data_2VN0 # _model_server_result.job_id RDGwPHDtFkt9QLvhP8-05Q _model_server_result.datetime_utc '2024-11-27 16:43:58' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2vn0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 2VN0 # _exptl.entry_id 2VN0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2VN0 _cell.length_a 74.2 _cell.length_b 136.09 _cell.length_c 163.24 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VN0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 417 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 435 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 500 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 2.269 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C34 H32 Fe N4 O4' _chem_comp.formula_weight 616.487 _chem_comp.id HEM _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEME # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag CHA C1A HEM sing 129 n n CHA C4D HEM doub 130 n n CHA HHA HEM sing 131 n n CHB C4A HEM sing 132 n n CHB C1B HEM doub 133 n n CHB HHB HEM sing 134 n n CHC C4B HEM sing 135 n n CHC C1C HEM doub 136 n n CHC HHC HEM sing 137 n n CHD C4C HEM doub 138 n n CHD C1D HEM sing 139 n n CHD HHD HEM sing 140 n n C1A C2A HEM doub 141 n y C1A NA HEM sing 142 n y C2A C3A HEM sing 143 n y C2A CAA HEM sing 144 n n C3A C4A HEM doub 145 n y C3A CMA HEM sing 146 n n C4A NA HEM sing 147 n y CMA HMA HEM sing 148 n n CMA HMAA HEM sing 149 n n CMA HMAB HEM sing 150 n n CAA CBA HEM sing 151 n n CAA HAA HEM sing 152 n n CAA HAAA HEM sing 153 n n CBA CGA HEM sing 154 n n CBA HBA HEM sing 155 n n CBA HBAA HEM sing 156 n n CGA O1A HEM doub 157 n n CGA O2A HEM sing 158 n n C1B C2B HEM sing 159 n n C1B NB HEM sing 160 n n C2B C3B HEM doub 161 n n C2B CMB HEM sing 162 n n C3B C4B HEM sing 163 n n C3B CAB HEM sing 164 n n C4B NB HEM doub 165 n n CMB HMB HEM sing 166 n n CMB HMBA HEM sing 167 n n CMB HMBB HEM sing 168 n n CAB CBB HEM doub 169 n n CAB HAB HEM sing 170 n n CBB HBB HEM sing 171 n n CBB HBBA HEM sing 172 n n C1C C2C HEM sing 173 n y C1C NC HEM sing 174 n y C2C C3C HEM doub 175 n y C2C CMC HEM sing 176 n n C3C C4C HEM sing 177 n y C3C CAC HEM sing 178 n n C4C NC HEM sing 179 n y CMC HMC HEM sing 180 n n CMC HMCA HEM sing 181 n n CMC HMCB HEM sing 182 n n CAC CBC HEM doub 183 n n CAC HAC HEM sing 184 n n CBC HBC HEM sing 185 n n CBC HBCA HEM sing 186 n n C1D C2D HEM sing 187 n n C1D ND HEM doub 188 n n C2D C3D HEM doub 189 n n C2D CMD HEM sing 190 n n C3D C4D HEM sing 191 n n C3D CAD HEM sing 192 n n C4D ND HEM sing 193 n n CMD HMD HEM sing 194 n n CMD HMDA HEM sing 195 n n CMD HMDB HEM sing 196 n n CAD CBD HEM sing 197 n n CAD HAD HEM sing 198 n n CAD HADA HEM sing 199 n n CBD CGD HEM sing 200 n n CBD HBD HEM sing 201 n n CBD HBDA HEM sing 202 n n CGD O1D HEM doub 203 n n CGD O2D HEM sing 204 n n O2A H2A HEM sing 205 n n O2D H2D HEM sing 206 n n FE NA HEM sing 207 n n FE NB HEM sing 208 n n FE NC HEM sing 209 n n FE ND HEM sing 210 n n # _atom_sites.entry_id 2VN0 _atom_sites.fract_transf_matrix[1][1] 0.013477 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007348 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006126 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HEM A 1 500 500 HEM HEM . C 3 TDZ A 1 501 501 TDZ TDZ . D 4 PLM A 1 502 502 PLM PLM . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C CHA HEM . . . B 2 52.743 20.739 -25.976 1 45.18 ? CHA HEM 500 A 1 HETATM 2 C CHB HEM . . . B 2 48.725 23.164 -26.556 1 42.71 ? CHB HEM 500 A 1 HETATM 3 C CHC HEM . . . B 2 48.709 22.049 -31.116 1 40.56 ? CHC HEM 500 A 1 HETATM 4 C CHD HEM . . . B 2 53.056 20.253 -30.635 1 45.25 ? CHD HEM 500 A 1 HETATM 5 C C1A HEM . . . B 2 51.549 21.387 -25.641 1 45.42 ? C1A HEM 500 A 1 HETATM 6 C C2A HEM . . . B 2 51.109 21.727 -24.352 1 45.67 ? C2A HEM 500 A 1 HETATM 7 C C3A HEM . . . B 2 49.92 22.415 -24.529 1 44.48 ? C3A HEM 500 A 1 HETATM 8 C C4A HEM . . . B 2 49.705 22.459 -25.912 1 44.68 ? C4A HEM 500 A 1 HETATM 9 C CMA HEM . . . B 2 48.982 23.035 -23.43 1 44.52 ? CMA HEM 500 A 1 HETATM 10 C CAA HEM . . . B 2 51.842 21.383 -23.053 1 48.06 ? CAA HEM 500 A 1 HETATM 11 C CBA HEM . . . B 2 52.824 22.413 -22.595 1 47.64 ? CBA HEM 500 A 1 HETATM 12 C CGA HEM . . . B 2 53.515 22.048 -21.315 1 48 ? CGA HEM 500 A 1 HETATM 13 O O1A HEM . . . B 2 54.395 21.217 -21.305 1 48.86 ? O1A HEM 500 A 1 HETATM 14 O O2A HEM . . . B 2 53.184 22.593 -20.27 1 47.91 ? O2A HEM 500 A 1 HETATM 15 C C1B HEM . . . B 2 48.186 22.97 -27.819 1 40.49 ? C1B HEM 500 A 1 HETATM 16 C C2B HEM . . . B 2 46.959 23.466 -28.3 1 38.36 ? C2B HEM 500 A 1 HETATM 17 C C3B HEM . . . B 2 46.921 23.06 -29.657 1 38.73 ? C3B HEM 500 A 1 HETATM 18 C C4B HEM . . . B 2 48.146 22.349 -29.865 1 41.48 ? C4B HEM 500 A 1 HETATM 19 C CMB HEM . . . B 2 45.962 24.253 -27.466 1 38.33 ? CMB HEM 500 A 1 HETATM 20 C CAB HEM . . . B 2 45.921 23.274 -30.645 1 38.63 ? CAB HEM 500 A 1 HETATM 21 C CBB HEM . . . B 2 45.001 24.419 -30.852 1 37.11 ? CBB HEM 500 A 1 HETATM 22 C C1C HEM . . . B 2 50.005 21.702 -31.488 1 42.8 ? C1C HEM 500 A 1 HETATM 23 C C2C HEM . . . B 2 50.408 21.402 -32.785 1 43.95 ? C2C HEM 500 A 1 HETATM 24 C C3C HEM . . . B 2 51.656 20.755 -32.678 1 44.87 ? C3C HEM 500 A 1 HETATM 25 C C4C HEM . . . B 2 51.916 20.715 -31.282 1 44.36 ? C4C HEM 500 A 1 HETATM 26 C CMC HEM . . . B 2 49.627 21.717 -34.097 1 43.54 ? CMC HEM 500 A 1 HETATM 27 C CAC HEM . . . B 2 52.512 20.235 -33.63 1 46.04 ? CAC HEM 500 A 1 HETATM 28 C CBC HEM . . . B 2 53.739 20.735 -34.155 1 45.64 ? CBC HEM 500 A 1 HETATM 29 C C1D HEM . . . B 2 53.341 20.152 -29.32 1 45.95 ? C1D HEM 500 A 1 HETATM 30 C C2D HEM . . . B 2 54.46 19.486 -28.79 1 46.24 ? C2D HEM 500 A 1 HETATM 31 C C3D HEM . . . B 2 54.394 19.607 -27.438 1 46.21 ? C3D HEM 500 A 1 HETATM 32 C C4D HEM . . . B 2 53.217 20.353 -27.214 1 45.65 ? C4D HEM 500 A 1 HETATM 33 C CMD HEM . . . B 2 55.565 18.751 -29.569 1 47.03 ? CMD HEM 500 A 1 HETATM 34 C CAD HEM . . . B 2 55.379 19.053 -26.357 1 48.44 ? CAD HEM 500 A 1 HETATM 35 C CBD HEM . . . B 2 56.521 20.057 -25.998 1 50.18 ? CBD HEM 500 A 1 HETATM 36 C CGD HEM . . . B 2 57.539 19.628 -24.915 1 50.99 ? CGD HEM 500 A 1 HETATM 37 O O1D HEM . . . B 2 57.289 18.698 -24.174 1 53.51 ? O1D HEM 500 A 1 HETATM 38 O O2D HEM . . . B 2 58.607 20.255 -24.789 1 49.84 ? O2D HEM 500 A 1 HETATM 39 N NA HEM . . . B 2 50.666 21.853 -26.57 1 44.11 ? NA HEM 500 A 1 HETATM 40 N NB HEM . . . B 2 48.856 22.322 -28.761 1 41.95 ? NB HEM 500 A 1 HETATM 41 N NC HEM . . . B 2 50.901 21.292 -30.604 1 43.83 ? NC HEM 500 A 1 HETATM 42 N ND HEM . . . B 2 52.624 20.653 -28.367 1 45.07 ? ND HEM 500 A 1 HETATM 43 FE FE HEM . . . B 2 50.732 21.495 -28.586 1 42.17 ? FE HEM 500 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #