data_2VYW # _model_server_result.job_id A0iLAu3qqhbVU2NVeQJNaA _model_server_result.datetime_utc '2024-11-05 00:40:15' _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 2vyw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":149}' # _entry.id 2VYW # _exptl.entry_id 2VYW _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 94.55 _cell.angle_gamma 90 _cell.entry_id 2VYW _cell.length_a 26.677 _cell.length_b 59.604 _cell.length_c 42.626 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VYW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 99 A HIS 99 1_555 B FE HEM . A HEM 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc2 B FE HEM . A HEM 149 1_555 C O1 OXY . A OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc3 B FE HEM . A HEM 149 1_555 C O2 OXY . A OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? # _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 116 n n CHA C4D HEM doub 117 n n CHA HHA HEM sing 118 n n CHB C4A HEM sing 119 n n CHB C1B HEM doub 120 n n CHB HHB HEM sing 121 n n CHC C4B HEM sing 122 n n CHC C1C HEM doub 123 n n CHC HHC HEM sing 124 n n CHD C4C HEM doub 125 n n CHD C1D HEM sing 126 n n CHD HHD HEM sing 127 n n C1A C2A HEM doub 128 n y C1A NA HEM sing 129 n y C2A C3A HEM sing 130 n y C2A CAA HEM sing 131 n n C3A C4A HEM doub 132 n y C3A CMA HEM sing 133 n n C4A NA HEM sing 134 n y CMA HMA HEM sing 135 n n CMA HMAA HEM sing 136 n n CMA HMAB HEM sing 137 n n CAA CBA HEM sing 138 n n CAA HAA HEM sing 139 n n CAA HAAA HEM sing 140 n n CBA CGA HEM sing 141 n n CBA HBA HEM sing 142 n n CBA HBAA HEM sing 143 n n CGA O1A HEM doub 144 n n CGA O2A HEM sing 145 n n C1B C2B HEM sing 146 n n C1B NB HEM sing 147 n n C2B C3B HEM doub 148 n n C2B CMB HEM sing 149 n n C3B C4B HEM sing 150 n n C3B CAB HEM sing 151 n n C4B NB HEM doub 152 n n CMB HMB HEM sing 153 n n CMB HMBA HEM sing 154 n n CMB HMBB HEM sing 155 n n CAB CBB HEM doub 156 n n CAB HAB HEM sing 157 n n CBB HBB HEM sing 158 n n CBB HBBA HEM sing 159 n n C1C C2C HEM sing 160 n y C1C NC HEM sing 161 n y C2C C3C HEM doub 162 n y C2C CMC HEM sing 163 n n C3C C4C HEM sing 164 n y C3C CAC HEM sing 165 n n C4C NC HEM sing 166 n y CMC HMC HEM sing 167 n n CMC HMCA HEM sing 168 n n CMC HMCB HEM sing 169 n n CAC CBC HEM doub 170 n n CAC HAC HEM sing 171 n n CBC HBC HEM sing 172 n n CBC HBCA HEM sing 173 n n C1D C2D HEM sing 174 n n C1D ND HEM doub 175 n n C2D C3D HEM doub 176 n n C2D CMD HEM sing 177 n n C3D C4D HEM sing 178 n n C3D CAD HEM sing 179 n n C4D ND HEM sing 180 n n CMD HMD HEM sing 181 n n CMD HMDA HEM sing 182 n n CMD HMDB HEM sing 183 n n CAD CBD HEM sing 184 n n CAD HAD HEM sing 185 n n CAD HADA HEM sing 186 n n CBD CGD HEM sing 187 n n CBD HBD HEM sing 188 n n CBD HBDA HEM sing 189 n n CGD O1D HEM doub 190 n n CGD O2D HEM sing 191 n n O2A H2A HEM sing 192 n n O2D H2D HEM sing 193 n n FE NA HEM sing 194 n n FE NB HEM sing 195 n n FE NC HEM sing 196 n n FE ND HEM sing 197 n n # _atom_sites.entry_id 2VYW _atom_sites.fract_transf_matrix[1][1] 0.037485 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002983 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016777 _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] 0.023534 _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 1 149 149 HEM HEM . C 3 OXY A 1 150 150 OXY OXY . D 4 HOH A 1 2001 2001 HOH HOH . D 4 HOH A 2 2002 2002 HOH HOH . D 4 HOH A 3 2003 2003 HOH HOH . D 4 HOH A 4 2004 2004 HOH HOH . D 4 HOH A 5 2005 2005 HOH HOH . D 4 HOH A 6 2006 2006 HOH HOH . D 4 HOH A 7 2007 2007 HOH HOH . D 4 HOH A 8 2008 2008 HOH HOH . D 4 HOH A 9 2009 2009 HOH HOH . D 4 HOH A 10 2010 2010 HOH HOH . D 4 HOH A 11 2011 2011 HOH HOH . D 4 HOH A 12 2012 2012 HOH HOH . D 4 HOH A 13 2013 2013 HOH HOH . D 4 HOH A 14 2014 2014 HOH HOH . D 4 HOH A 15 2015 2015 HOH HOH . D 4 HOH A 16 2016 2016 HOH HOH . D 4 HOH A 17 2017 2017 HOH HOH . D 4 HOH A 18 2018 2018 HOH HOH . D 4 HOH A 19 2019 2019 HOH HOH . D 4 HOH A 20 2020 2020 HOH HOH . D 4 HOH A 21 2021 2021 HOH HOH . D 4 HOH A 22 2022 2022 HOH HOH . D 4 HOH A 23 2023 2023 HOH HOH . D 4 HOH A 24 2024 2024 HOH HOH . D 4 HOH A 25 2025 2025 HOH HOH . D 4 HOH A 26 2026 2026 HOH HOH . D 4 HOH A 27 2027 2027 HOH HOH . D 4 HOH A 28 2028 2028 HOH HOH . D 4 HOH A 29 2029 2029 HOH HOH . D 4 HOH A 30 2030 2030 HOH HOH . D 4 HOH A 31 2031 2031 HOH HOH . D 4 HOH A 32 2032 2032 HOH HOH . D 4 HOH A 33 2033 2033 HOH HOH . D 4 HOH A 34 2034 2034 HOH HOH . D 4 HOH A 35 2035 2035 HOH HOH . D 4 HOH A 36 2036 2036 HOH HOH . D 4 HOH A 37 2037 2037 HOH HOH . D 4 HOH A 38 2038 2038 HOH HOH . D 4 HOH A 39 2039 2039 HOH HOH . D 4 HOH A 40 2040 2040 HOH HOH . D 4 HOH A 41 2041 2041 HOH HOH . D 4 HOH A 42 2042 2042 HOH HOH . D 4 HOH A 43 2043 2043 HOH HOH . D 4 HOH A 44 2044 2044 HOH HOH . D 4 HOH A 45 2045 2045 HOH HOH . D 4 HOH A 46 2046 2046 HOH HOH . D 4 HOH A 47 2047 2047 HOH HOH . D 4 HOH A 48 2048 2048 HOH HOH . D 4 HOH A 49 2049 2049 HOH HOH . D 4 HOH A 50 2050 2050 HOH HOH . D 4 HOH A 51 2051 2051 HOH HOH . D 4 HOH A 52 2052 2052 HOH HOH . D 4 HOH A 53 2053 2053 HOH HOH . D 4 HOH A 54 2054 2054 HOH HOH . D 4 HOH A 55 2055 2055 HOH HOH . D 4 HOH A 56 2056 2056 HOH HOH . D 4 HOH A 57 2057 2057 HOH HOH . D 4 HOH A 58 2058 2058 HOH HOH . D 4 HOH A 59 2059 2059 HOH HOH . D 4 HOH A 60 2060 2060 HOH HOH . D 4 HOH A 61 2061 2061 HOH HOH . D 4 HOH A 62 2062 2062 HOH HOH . D 4 HOH A 63 2063 2063 HOH HOH . D 4 HOH A 64 2064 2064 HOH HOH . D 4 HOH A 65 2065 2065 HOH HOH . D 4 HOH A 66 2066 2066 HOH HOH . D 4 HOH A 67 2067 2067 HOH HOH . D 4 HOH A 68 2068 2068 HOH HOH . D 4 HOH A 69 2069 2069 HOH HOH . D 4 HOH A 70 2070 2070 HOH HOH . D 4 HOH A 71 2071 2071 HOH HOH . D 4 HOH A 72 2072 2072 HOH HOH . D 4 HOH A 73 2073 2073 HOH HOH . D 4 HOH A 74 2074 2074 HOH HOH . D 4 HOH A 75 2075 2075 HOH HOH . D 4 HOH A 76 2076 2076 HOH HOH . D 4 HOH A 77 2077 2077 HOH HOH . D 4 HOH A 78 2078 2078 HOH HOH . D 4 HOH A 79 2079 2079 HOH HOH . D 4 HOH A 80 2080 2080 HOH HOH . D 4 HOH A 81 2081 2081 HOH HOH . D 4 HOH A 82 2082 2082 HOH HOH . D 4 HOH A 83 2083 2083 HOH HOH . D 4 HOH A 84 2084 2084 HOH HOH . D 4 HOH A 85 2085 2085 HOH HOH . D 4 HOH A 86 2086 2086 HOH HOH . D 4 HOH A 87 2087 2087 HOH HOH . D 4 HOH A 88 2088 2088 HOH HOH . D 4 HOH A 89 2089 2089 HOH HOH . D 4 HOH A 90 2090 2090 HOH HOH . D 4 HOH A 91 2091 2091 HOH HOH . D 4 HOH A 92 2092 2092 HOH HOH . D 4 HOH A 93 2093 2093 HOH HOH . D 4 HOH A 94 2094 2094 HOH HOH . D 4 HOH A 95 2095 2095 HOH HOH . D 4 HOH A 96 2096 2096 HOH HOH . D 4 HOH A 97 2097 2097 HOH HOH . D 4 HOH A 98 2098 2098 HOH HOH . D 4 HOH A 99 2099 2099 HOH HOH . D 4 HOH A 100 2100 2100 HOH HOH . D 4 HOH A 101 2101 2101 HOH HOH . D 4 HOH A 102 2102 2102 HOH HOH . D 4 HOH A 103 2103 2103 HOH HOH . D 4 HOH A 104 2104 2104 HOH HOH . D 4 HOH A 105 2105 2105 HOH HOH . D 4 HOH A 106 2106 2106 HOH HOH . D 4 HOH A 107 2107 2107 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 5.319 7.671 -1.315 1 14.15 ? CHA HEM 149 A 1 HETATM 2 C CHB HEM . . . B 2 5.06 4.817 2.575 1 13.94 ? CHB HEM 149 A 1 HETATM 3 C CHC HEM . . . B 2 0.254 4.438 2.106 1 12.52 ? CHC HEM 149 A 1 HETATM 4 C CHD HEM . . . B 2 0.585 6.835 -2.087 1 14.03 ? CHD HEM 149 A 1 HETATM 5 C C1A HEM . . . B 2 5.669 6.908 -0.232 1 14.19 ? C1A HEM 149 A 1 HETATM 6 C C2A HEM . . . B 2 7.016 6.676 0.247 1 15.44 ? C2A HEM 149 A 1 HETATM 7 C C3A HEM . . . B 2 6.947 5.88 1.316 1 15.1 ? C3A HEM 149 A 1 HETATM 8 C C4A HEM . . . B 2 5.549 5.587 1.552 1 15.38 ? C4A HEM 149 A 1 HETATM 9 C CMA HEM . . . B 2 8.118 5.355 2.184 1 15.6 ? CMA HEM 149 A 1 HETATM 10 C CAA HEM . . . B 2 8.3 7.261 -0.383 1 18.3 ? CAA HEM 149 A 1 HETATM 11 C CBA HEM . . . B 2 8.692 6.428 -1.593 1 23.27 ? CBA HEM 149 A 1 HETATM 12 C CGA HEM . . . B 2 9.785 7.137 -2.361 1 27.9 ? CGA HEM 149 A 1 HETATM 13 O O1A HEM . . . B 2 9.507 7.683 -3.464 1 30.16 ? O1A HEM 149 A 1 HETATM 14 O O2A HEM . . . B 2 10.936 7.139 -1.858 1 29.75 ? O2A HEM 149 A 1 HETATM 15 C C1B HEM . . . B 2 3.734 4.558 2.824 1 13.29 ? C1B HEM 149 A 1 HETATM 16 C C2B HEM . . . B 2 3.223 3.925 4.018 1 13.79 ? C2B HEM 149 A 1 HETATM 17 C C3B HEM . . . B 2 1.889 3.829 3.903 1 13.41 ? C3B HEM 149 A 1 HETATM 18 C C4B HEM . . . B 2 1.528 4.375 2.613 1 13.93 ? C4B HEM 149 A 1 HETATM 19 C CMB HEM . . . B 2 4.101 3.484 5.205 1 15.17 ? CMB HEM 149 A 1 HETATM 20 C CAB HEM . . . B 2 0.883 3.219 4.905 1 13 ? CAB HEM 149 A 1 HETATM 21 C CBB HEM . . . B 2 1.029 3.341 6.241 1 15.29 ? CBB HEM 149 A 1 HETATM 22 C C1C HEM . . . B 2 -0.071 5.001 0.896 1 13.32 ? C1C HEM 149 A 1 HETATM 23 C C2C HEM . . . B 2 -1.386 5.016 0.287 1 12.93 ? C2C HEM 149 A 1 HETATM 24 C C3C HEM . . . B 2 -1.298 5.652 -0.882 1 13.8 ? C3C HEM 149 A 1 HETATM 25 C C4C HEM . . . B 2 0.081 6.097 -1.043 1 14.68 ? C4C HEM 149 A 1 HETATM 26 C CMC HEM . . . B 2 -2.653 4.371 0.885 1 13.41 ? CMC HEM 149 A 1 HETATM 27 C CAC HEM . . . B 2 -2.494 5.875 -1.843 1 14.08 ? CAC HEM 149 A 1 HETATM 28 C CBC HEM . . . B 2 -2.33 5.947 -3.173 1 14.04 ? CBC HEM 149 A 1 HETATM 29 C C1D HEM . . . B 2 1.847 7.352 -2.237 1 13.65 ? C1D HEM 149 A 1 HETATM 30 C C2D HEM . . . B 2 2.243 8.244 -3.298 1 13.46 ? C2D HEM 149 A 1 HETATM 31 C C3D HEM . . . B 2 3.72 8.504 -3.059 1 16 ? C3D HEM 149 A 1 HETATM 32 C C4D HEM . . . B 2 4.071 7.727 -1.889 1 14.74 ? C4D HEM 149 A 1 HETATM 33 C CMD HEM . . . B 2 1.318 8.801 -4.413 1 13.7 ? CMD HEM 149 A 1 HETATM 34 C CAD HEM . . . B 2 4.672 9.372 -3.893 1 15.94 ? CAD HEM 149 A 1 HETATM 35 C CBD HEM . . . B 2 5.32 8.423 -4.89 1 20.94 ? CBD HEM 149 A 1 HETATM 36 C CGD HEM . . . B 2 6.183 9.135 -5.903 1 22.64 ? CGD HEM 149 A 1 HETATM 37 O O1D HEM . . . B 2 7.396 9.268 -5.656 1 26.91 ? O1D HEM 149 A 1 HETATM 38 O O2D HEM . . . B 2 5.684 9.549 -6.973 1 22.26 ? O2D HEM 149 A 1 HETATM 39 N NA HEM . . . B 2 4.804 6.222 0.576 1 11.47 ? NA HEM 149 A 1 HETATM 40 N NB HEM . . . B 2 2.669 4.821 1.97 1 12.79 ? NB HEM 149 A 1 HETATM 41 N NC HEM . . . B 2 0.796 5.672 0.065 1 11.86 ? NC HEM 149 A 1 HETATM 42 N ND HEM . . . B 2 2.947 7.074 -1.429 1 14.01 ? ND HEM 149 A 1 HETATM 43 FE FE HEM . . . B 2 2.823 5.92 0.286 1 13.43 ? FE HEM 149 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #