data_1EBV # _model_server_result.job_id kc0zwysnx5UJtyJRGr3V9w _model_server_result.datetime_utc '2024-10-30 00:30:05' _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 1ebv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 1EBV # _exptl.entry_id 1EBV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 5 _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 1EBV _cell.length_a 98.87 _cell.length_b 207.46 _cell.length_c 221.98 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1EBV _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 ? _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,F _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 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 NAG 1 B 1 NAG A 671 NAG 2 n B NAG 2 B 2 NAG A 672 NAG # 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 disulf ? disulf1 A SG CYS 4 A CYS 36 1_555 A SG CYS 15 A CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 5 A CYS 37 1_555 A SG CYS 127 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 9 A CYS 41 1_555 A SG CYS 25 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 A SG CYS 27 A CYS 59 1_555 A SG CYS 37 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 537 A CYS 569 1_555 A SG CYS 543 A CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 A ND2 ASN 36 A ASN 68 1_555 C C1 NAG . A NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 A ND2 ASN 112 A ASN 144 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 A ND2 ASN 378 A ASN 410 1_555 D C1 NAG . A NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale4 A C PHE 497 A PHE 529 1_555 A N OAS 498 A OAS 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C OAS 498 A OAS 530 1_555 A N LEU 499 A LEU 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale6 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? metalc ? metalc1 A NE2 HIS 356 A HIS 388 1_555 F FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _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 1EBV _atom_sites.fract_transf_matrix[1][1] 0.010114 _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] 0.00482 _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] 0.004505 _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 NAG A 1 661 661 NAG NAG . D 3 NAG A 1 681 681 NAG NAG . E 4 SCL A 1 700 700 SCL SAL . F 5 HEM A 1 601 601 HEM HEM . # 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 5 23.253 44.572 183.508 1 21.52 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . F 5 20.252 48.218 184.107 1 20.17 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . F 5 20.289 47.522 188.894 1 18 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . F 5 23.258 43.746 188.265 1 19.44 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . F 5 22.422 45.609 183.247 1 23 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . F 5 22.149 46.122 181.895 1 24.97 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . F 5 21.314 47.12 182.111 1 23.34 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . F 5 21.069 47.246 183.531 1 22.03 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . F 5 20.721 48 181.043 1 23.83 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . F 5 22.65 45.703 180.523 1 28.88 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . F 5 21.967 44.549 179.779 1 35.42 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . F 5 21.349 44.933 178.418 1 39.56 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . F 5 22.031 45.599 177.58 1 41.65 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . F 5 20.171 44.566 178.182 1 41.49 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . F 5 20.015 48.38 185.479 1 18.73 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . F 5 19.181 49.459 186.047 1 17.55 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . F 5 19.183 49.283 187.412 1 16.75 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . F 5 20.029 48.071 187.642 1 17.51 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . F 5 18.483 50.525 185.193 1 17.56 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . F 5 18.562 50.025 188.424 1 15.5 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . F 5 17.722 51.216 188.347 1 13.98 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . F 5 21.091 46.404 189.125 1 19.2 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . F 5 21.332 45.812 190.469 1 19.27 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . F 5 22.164 44.736 190.305 1 19.34 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . F 5 22.429 44.688 188.85 1 19.56 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . F 5 20.759 46.299 191.813 1 19.47 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . F 5 22.631 43.89 191.333 1 18.87 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . F 5 24.003 43.706 191.769 1 17.93 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . F 5 23.53 43.676 186.922 1 19.69 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . F 5 24.451 42.712 186.377 1 19.33 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . F 5 24.447 42.959 185.039 1 19.55 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . F 5 23.515 44.061 184.773 1 20.18 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . F 5 25.252 41.664 187.139 1 19.25 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . F 5 25.261 42.241 183.975 1 18.98 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . F 5 26.441 43.138 183.56 1 17.98 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . F 5 27.352 42.587 182.48 1 17.77 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . F 5 27.136 41.462 181.965 1 19 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . F 5 28.305 43.301 182.133 1 16.35 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . F 5 21.75 46.308 184.236 1 21.57 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . F 5 20.526 47.544 186.45 1 18.77 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . F 5 21.77 45.701 188.13 1 19.54 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . F 5 22.951 44.507 185.947 1 20.08 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . F 5 21.619 45.896 186.179 1 18.91 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #