Two-Dimensional NMR ; _BMRB_accession_number 17340 _BMRB_flat_file_name bmr17340.str _Entry_type original _Submission_date 2010-12-02 _Accession_date 2010-12-02 _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 Paterson Yvonne S. . 2 Englander S. W. . 3 Roder Heinrich . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count chemical_rates 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-06 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'An Antibody Binding Site on Cytochrome c Defined by Hydrogen Exchange and Two-Dimensional NMR' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 1697101 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Paterson Yvonne . . 2 Englander S. W. . 3 Roder Heinrich . . stop_ _Journal_abbreviation Science _Journal_volume 249 _Journal_issue 4970 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 755 _Page_last 759 _Year 1990 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'cytc/MABE8 complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label cytc $cytc MABE8 $MABE8 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_cytc _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common cytc _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 104 _Mol_residue_sequence ; GDVEKGKKIFVQKCAQCHTV EKGGKHKTGPNLHGLFGRKT GQAPGFTYTDANKNKGITWK EETLMEYLENPKKYIPGTKM IFAGIKKKTEREDLIAYLKK ATNE ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 ASP 3 VAL 4 GLU 5 LYS 6 GLY 7 LYS 8 LYS 9 ILE 10 PHE 11 VAL 12 GLN 13 LYS 14 CYS 15 ALA 16 GLN 17 CYS 18 HIS 19 THR 20 VAL 21 GLU 22 LYS 23 GLY 24 GLY 25 LYS 26 HIS 27 LYS 28 THR 29 GLY 30 PRO 31 ASN 32 LEU 33 HIS 34 GLY 35 LEU 36 PHE 37 GLY 38 ARG 39 LYS 40 THR 41 GLY 42 GLN 43 ALA 44 PRO 45 GLY 46 PHE 47 THR 48 TYR 49 THR 50 ASP 51 ALA 52 ASN 53 LYS 54 ASN 55 LYS 56 GLY 57 ILE 58 THR 59 TRP 60 LYS 61 GLU 62 GLU 63 THR 64 LEU 65 MET 66 GLU 67 TYR 68 LEU 69 GLU 70 ASN 71 PRO 72 LYS 73 LYS 74 TYR 75 ILE 76 PRO 77 GLY 78 THR 79 LYS 80 MET 81 ILE 82 PHE 83 ALA 84 GLY 85 ILE 86 LYS 87 LYS 88 LYS 89 THR 90 GLU 91 ARG 92 GLU 93 ASP 94 LEU 95 ILE 96 ALA 97 TYR 98 LEU 99 LYS 100 LYS 101 ALA 102 THR 103 ASN 104 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-04 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 1058 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 1107 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 1108 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 1109 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 1110 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 1111 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 1112 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 1113 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 1114 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 1116 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 1170 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 1171 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 1404 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 16759 cytochrome_c 100.00 104 100.00 100.00 4.24e-68 BMRB 17120 cytc 100.00 105 99.04 100.00 6.69e-68 BMRB 1736 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 1783 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 17847 hCc 100.00 104 100.00 100.00 4.24e-68 BMRB 17848 hCc 100.00 104 100.00 100.00 4.24e-68 BMRB 1785 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 1787 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 1789 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 216 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 220 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 224 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 2366 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 2367 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 2368 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 243 "cytochrome c" 100.00 104 100.00 100.00 4.24e-68 BMRB 244 "cytochrome c" 100.00 104 100.00 100.00 4.24e-68 BMRB 25640 entity_1 100.00 105 99.04 99.04 8.50e-67 BMRB 274 "cytochrome c" 100.00 104 100.00 100.00 4.24e-68 BMRB 285 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 286 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 316 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 317 "cytochrome c" 99.04 104 100.00 100.00 2.13e-67 BMRB 336 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 4189 "cytochrome c" 100.00 104 100.00 100.00 4.24e-68 BMRB 436 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 437 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 438 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 BMRB 439 "cytochrome c" 99.04 104 98.06 98.06 9.26e-65 PDB 1AKK "Solution Structure Of Oxidized Horse Heart Cytochrome C, Nmr, Minimized Average Structure" 100.00 104 100.00 100.00 4.24e-68 PDB 1CRC "Cytochrome C At Low Ionic Strength" 100.00 105 100.00 100.00 4.37e-68 PDB 1FI7 "Solution Structure Of The Imidazole Complex Of Cytochrome C" 100.00 104 100.00 100.00 4.24e-68 PDB 1FI9 "Solution Structure Of The Imidazole Complex Of Cytochrome C" 100.00 104 100.00 100.00 4.24e-68 PDB 1GIW "Solution Structure Of Reduced Horse Heart Cytochrome C, Nmr, Minimized Average Structure" 99.04 104 100.00 100.00 2.13e-67 PDB 1HRC "High-Resolution Three-Dimensional Structure Of Horse Heart Cytochrome C" 100.00 105 100.00 100.00 4.37e-68 PDB 1I5T "Solution Structure Of Cyanoferricytochrome C" 100.00 104 100.00 100.00 4.24e-68 PDB 1LC1 "Solution Structure Of Reduced Horse Heart Cytochrome C In 30% Acetonitrile Solution, Nmr Minimized Average Structure" 100.00 104 100.00 100.00 4.24e-68 PDB 1LC2 "Solution Structure Of Reduced Horse Heart Cytochrome C In 30% Acetonitrile Solution, Nmr 30 Structures" 100.00 104 100.00 100.00 4.24e-68 PDB 1M60 "Solution Structure Of Zinc-Substituted Cytochrome C" 100.00 104 100.00 100.00 4.24e-68 PDB 1OCD "Cytochrome C (Oxidized) From Equus Caballus, Nmr, Minimized Average Structure" 100.00 104 100.00 100.00 4.24e-68 PDB 1U75 "Electron Transfer Complex Between Horse Heart Cytochrome C And Zinc- Porphyrin Substituted Cytochrome C Peroxidase" 100.00 104 100.00 100.00 4.24e-68 PDB 1WEJ "Igg1 Fab Fragment (Of E8 Antibody) Complexed With Horse Cytochrome C At 1.8 A Resolution" 100.00 105 100.00 100.00 4.37e-68 PDB 2B4Z "Crystal Structure Of Cytochrome C From Bovine Heart At 1.5 A Resolution." 100.00 104 97.12 98.08 8.23e-66 PDB 2FRC "Cytochrome C (Reduced) From Equus Caballus, Nmr, Minimized Average Structure" 100.00 104 100.00 100.00 4.24e-68 PDB 2GIW "Solution Structure Of Reduced Horse Heart Cytochrome C, Nmr, 40 Structures" 100.00 104 100.00 100.00 4.24e-68 PDB 2PCB "Crystal Structure Of A Complex Between Electron Transfer Partners, Cytochrome C Peroxidase And Cytochrome C" 100.00 104 100.00 100.00 4.24e-68 PDB 2YBB "Fitted Model For Bovine Mitochondrial Supercomplex I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)" 100.00 104 97.12 98.08 8.23e-66 PDB 3J2T "An Improved Model Of The Human Apoptosome" 100.00 104 97.12 98.08 8.23e-66 PDB 3NBS "Crystal Structure Of Dimeric Cytochrome C From Horse Heart" 100.00 104 100.00 100.00 4.24e-68 PDB 3NBT "Crystal Structure Of Trimeric Cytochrome C From Horse Heart" 100.00 104 100.00 100.00 4.24e-68 PDB 3O1Y "Electron Transfer Complexes: Experimental Mapping Of The Redox- Dependent Cytochrome C Electrostatic Surface" 100.00 105 100.00 100.00 4.37e-68 PDB 3O20 "Electron Transfer Complexes:experimental Mapping Of The Redox- Dependent Cytochrome C Electrostatic Surface" 100.00 105 100.00 100.00 4.37e-68 PDB 3WC8 "Dimeric Horse Cytochrome C Obtained By Refolding With Desalting Method" 100.00 104 100.00 100.00 4.24e-68 PDB 3WUI "Dimeric Horse Cytochrome C Formed By Refolding From Molten Globule State" 100.00 104 100.00 100.00 4.24e-68 PDB 4NFG "K13r Mutant Of Horse Cytochrome C And Yeast Cytochrome C Peroxidase Complex" 100.00 104 97.12 100.00 3.92e-66 PDB 4RSZ "The X-ray Structure Of The Primary Adduct Formed In The Reaction Between Cisplatin And Cytochrome C" 100.00 104 100.00 100.00 4.24e-68 GB AAB33495 "apocytochrome c [horses, heart, Peptide, 104 aa]" 100.00 104 98.08 98.08 4.42e-66 GB AAI05398 "Cytochrome c, somatic [Bos taurus]" 100.00 105 97.12 98.08 6.75e-66 GB AAX77008 "cytochrome c-like protein [Sus scrofa]" 100.00 105 97.12 98.08 6.75e-66 GB ABA06541 "mitochondrial cytochrome c [Bubalus bubalis]" 100.00 104 97.12 98.08 8.23e-66 GB AEB61027 "cytochrome c-like protein, partial [Equus caballus]" 100.00 127 100.00 100.00 1.25e-68 PRF 610169A "cytochrome c" 100.00 104 100.00 100.00 4.24e-68 PRF 711086A "cytochrome c" 100.00 104 97.12 100.00 2.40e-67 REF NP_001039526 "cytochrome c [Bos taurus]" 100.00 105 97.12 98.08 6.75e-66 REF NP_001123442 "cytochrome c [Sus scrofa]" 100.00 105 97.12 98.08 6.75e-66 REF NP_001157486 "cytochrome c [Equus caballus]" 100.00 105 99.04 100.00 6.69e-68 REF XP_004007999 "PREDICTED: cytochrome c [Ovis aries]" 100.00 105 97.12 98.08 6.75e-66 REF XP_004418964 "PREDICTED: cytochrome c-like [Ceratotherium simum simum]" 100.00 105 98.08 99.04 2.53e-67 SP P00004 "RecName: Full=Cytochrome c" 100.00 105 100.00 100.00 3.36e-68 SP P62894 "RecName: Full=Cytochrome c" 100.00 105 97.12 98.08 6.75e-66 SP P62895 "RecName: Full=Cytochrome c" 100.00 105 97.12 98.08 6.75e-66 SP P62896 "RecName: Full=Cytochrome c" 100.00 105 97.12 98.08 6.75e-66 SP P68096 "RecName: Full=Cytochrome c" 100.00 105 99.04 100.00 6.69e-68 TPG DAA30512 "TPA: cytochrome c [Bos taurus]" 100.00 105 97.12 98.08 6.75e-66 stop_ save_ save_MABE8 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common MABE8 _Molecular_mass . _Mol_thiol_state 'not reported' _Details . _Residue_count 219 _Mol_residue_sequence ; EVQLQQSGAELVKPGASVKL SCTASGFNIKDTYMHWVKQR PEKGLEWIGRIDPASGNTKY DPKFQDKATITADTSSNTAY LQLSSLTSEDTAVYYCAGYD YGNFDYWGQGTTLTVSSAET TPPSVYPLAPGTAALKSSMV TLGCLVKGYFPEPVTVTWNS GSLSSGVHTFPAVLQSDLYT LSSSVTVPSSTWPSQTVTCN VAHPASSTKVDKKIVPRNC ; loop_ _Residue_seq_code _Residue_label 1 GLU 2 VAL 3 GLN 4 LEU 5 GLN 6 GLN 7 SER 8 GLY 9 ALA 10 GLU 11 LEU 12 VAL 13 LYS 14 PRO 15 GLY 16 ALA 17 SER 18 VAL 19 LYS 20 LEU 21 SER 22 CYS 23 THR 24 ALA 25 SER 26 GLY 27 PHE 28 ASN 29 ILE 30 LYS 31 ASP 32 THR 33 TYR 34 MET 35 HIS 36 TRP 37 VAL 38 LYS 39 GLN 40 ARG 41 PRO 42 GLU 43 LYS 44 GLY 45 LEU 46 GLU 47 TRP 48 ILE 49 GLY 50 ARG 51 ILE 52 ASP 53 PRO 54 ALA 55 SER 56 GLY 57 ASN 58 THR 59 LYS 60 TYR 61 ASP 62 PRO 63 LYS 64 PHE 65 GLN 66 ASP 67 LYS 68 ALA 69 THR 70 ILE 71 THR 72 ALA 73 ASP 74 THR 75 SER 76 SER 77 ASN 78 THR 79 ALA 80 TYR 81 LEU 82 GLN 83 LEU 84 SER 85 SER 86 LEU 87 THR 88 SER 89 GLU 90 ASP 91 THR 92 ALA 93 VAL 94 TYR 95 TYR 96 CYS 97 ALA 98 GLY 99 TYR 100 ASP 101 TYR 102 GLY 103 ASN 104 PHE 105 ASP 106 TYR 107 TRP 108 GLY 109 GLN 110 GLY 111 THR 112 THR 113 LEU 114 THR 115 VAL 116 SER 117 SER 118 ALA 119 GLU 120 THR 121 THR 122 PRO 123 PRO 124 SER 125 VAL 126 TYR 127 PRO 128 LEU 129 ALA 130 PRO 131 GLY 132 THR 133 ALA 134 ALA 135 LEU 136 LYS 137 SER 138 SER 139 MET 140 VAL 141 THR 142 LEU 143 GLY 144 CYS 145 LEU 146 VAL 147 LYS 148 GLY 149 TYR 150 PHE 151 PRO 152 GLU 153 PRO 154 VAL 155 THR 156 VAL 157 THR 158 TRP 159 ASN 160 SER 161 GLY 162 SER 163 LEU 164 SER 165 SER 166 GLY 167 VAL 168 HIS 169 THR 170 PHE 171 PRO 172 ALA 173 VAL 174 LEU 175 GLN 176 SER 177 ASP 178 LEU 179 TYR 180 THR 181 LEU 182 SER 183 SER 184 SER 185 VAL 186 THR 187 VAL 188 PRO 189 SER 190 SER 191 THR 192 TRP 193 PRO 194 SER 195 GLN 196 THR 197 VAL 198 THR 199 CYS 200 ASN 201 VAL 202 ALA 203 HIS 204 PRO 205 ALA 206 SER 207 SER 208 THR 209 LYS 210 VAL 211 ASP 212 LYS 213 LYS 214 ILE 215 VAL 216 PRO 217 ARG 218 ASN 219 CYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-10 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 1QBL "Fab E8 (Fabe8a) X-Ray Structure At 2.26 Angstrom Resolution" 100.00 219 99.54 100.00 5.39e-157 PDB 1QBM "Fab E8b Antibody, X-Ray Structure At 2.37 Angstroms Resolution" 100.00 219 100.00 100.00 1.80e-157 PDB 1WEJ "Igg1 Fab Fragment (Of E8 Antibody) Complexed With Horse Cytochrome C At 1.8 A Resolution" 100.00 223 99.54 100.00 1.11e-156 EMBL CAA43095 "E8 variable heavy chain [Mus musculus]" 53.42 117 100.00 100.00 3.03e-79 PIR S17586 "Ig heavy chain V region (E8) - mouse (fragment)" 53.42 117 100.00 100.00 3.03e-79 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $cytc Horse 9796 Eukaryota Metazoa Equus caballus $MABE8 Mouse 10090 Eukaryota Metazoa Mus musculus 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 $cytc 'purified from the natural source' . . . . . $MABE8 'purified from the natural source' . . . . . 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 $cytc 1.5 mM . . 'natural abundance' $MABE8 . mM 0 1.5 'natural abundance' 'potassium phosphate' .1 M . . 'natural abundance' 'ascorbic acid' 9 mM . . 'natural abundance' D2O 100 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_FTNMR _Saveframe_category software _Name FTNMR _Version . loop_ _Vendor _Address _Electronic_address 'Hare Research, Woodinville, Washington' . . stop_ loop_ _Task processing stop_ _Details . save_ save_ModelFree _Saveframe_category software _Name ModelFree _Version . _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AM _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NMR_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NMR' _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 293 . K pH 5.3 . pH pressure 1 . atm stop_ save_