data_3NVR # _model_server_result.job_id bwhRjnv5eXq5YGyta4dc6Q _model_server_result.datetime_utc '2024-11-28 16:26:18' _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 3nvr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":200}' # _entry.id 3NVR # _exptl.entry_id 3NVR _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 2 _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 3NVR _cell.length_a 79.825 _cell.length_b 126.095 _cell.length_c 42.742 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NVR _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F,G,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N 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 102 A HIS 102 1_555 C FE HEM . A HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc2 C FE HEM . A HEM 200 1_555 D O1 OXY . A OXY 493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc3 C FE HEM . A HEM 200 1_555 D O2 OXY . A OXY 493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? metalc ? metalc4 B NE2 HIS 102 B HIS 102 1_555 F FE HEM . B HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc5 F FE HEM . B HEM 200 1_555 G O1 OXY . B OXY 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc6 F FE HEM . B HEM 200 1_555 G O2 OXY . B OXY 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? # _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 3NVR _atom_sites.fract_transf_matrix[1][1] 0.012527 _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] 0.007931 _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] 0.023396 _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 C 2 HEM A 1 200 200 HEM HEM . D 3 OXY A 1 493 493 OXY OXY . E 4 CL A 1 189 2 CL CL . F 2 HEM B 1 200 200 HEM HEM . G 3 OXY B 1 494 494 OXY OXY . H 4 CL B 1 189 1 CL CL . I 5 HOH A 1 190 1 HOH HOH . I 5 HOH A 2 191 2 HOH HOH . I 5 HOH A 3 192 4 HOH HOH . I 5 HOH A 4 193 6 HOH HOH . I 5 HOH A 5 194 9 HOH HOH . I 5 HOH A 6 195 10 HOH HOH . I 5 HOH A 7 196 11 HOH HOH . I 5 HOH A 8 197 12 HOH HOH . I 5 HOH A 9 198 13 HOH HOH . I 5 HOH A 10 199 18 HOH HOH . I 5 HOH A 11 201 22 HOH HOH . I 5 HOH A 12 202 23 HOH HOH . I 5 HOH A 13 203 25 HOH HOH . I 5 HOH A 14 204 27 HOH HOH . I 5 HOH A 15 205 31 HOH HOH . I 5 HOH A 16 206 32 HOH HOH . I 5 HOH A 17 207 36 HOH HOH . I 5 HOH A 18 208 37 HOH HOH . I 5 HOH A 19 209 38 HOH HOH . I 5 HOH A 20 210 39 HOH HOH . I 5 HOH A 21 211 41 HOH HOH . I 5 HOH A 22 212 42 HOH HOH . I 5 HOH A 23 213 43 HOH HOH . I 5 HOH A 24 214 48 HOH HOH . I 5 HOH A 25 215 49 HOH HOH . I 5 HOH A 26 216 50 HOH HOH . I 5 HOH A 27 217 51 HOH HOH . I 5 HOH A 28 218 52 HOH HOH . I 5 HOH A 29 219 54 HOH HOH . I 5 HOH A 30 220 55 HOH HOH . J 5 HOH B 1 190 3 HOH HOH . J 5 HOH B 2 191 5 HOH HOH . J 5 HOH B 3 192 7 HOH HOH . J 5 HOH B 4 193 8 HOH HOH . J 5 HOH B 5 194 14 HOH HOH . J 5 HOH B 6 195 15 HOH HOH . J 5 HOH B 7 196 16 HOH HOH . J 5 HOH B 8 197 17 HOH HOH . J 5 HOH B 9 198 19 HOH HOH . J 5 HOH B 10 199 20 HOH HOH . J 5 HOH B 11 201 21 HOH HOH . J 5 HOH B 12 202 24 HOH HOH . J 5 HOH B 13 203 26 HOH HOH . J 5 HOH B 14 204 28 HOH HOH . J 5 HOH B 15 205 29 HOH HOH . J 5 HOH B 16 206 30 HOH HOH . J 5 HOH B 17 207 33 HOH HOH . J 5 HOH B 18 208 34 HOH HOH . J 5 HOH B 19 209 35 HOH HOH . J 5 HOH B 20 210 40 HOH HOH . J 5 HOH B 21 211 44 HOH HOH . J 5 HOH B 22 212 45 HOH HOH . J 5 HOH B 23 213 46 HOH HOH . J 5 HOH B 24 214 47 HOH HOH . J 5 HOH B 25 215 53 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 . . . F 2 -18.549 44.508 3.379 1 35.62 ? CHA HEM 200 B 1 HETATM 2 C CHB HEM . . . F 2 -19.066 40.511 6.057 1 35.28 ? CHB HEM 200 B 1 HETATM 3 C CHC HEM . . . F 2 -19.369 43.194 10.067 1 37.65 ? CHC HEM 200 B 1 HETATM 4 C CHD HEM . . . F 2 -17.681 46.901 7.504 1 29.64 ? CHD HEM 200 B 1 HETATM 5 C C1A HEM . . . F 2 -18.619 43.203 3.763 1 33.2 ? C1A HEM 200 B 1 HETATM 6 C C2A HEM . . . F 2 -18.504 42.072 2.877 1 29.25 ? C2A HEM 200 B 1 HETATM 7 C C3A HEM . . . F 2 -18.633 40.965 3.616 1 36.85 ? C3A HEM 200 B 1 HETATM 8 C C4A HEM . . . F 2 -18.856 41.364 4.993 1 42.02 ? C4A HEM 200 B 1 HETATM 9 C CMA HEM . . . F 2 -18.572 39.514 3.081 1 40.87 ? CMA HEM 200 B 1 HETATM 10 C CAA HEM . . . F 2 -18.235 42.136 1.351 1 47.67 ? CAA HEM 200 B 1 HETATM 11 C CBA HEM . . . F 2 -16.812 42.636 1.081 1 49.72 ? CBA HEM 200 B 1 HETATM 12 C CGA HEM . . . F 2 -16.468 42.668 -0.397 1 43.77 ? CGA HEM 200 B 1 HETATM 13 O O1A HEM . . . F 2 -15.415 43.265 -0.744 1 54.97 ? O1A HEM 200 B 1 HETATM 14 O O2A HEM . . . F 2 -17.241 42.123 -1.23 1 52.18 ? O2A HEM 200 B 1 HETATM 15 C C1B HEM . . . F 2 -19.286 40.876 7.367 1 31.42 ? C1B HEM 200 B 1 HETATM 16 C C2B HEM . . . F 2 -19.701 40.018 8.468 1 41.73 ? C2B HEM 200 B 1 HETATM 17 C C3B HEM . . . F 2 -19.792 40.774 9.569 1 41.91 ? C3B HEM 200 B 1 HETATM 18 C C4B HEM . . . F 2 -19.418 42.125 9.209 1 38.72 ? C4B HEM 200 B 1 HETATM 19 C CMB HEM . . . F 2 -20.003 38.505 8.371 1 39.88 ? CMB HEM 200 B 1 HETATM 20 C CAB HEM . . . F 2 -20.18 40.348 11.005 1 46.31 ? CAB HEM 200 B 1 HETATM 21 C CBB HEM . . . F 2 -20.141 39.069 11.399 1 52.62 ? CBB HEM 200 B 1 HETATM 22 C C1C HEM . . . F 2 -18.844 44.416 9.737 1 37.98 ? C1C HEM 200 B 1 HETATM 23 C C2C HEM . . . F 2 -18.498 45.476 10.663 1 38.93 ? C2C HEM 200 B 1 HETATM 24 C C3C HEM . . . F 2 -18.026 46.495 9.938 1 33.49 ? C3C HEM 200 B 1 HETATM 25 C C4C HEM . . . F 2 -18.069 46.109 8.548 1 34.69 ? C4C HEM 200 B 1 HETATM 26 C CMC HEM . . . F 2 -18.646 45.417 12.201 1 36.87 ? CMC HEM 200 B 1 HETATM 27 C CAC HEM . . . F 2 -17.518 47.861 10.437 1 38.64 ? CAC HEM 200 B 1 HETATM 28 C CBC HEM . . . F 2 -17.536 48.191 11.728 1 47.27 ? CBC HEM 200 B 1 HETATM 29 C C1D HEM . . . F 2 -17.958 46.673 6.183 1 29.29 ? C1D HEM 200 B 1 HETATM 30 C C2D HEM . . . F 2 -18.089 47.697 5.169 1 29.82 ? C2D HEM 200 B 1 HETATM 31 C C3D HEM . . . F 2 -18.355 46.938 3.874 1 36.93 ? C3D HEM 200 B 1 HETATM 32 C C4D HEM . . . F 2 -18.362 45.547 4.251 1 32.24 ? C4D HEM 200 B 1 HETATM 33 C CMD HEM . . . F 2 -17.984 49.225 5.354 1 26.65 ? CMD HEM 200 B 1 HETATM 34 C CAD HEM . . . F 2 -18.589 47.527 2.466 1 32.69 ? CAD HEM 200 B 1 HETATM 35 C CBD HEM . . . F 2 -17.411 47.145 1.583 1 41.39 ? CBD HEM 200 B 1 HETATM 36 C CGD HEM . . . F 2 -16.553 48.368 1.359 1 45.9 ? CGD HEM 200 B 1 HETATM 37 O O1D HEM . . . F 2 -15.523 48.262 0.64 1 49.92 ? O1D HEM 200 B 1 HETATM 38 O O2D HEM . . . F 2 -16.897 49.447 1.913 1 35.84 ? O2D HEM 200 B 1 HETATM 39 N NA HEM . . . F 2 -18.827 42.749 5.044 1 29.68 ? NA HEM 200 B 1 HETATM 40 N NB HEM . . . F 2 -19.125 42.151 7.863 1 36.25 ? NB HEM 200 B 1 HETATM 41 N NC HEM . . . F 2 -18.567 44.833 8.449 1 30.74 ? NC HEM 200 B 1 HETATM 42 N ND HEM . . . F 2 -18.123 45.431 5.605 1 35.35 ? ND HEM 200 B 1 HETATM 43 FE FE HEM . . . F 2 -18.727 43.792 6.703 1 35.56 ? FE HEM 200 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #