data_3JUV # _model_server_result.job_id HaoaF4iXIC71vawJHGRd0A _model_server_result.datetime_utc '2024-12-02 11:47:42' _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 3juv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 3JUV # _exptl.entry_id 3JUV _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 90 _cell.angle_gamma 120 _cell.entry_id 3JUV _cell.length_a 174.144 _cell.length_b 174.144 _cell.length_c 244.269 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JUV _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 18_444 -x-2/3,-x+y-1/3,-z-1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 -87.072 -50.271043 -81.423 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 1 7 GLC GLC C1 O1 . O4 HO4 . sing 2 ? 2 2 1 GLC GLC C1 O1 . O4 HO4 . sing 3 ? 2 3 2 GLC GLC C1 O1 . O4 HO4 . sing 4 ? 2 4 3 GLC GLC C1 O1 . O4 HO4 . sing 5 ? 2 5 4 GLC GLC C1 O1 . O4 HO4 . sing 6 ? 2 6 5 GLC GLC C1 O1 . O4 HO4 . sing 7 ? 2 7 6 GLC GLC C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC A 603 BCD 2 n B GLC 2 B 2 GLC A 603 BCD 2 n B GLC 3 B 3 GLC A 603 BCD 2 n B GLC 4 B 4 GLC A 603 BCD 2 n B GLC 5 B 5 GLC A 603 BCD 2 n B GLC 6 B 6 GLC A 603 BCD 2 n B GLC 7 B 7 GLC A 603 BCD # 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 covale ? covale1 B O4 GLC . B GLC 1 1_555 B C1 GLC . B GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 sing covale ? covale2 B C1 GLC . B GLC 1 1_555 B O4 GLC . B GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 sing covale ? covale3 B O4 GLC . B GLC 2 1_555 B C1 GLC . B GLC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 sing covale ? covale4 B O4 GLC . B GLC 3 1_555 B C1 GLC . B GLC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 sing covale ? covale5 B O4 GLC . B GLC 4 1_555 B C1 GLC . B GLC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 sing covale ? covale6 B O4 GLC . B GLC 5 1_555 B C1 GLC . B GLC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 sing covale ? covale7 B O4 GLC . B GLC 6 1_555 B C1 GLC . B GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 sing metalc ? metalc1 A SG CYS 401 A CYS 449 1_555 C FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? # _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 153 n n CHA C4D HEM doub 154 n n CHA HHA HEM sing 155 n n CHB C4A HEM sing 156 n n CHB C1B HEM doub 157 n n CHB HHB HEM sing 158 n n CHC C4B HEM sing 159 n n CHC C1C HEM doub 160 n n CHC HHC HEM sing 161 n n CHD C4C HEM doub 162 n n CHD C1D HEM sing 163 n n CHD HHD HEM sing 164 n n C1A C2A HEM doub 165 n y C1A NA HEM sing 166 n y C2A C3A HEM sing 167 n y C2A CAA HEM sing 168 n n C3A C4A HEM doub 169 n y C3A CMA HEM sing 170 n n C4A NA HEM sing 171 n y CMA HMA HEM sing 172 n n CMA HMAA HEM sing 173 n n CMA HMAB HEM sing 174 n n CAA CBA HEM sing 175 n n CAA HAA HEM sing 176 n n CAA HAAA HEM sing 177 n n CBA CGA HEM sing 178 n n CBA HBA HEM sing 179 n n CBA HBAA HEM sing 180 n n CGA O1A HEM doub 181 n n CGA O2A HEM sing 182 n n C1B C2B HEM sing 183 n n C1B NB HEM sing 184 n n C2B C3B HEM doub 185 n n C2B CMB HEM sing 186 n n C3B C4B HEM sing 187 n n C3B CAB HEM sing 188 n n C4B NB HEM doub 189 n n CMB HMB HEM sing 190 n n CMB HMBA HEM sing 191 n n CMB HMBB HEM sing 192 n n CAB CBB HEM doub 193 n n CAB HAB HEM sing 194 n n CBB HBB HEM sing 195 n n CBB HBBA HEM sing 196 n n C1C C2C HEM sing 197 n y C1C NC HEM sing 198 n y C2C C3C HEM doub 199 n y C2C CMC HEM sing 200 n n C3C C4C HEM sing 201 n y C3C CAC HEM sing 202 n n C4C NC HEM sing 203 n y CMC HMC HEM sing 204 n n CMC HMCA HEM sing 205 n n CMC HMCB HEM sing 206 n n CAC CBC HEM doub 207 n n CAC HAC HEM sing 208 n n CBC HBC HEM sing 209 n n CBC HBCA HEM sing 210 n n C1D C2D HEM sing 211 n n C1D ND HEM doub 212 n n C2D C3D HEM doub 213 n n C2D CMD HEM sing 214 n n C3D C4D HEM sing 215 n n C3D CAD HEM sing 216 n n C4D ND HEM sing 217 n n CMD HMD HEM sing 218 n n CMD HMDA HEM sing 219 n n CMD HMDB HEM sing 220 n n CAD CBD HEM sing 221 n n CAD HAD HEM sing 222 n n CAD HADA HEM sing 223 n n CBD CGD HEM sing 224 n n CBD HBD HEM sing 225 n n CBD HBDA HEM sing 226 n n CGD O1D HEM doub 227 n n CGD O2D HEM sing 228 n n O2A H2A HEM sing 229 n n O2D H2D HEM sing 230 n n FE NA HEM sing 231 n n FE NB HEM sing 232 n n FE NC HEM sing 233 n n FE ND HEM sing 234 n n # _atom_sites.entry_id 3JUV _atom_sites.fract_transf_matrix[1][1] 0.005742 _atom_sites.fract_transf_matrix[1][2] 0.003315 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006631 _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] 0.004094 _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 3 HEM A 1 601 601 HEM HEM . D 4 HOH A 1 604 604 HOH HOH . D 4 HOH A 2 605 605 HOH HOH . D 4 HOH A 3 606 606 HOH HOH . D 4 HOH A 4 607 607 HOH HOH . D 4 HOH A 5 608 608 HOH HOH . D 4 HOH A 6 609 609 HOH HOH . D 4 HOH A 7 610 610 HOH HOH . D 4 HOH A 8 611 611 HOH HOH . D 4 HOH A 9 612 612 HOH HOH . D 4 HOH A 10 613 613 HOH HOH . D 4 HOH A 11 614 614 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 . . . C 3 -75.664 26.16 -6.692 1 59.44 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . C 3 -79.734 23.959 -7.924 1 55.5 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . C 3 -80.748 23.415 -3.198 1 57.81 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . C 3 -76.565 25.481 -1.956 1 60.37 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . C 3 -76.647 25.593 -7.448 1 57.48 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . C 3 -76.655 25.502 -8.884 1 56.34 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . C 3 -77.788 24.894 -9.256 1 55.65 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . C 3 -78.521 24.587 -8.035 1 55.88 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . C 3 -78.231 24.573 -10.709 1 53.53 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . C 3 -75.537 26.048 -9.785 1 57.12 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . C 3 -74.423 25.04 -9.979 1 59.85 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . C 3 -73.237 25.762 -10.56 1 62.25 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . C 3 -73.403 26.466 -11.6 1 62.7 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . C 3 -72.123 25.635 -9.972 1 64.74 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . C 3 -80.349 23.604 -6.743 1 56.15 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . C 3 -81.578 22.846 -6.64 1 56.05 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . C 3 -81.868 22.696 -5.349 1 56.08 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . C 3 -80.831 23.352 -4.57 1 56.59 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . C 3 -82.409 22.303 -7.825 1 55.62 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . C 3 -83.097 21.928 -4.822 1 55.09 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . C 3 -83.975 22.53 -4.025 1 56.06 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . C 3 -79.689 23.886 -2.44 1 58.91 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . C 3 -79.546 23.828 -0.987 1 59.35 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . C 3 -78.384 24.405 -0.658 1 60.06 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . C 3 -77.768 24.842 -1.879 1 59.76 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . C 3 -80.565 23.211 -0.004 1 59.26 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . C 3 -77.752 24.632 0.737 1 61.48 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . C 3 -77.45 23.628 1.564 1 62.99 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . C 3 -75.998 25.952 -3.11 1 60.42 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . C 3 -74.889 26.873 -3.152 1 61.34 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . C 3 -74.626 27.057 -4.631 1 61.75 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . C 3 -75.593 26.251 -5.324 1 60.17 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . C 3 -74.115 27.531 -1.981 1 61.64 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . C 3 -73.567 27.968 -5.249 1 64.81 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . C 3 -74.313 29.288 -5.403 1 67.09 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . C 3 -73.782 30.071 -6.568 1 69.53 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . C 3 -72.735 29.671 -7.174 1 70.15 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . C 3 -74.425 31.116 -6.869 1 71.27 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . C 3 -77.787 25.024 -6.954 1 57.26 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . C 3 -79.923 23.894 -5.455 1 57.03 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . C 3 -78.57 24.508 -2.947 1 58.75 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . C 3 -76.383 25.607 -4.399 1 59.03 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . C 3 -78.154 24.775 -4.912 1 58.55 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 43 #