data_1VXB # _model_server_result.job_id '_CNroQuqdyzuBbsfbbEhhQ' _model_server_result.datetime_utc '2025-02-28 20:56:08' _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 1vxb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":156}' # _entry.id 1VXB # _exptl.entry_id 1VXB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _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 106.75 _cell.angle_gamma 90 _cell.entry_id 1VXB _cell.length_a 64.35 _cell.length_b 30.924 _cell.length_c 35.531 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VXB _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 3 _struct_asym.id D _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 93 A HIS 93 1_555 D FE HEM . A HEM 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc2 D FE HEM . A HEM 156 1_555 E O HOH . A HOH 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? # _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 1VXB _atom_sites.fract_transf_matrix[1][1] 0.01554 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004677 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.032337 _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] 0.029391 _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 SO4 A 1 154 3 SO4 SO4 . C 2 SO4 A 1 155 4 SO4 SO4 . D 3 HEM A 1 156 1 HEM HEM . E 4 HOH A 1 157 2 HOH MTO . E 4 HOH A 2 158 5 HOH HOH . E 4 HOH A 3 159 6 HOH HOH . E 4 HOH A 4 160 7 HOH HOH . E 4 HOH A 5 161 8 HOH HOH . E 4 HOH A 6 162 9 HOH HOH . E 4 HOH A 7 163 10 HOH HOH . E 4 HOH A 8 164 11 HOH HOH . E 4 HOH A 9 165 12 HOH HOH . E 4 HOH A 10 166 13 HOH HOH . E 4 HOH A 11 167 14 HOH HOH . E 4 HOH A 12 168 15 HOH HOH . E 4 HOH A 13 169 16 HOH HOH . E 4 HOH A 14 170 17 HOH HOH . E 4 HOH A 15 171 18 HOH HOH . E 4 HOH A 16 172 19 HOH HOH . E 4 HOH A 17 173 20 HOH HOH . E 4 HOH A 18 174 21 HOH HOH . E 4 HOH A 19 175 22 HOH HOH . E 4 HOH A 20 176 23 HOH HOH . E 4 HOH A 21 177 24 HOH HOH . E 4 HOH A 22 178 25 HOH HOH . E 4 HOH A 23 179 26 HOH HOH . E 4 HOH A 24 180 27 HOH HOH . E 4 HOH A 25 181 28 HOH HOH . E 4 HOH A 26 182 29 HOH HOH . E 4 HOH A 27 183 30 HOH HOH . E 4 HOH A 28 184 31 HOH HOH . E 4 HOH A 29 185 32 HOH HOH . E 4 HOH A 30 186 33 HOH HOH . E 4 HOH A 31 187 34 HOH HOH . E 4 HOH A 32 188 35 HOH HOH . E 4 HOH A 33 189 36 HOH HOH . E 4 HOH A 34 190 37 HOH HOH . E 4 HOH A 35 191 38 HOH HOH . E 4 HOH A 36 192 39 HOH HOH . E 4 HOH A 37 193 40 HOH HOH . E 4 HOH A 38 194 41 HOH HOH . E 4 HOH A 39 195 42 HOH HOH . E 4 HOH A 40 196 43 HOH HOH . E 4 HOH A 41 197 44 HOH HOH . E 4 HOH A 42 198 45 HOH HOH . E 4 HOH A 43 199 46 HOH HOH . E 4 HOH A 44 200 47 HOH HOH . E 4 HOH A 45 201 48 HOH HOH . E 4 HOH A 46 202 49 HOH HOH . E 4 HOH A 47 203 50 HOH HOH . E 4 HOH A 48 204 51 HOH HOH . E 4 HOH A 49 205 52 HOH HOH . E 4 HOH A 50 206 53 HOH HOH . E 4 HOH A 51 207 54 HOH HOH . E 4 HOH A 52 208 55 HOH HOH . E 4 HOH A 53 209 56 HOH HOH . E 4 HOH A 54 210 57 HOH HOH . E 4 HOH A 55 211 58 HOH HOH . E 4 HOH A 56 212 59 HOH HOH . E 4 HOH A 57 213 60 HOH HOH . E 4 HOH A 58 214 61 HOH HOH . E 4 HOH A 59 215 62 HOH HOH . E 4 HOH A 60 216 63 HOH HOH . E 4 HOH A 61 217 64 HOH HOH . E 4 HOH A 62 218 65 HOH HOH . E 4 HOH A 63 219 66 HOH HOH . E 4 HOH A 64 220 67 HOH HOH . E 4 HOH A 65 221 68 HOH HOH . E 4 HOH A 66 222 69 HOH HOH . E 4 HOH A 67 223 70 HOH HOH . E 4 HOH A 68 224 71 HOH HOH . E 4 HOH A 69 225 72 HOH HOH . E 4 HOH A 70 226 73 HOH HOH . E 4 HOH A 71 227 74 HOH HOH . E 4 HOH A 72 228 75 HOH HOH . E 4 HOH A 73 229 76 HOH HOH . E 4 HOH A 74 230 77 HOH HOH . E 4 HOH A 75 231 78 HOH HOH . E 4 HOH A 76 232 79 HOH HOH . E 4 HOH A 77 233 80 HOH HOH . E 4 HOH A 78 234 81 HOH HOH . E 4 HOH A 79 235 82 HOH HOH . E 4 HOH A 80 236 83 HOH HOH . E 4 HOH A 81 237 84 HOH HOH . E 4 HOH A 82 238 85 HOH HOH . E 4 HOH A 83 239 86 HOH HOH . E 4 HOH A 84 240 87 HOH HOH . E 4 HOH A 85 241 88 HOH HOH . E 4 HOH A 86 242 89 HOH HOH . E 4 HOH A 87 243 90 HOH HOH . E 4 HOH A 88 244 91 HOH HOH . E 4 HOH A 89 245 92 HOH HOH . E 4 HOH A 90 246 93 HOH HOH . E 4 HOH A 91 247 94 HOH HOH . E 4 HOH A 92 248 95 HOH HOH . E 4 HOH A 93 249 96 HOH HOH . E 4 HOH A 94 250 97 HOH HOH . E 4 HOH A 95 251 98 HOH HOH . E 4 HOH A 96 252 99 HOH HOH . E 4 HOH A 97 253 100 HOH HOH . E 4 HOH A 98 254 101 HOH HOH . E 4 HOH A 99 255 102 HOH HOH . E 4 HOH A 100 256 103 HOH HOH . E 4 HOH A 101 257 104 HOH HOH . E 4 HOH A 102 258 105 HOH HOH . E 4 HOH A 103 259 106 HOH HOH . E 4 HOH A 104 260 107 HOH HOH . E 4 HOH A 105 261 108 HOH HOH . E 4 HOH A 106 262 109 HOH HOH . E 4 HOH A 107 263 110 HOH HOH . E 4 HOH A 108 264 111 HOH HOH . E 4 HOH A 109 265 112 HOH HOH . E 4 HOH A 110 266 113 HOH HOH . E 4 HOH A 111 267 114 HOH HOH . E 4 HOH A 112 268 115 HOH HOH . E 4 HOH A 113 269 116 HOH HOH . E 4 HOH A 114 270 117 HOH HOH . E 4 HOH A 115 271 118 HOH HOH . E 4 HOH A 116 272 119 HOH HOH . E 4 HOH A 117 273 120 HOH HOH . E 4 HOH A 118 274 121 HOH HOH . E 4 HOH A 119 275 122 HOH HOH . E 4 HOH A 120 276 123 HOH HOH . E 4 HOH A 121 277 124 HOH HOH . E 4 HOH A 122 278 125 HOH HOH . E 4 HOH A 123 279 126 HOH HOH . E 4 HOH A 124 280 127 HOH HOH . E 4 HOH A 125 281 128 HOH HOH . E 4 HOH A 126 282 129 HOH HOH . E 4 HOH A 127 283 130 HOH HOH . E 4 HOH A 128 284 131 HOH HOH . E 4 HOH A 129 285 132 HOH HOH . E 4 HOH A 130 286 133 HOH HOH . E 4 HOH A 131 287 134 HOH HOH . E 4 HOH A 132 288 135 HOH HOH . E 4 HOH A 133 289 136 HOH HOH . E 4 HOH A 134 290 137 HOH HOH . E 4 HOH A 135 291 138 HOH HOH . E 4 HOH A 136 292 139 HOH HOH . E 4 HOH A 137 293 140 HOH HOH . E 4 HOH A 138 294 141 HOH HOH . E 4 HOH A 139 295 142 HOH HOH . E 4 HOH A 140 296 143 HOH HOH . E 4 HOH A 141 297 144 HOH HOH . E 4 HOH A 142 298 145 HOH HOH . E 4 HOH A 143 299 146 HOH HOH . E 4 HOH A 144 300 147 HOH HOH . E 4 HOH A 145 301 148 HOH HOH . E 4 HOH A 146 302 149 HOH HOH . E 4 HOH A 147 303 150 HOH HOH . E 4 HOH A 148 304 151 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 . . . D 3 16.463 31.048 4.614 1 19.7 ? CHA HEM 156 A 1 HETATM 2 C CHB HEM . . . D 3 13.985 28.114 7.649 1 17.9 ? CHB HEM 156 A 1 HETATM 3 C CHC HEM . . . D 3 13.379 24.972 4.092 1 12.6 ? CHC HEM 156 A 1 HETATM 4 C CHD HEM . . . D 3 15.639 27.63 1.087 1 15.8 ? CHD HEM 156 A 1 HETATM 5 C C1A HEM . . . D 3 15.896 30.511 5.83 1 20.5 ? C1A HEM 156 A 1 HETATM 6 C C2A HEM . . . D 3 16.019 31.072 7.118 1 18.8 ? C2A HEM 156 A 1 HETATM 7 C C3A HEM . . . D 3 15.257 30.36 8.028 1 21.6 ? C3A HEM 156 A 1 HETATM 8 C C4A HEM . . . D 3 14.545 29.298 7.155 1 21.4 ? C4A HEM 156 A 1 HETATM 9 C CMA HEM . . . D 3 14.861 30.809 9.393 1 16.3 ? CMA HEM 156 A 1 HETATM 10 C CAA HEM . . . D 3 16.332 32.502 7.354 1 25 ? CAA HEM 156 A 1 HETATM 11 C CBA HEM . . . D 3 15.123 33.437 7.487 1 23.1 ? CBA HEM 156 A 1 HETATM 12 C CGA HEM . . . D 3 14.415 33.611 6.156 1 26.7 ? CGA HEM 156 A 1 HETATM 13 O O1A HEM . . . D 3 15.163 33.776 5.194 1 28.4 ? O1A HEM 156 A 1 HETATM 14 O O2A HEM . . . D 3 13.172 33.5 6.058 1 24 ? O2A HEM 156 A 1 HETATM 15 C C1B HEM . . . D 3 13.756 26.994 6.767 1 17.4 ? C1B HEM 156 A 1 HETATM 16 C C2B HEM . . . D 3 13.006 25.731 7.286 1 7.8 ? C2B HEM 156 A 1 HETATM 17 C C3B HEM . . . D 3 13 24.861 6.295 1 11.4 ? C3B HEM 156 A 1 HETATM 18 C C4B HEM . . . D 3 13.465 25.635 5.159 1 11.1 ? C4B HEM 156 A 1 HETATM 19 C CMB HEM . . . D 3 12.492 25.727 8.688 1 10.5 ? CMB HEM 156 A 1 HETATM 20 C CAB HEM . . . D 3 12.714 23.387 6.301 1 12.4 ? CAB HEM 156 A 1 HETATM 21 C CBB HEM . . . D 3 12.611 22.477 7.619 1 19.3 ? CBB HEM 156 A 1 HETATM 22 C C1C HEM . . . D 3 13.868 25.391 2.974 1 11.8 ? C1C HEM 156 A 1 HETATM 23 C C2C HEM . . . D 3 14.009 24.566 1.813 1 7.5 ? C2C HEM 156 A 1 HETATM 24 C C3C HEM . . . D 3 14.687 25.283 1.009 1 12.2 ? C3C HEM 156 A 1 HETATM 25 C C4C HEM . . . D 3 14.957 26.566 1.632 1 12 ? C4C HEM 156 A 1 HETATM 26 C CMC HEM . . . D 3 14.273 23.111 1.692 1 14.4 ? CMC HEM 156 A 1 HETATM 27 C CAC HEM . . . D 3 15.275 24.912 -0.264 1 13.4 ? CAC HEM 156 A 1 HETATM 28 C CBC HEM . . . D 3 15.175 23.753 -1.218 1 10.2 ? CBC HEM 156 A 1 HETATM 29 C C1D HEM . . . D 3 15.753 28.853 1.748 1 16.8 ? C1D HEM 156 A 1 HETATM 30 C C2D HEM . . . D 3 16.482 29.862 1.163 1 19.9 ? C2D HEM 156 A 1 HETATM 31 C C3D HEM . . . D 3 16.783 30.853 2.094 1 21.5 ? C3D HEM 156 A 1 HETATM 32 C C4D HEM . . . D 3 16.194 30.451 3.356 1 19.2 ? C4D HEM 156 A 1 HETATM 33 C CMD HEM . . . D 3 17.186 29.815 -0.141 1 25 ? CMD HEM 156 A 1 HETATM 34 C CAD HEM . . . D 3 17.545 32.063 1.694 1 22.2 ? CAD HEM 156 A 1 HETATM 35 C CBD HEM . . . D 3 19.011 31.889 2.171 1 25.9 ? CBD HEM 156 A 1 HETATM 36 C CGD HEM . . . D 3 19.747 33.213 2.216 1 22.9 ? CGD HEM 156 A 1 HETATM 37 O O1D HEM . . . D 3 20.119 33.762 1.126 1 24.3 ? O1D HEM 156 A 1 HETATM 38 O O2D HEM . . . D 3 19.959 33.681 3.354 1 22.2 ? O2D HEM 156 A 1 HETATM 39 N NA HEM . . . D 3 14.916 29.412 5.809 1 18.4 ? NA HEM 156 A 1 HETATM 40 N NB HEM . . . D 3 14.025 26.838 5.399 1 9.2 ? NB HEM 156 A 1 HETATM 41 N NC HEM . . . D 3 14.46 26.59 2.945 1 14.1 ? NC HEM 156 A 1 HETATM 42 N ND HEM . . . D 3 15.434 29.197 3.135 1 17 ? ND HEM 156 A 1 HETATM 43 FE FE HEM . . . D 3 14.802 28.02 4.434 1 21.4 ? FE HEM 156 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 438 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #