data_1PTH # _model_server_result.job_id WYgOez9T5WV7kuTXu79hIQ _model_server_result.datetime_utc '2025-01-03 05:11:20' _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 1pth # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":601}' # _entry.id 1PTH # _exptl.entry_id 1PTH _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 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 1PTH _cell.length_a 99.57 _cell.length_b 209.8 _cell.length_c 235 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PTH _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 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,K,L,M,N,O _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 ? 5 H N N ? 5 M N 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 C NAG 1 C 1 NAG A 671 NAG 2 n C NAG 2 C 2 NAG A 672 NAG 2 n D NAG 1 D 1 NAG B 671 NAG 2 n D NAG 2 D 2 NAG B 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 12 A CYS 36 1_555 A SG CYS 23 A CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 13 A CYS 37 1_555 A SG CYS 135 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 17 A CYS 41 1_555 A SG CYS 33 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf4 A SG CYS 35 A CYS 59 1_555 A SG CYS 45 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf5 A SG CYS 545 A CYS 569 1_555 A SG CYS 551 A CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf6 B SG CYS 12 B CYS 36 1_555 B SG CYS 23 B CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 B SG CYS 13 B CYS 37 1_555 B SG CYS 135 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 B SG CYS 17 B CYS 41 1_555 B SG CYS 33 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf9 B SG CYS 35 B CYS 59 1_555 B SG CYS 45 B CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf10 B SG CYS 545 B CYS 569 1_555 B SG CYS 551 B CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? covale ? covale1 A ND2 ASN 44 A ASN 68 1_555 E C1 NAG . A NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 A ND2 ASN 120 A ASN 144 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 386 A ASN 410 1_555 F C1 NAG . A NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 A C PHE 505 A PHE 529 1_555 A N 0AH 506 A 0AH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A C 0AH 506 A 0AH 530 1_555 A N LEU 507 A LEU 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 B ND2 ASN 44 B ASN 68 1_555 J C1 NAG . B NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale7 B ND2 ASN 120 B ASN 144 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 B ND2 ASN 386 B ASN 410 1_555 K C1 NAG . B NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale9 B C PHE 505 B PHE 529 1_555 B N 0AH 506 B 0AH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale10 B C 0AH 506 B 0AH 530 1_555 B N LEU 507 B LEU 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale11 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale12 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? metalc ? metalc1 A NE2 HIS 364 A HIS 388 1_555 H FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc2 B NE2 HIS 364 B HIS 388 1_555 M FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? # _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 # _atom_sites.entry_id 1PTH _atom_sites.fract_transf_matrix[1][1] 0.010043 _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] 0.004766 _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] 0.004255 _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 E 3 NAG A 1 661 661 NAG NAG . F 3 NAG A 1 681 681 NAG NAG . G 4 BOG A 1 702 702 BOG BOG . H 5 HEM A 1 601 601 HEM HEM . I 6 SAL A 1 710 710 SAL SAL . J 3 NAG B 1 661 661 NAG NAG . K 3 NAG B 1 681 681 NAG NAG . L 4 BOG B 1 702 702 BOG BOG . M 5 HEM B 1 602 602 HEM HEM . N 6 SAL B 1 711 711 SAL SAL . O 7 HOH A 1 704 704 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 . . . H 5 23.398 44.667 193.297 1 15.76 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . H 5 20.155 48.144 193.85 1 10.84 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . H 5 20.538 47.937 198.6 1 17.01 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . H 5 23.425 44.081 198.012 1 17.56 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . H 5 22.641 45.799 193.046 1 11.67 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . H 5 22.256 46.194 191.66 1 11.14 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . H 5 21.291 47.047 191.866 1 16.1 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . H 5 21.053 47.237 193.303 1 16.99 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . H 5 20.579 47.612 190.686 1 6.11 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . H 5 22.706 45.676 190.273 1 10.66 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . H 5 22.037 44.455 189.586 1 42.29 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . H 5 20.83 44.825 188.717 1 55.96 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . H 5 21.03 45.325 187.581 1 66.47 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . H 5 19.681 44.609 189.17 1 64.78 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . H 5 20.055 48.505 195.178 1 8.39 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . H 5 19.349 49.73 195.683 1 8.96 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . H 5 19.43 49.686 197.039 1 7.58 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . H 5 20.259 48.441 197.341 1 14.94 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . H 5 18.663 50.833 194.873 1 13.34 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . H 5 18.765 50.532 197.963 1 11.28 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . H 5 18.363 51.934 197.857 1 11.42 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . H 5 21.338 46.825 198.804 1 18.09 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . H 5 21.709 46.356 200.075 1 15.98 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . H 5 22.592 45.38 199.923 1 21.8 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . H 5 22.711 45.151 198.55 1 20.97 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . H 5 21.132 46.875 201.363 1 15.42 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . H 5 23.269 44.716 200.876 1 21 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . H 5 22.574 43.614 201.413 1 23.44 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . H 5 23.656 43.91 196.665 1 16.86 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . H 5 24.647 43.011 196.116 1 17.47 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . H 5 24.648 43.18 194.787 1 15.16 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . H 5 23.652 44.186 194.54 1 16.7 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . H 5 25.669 42.235 196.926 1 12.7 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . H 5 25.608 42.599 193.762 1 19.49 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . H 5 26.672 43.594 193.319 1 20.23 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . H 5 27.63 43.052 192.25 1 16.23 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . H 5 27.779 41.818 192.114 1 20.61 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . H 5 28.258 43.875 191.549 1 28.91 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . H 5 21.923 46.481 194.031 1 11.08 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . H 5 20.69 47.788 196.171 1 12.95 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . H 5 21.991 46.093 197.831 1 16.32 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . H 5 23.113 44.718 195.689 1 17.22 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . H 5 22.007 46.34 195.911 1 15.1 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #