data_1PGF # _model_server_result.job_id qSF2iXsJnfBd_CB8Ty3k0A _model_server_result.datetime_utc '2024-11-24 01:04:23' _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 1pgf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":601}' # _entry.id 1PGF # _exptl.entry_id 1PGF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 4 _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 1PGF _cell.length_a 99.22 _cell.length_b 208.99 _cell.length_c 232.43 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PGF _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 _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 ? 4 G N N ? 4 K 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 13 A CYS 37 1_555 A SG CYS 135 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 17 A CYS 41 1_555 A SG CYS 33 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf4 A SG CYS 35 A CYS 59 1_555 A SG CYS 45 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf5 A SG CYS 545 A CYS 569 1_555 A SG CYS 551 A CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf6 B SG CYS 12 B CYS 36 1_555 B SG CYS 23 B CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 13 B CYS 37 1_555 B SG CYS 135 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 17 B CYS 41 1_555 B SG CYS 33 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf9 B SG CYS 35 B CYS 59 1_555 B SG CYS 45 B CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf10 B SG CYS 545 B CYS 569 1_555 B SG CYS 551 B CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? covale ? covale1 A ND2 ASN 44 A ASN 68 1_555 E C1 NAG . A NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 120 A ASN 144 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 386 A ASN 410 1_555 F C1 NAG . A NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale4 B ND2 ASN 44 B ASN 68 1_555 I C1 NAG . B NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 B ND2 ASN 120 B ASN 144 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 B ND2 ASN 386 B ASN 410 1_555 J C1 NAG . B NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? metalc ? metalc1 A NE2 HIS 364 A HIS 388 1_555 G FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc2 B NE2 HIS 364 B HIS 388 1_555 K FE HEM . B HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? # _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 1PGF _atom_sites.fract_transf_matrix[1][1] 0.010079 _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] 0.004785 _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] 0.004302 _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 HEM A 1 601 601 HEM HEM . H 5 IMM A 1 800 800 IMM IMM . I 3 NAG B 1 661 661 NAG NAG . J 3 NAG B 1 681 681 NAG NAG . K 4 HEM B 1 601 601 HEM HEM . L 5 IMM B 1 800 800 IMM IMM . # 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 . . . K 4 70.235 36.25 182.111 1 17.1 ? CHA HEM 601 B 1 HETATM 2 C CHB HEM . . . K 4 73.295 35.146 178.674 1 12.18 ? CHB HEM 601 B 1 HETATM 3 C CHC HEM . . . K 4 73.395 30.659 180.005 1 18.35 ? CHC HEM 601 B 1 HETATM 4 C CHD HEM . . . K 4 70.787 31.893 183.79 1 18.9 ? CHD HEM 601 B 1 HETATM 5 C C1A HEM . . . K 4 71.164 36.332 181.155 1 13.01 ? C1A HEM 601 B 1 HETATM 6 C C2A HEM . . . K 4 71.439 37.637 180.582 1 12.48 ? C2A HEM 601 B 1 HETATM 7 C C3A HEM . . . K 4 72.199 37.279 179.524 1 17.44 ? C3A HEM 601 B 1 HETATM 8 C C4A HEM . . . K 4 72.46 35.832 179.554 1 18.33 ? C4A HEM 601 B 1 HETATM 9 C CMA HEM . . . K 4 72.431 38.211 178.343 1 7.45 ? CMA HEM 601 B 1 HETATM 10 C CAA HEM . . . K 4 70.735 38.983 180.949 1 12 ? CAA HEM 601 B 1 HETATM 11 C CBA HEM . . . K 4 71.448 40.147 181.642 1 43.63 ? CBA HEM 601 B 1 HETATM 12 C CGA HEM . . . K 4 72.173 41.073 180.654 1 57.3 ? CGA HEM 601 B 1 HETATM 13 O O1A HEM . . . K 4 71.596 42.112 180.252 1 67.81 ? O1A HEM 601 B 1 HETATM 14 O O2A HEM . . . K 4 73.326 40.762 180.275 1 66.12 ? O2A HEM 601 B 1 HETATM 15 C C1B HEM . . . K 4 73.583 33.777 178.649 1 9.73 ? C1B HEM 601 B 1 HETATM 16 C C2B HEM . . . K 4 74.385 33.059 177.588 1 10.3 ? C2B HEM 601 B 1 HETATM 17 C C3B HEM . . . K 4 74.582 31.841 177.991 1 8.92 ? C3B HEM 601 B 1 HETATM 18 C C4B HEM . . . K 4 73.727 31.771 179.275 1 16.28 ? C4B HEM 601 B 1 HETATM 19 C CMB HEM . . . K 4 74.692 33.563 176.163 1 14.68 ? CMB HEM 601 B 1 HETATM 20 C CAB HEM . . . K 4 75.438 30.969 177.307 1 12.62 ? CAB HEM 601 B 1 HETATM 21 C CBB HEM . . . K 4 75.413 30.581 175.89 1 12.76 ? CBB HEM 601 B 1 HETATM 22 C C1C HEM . . . K 4 72.535 30.574 181.098 1 19.43 ? C1C HEM 601 B 1 HETATM 23 C C2C HEM . . . K 4 72.431 29.399 181.919 1 17.32 ? C2C HEM 601 B 1 HETATM 24 C C3C HEM . . . K 4 71.735 29.807 182.965 1 23.14 ? C3C HEM 601 B 1 HETATM 25 C C4C HEM . . . K 4 71.427 31.153 182.825 1 22.31 ? C4C HEM 601 B 1 HETATM 26 C CMC HEM . . . K 4 73.033 28.012 181.664 1 16.76 ? CMC HEM 601 B 1 HETATM 27 C CAC HEM . . . K 4 71.384 29.046 184.002 1 22.34 ? CAC HEM 601 B 1 HETATM 28 C CBC HEM . . . K 4 70.001 28.863 184.22 1 24.78 ? CBC HEM 601 B 1 HETATM 29 C C1D HEM . . . K 4 70.343 33.159 183.588 1 18.2 ? C1D HEM 601 B 1 HETATM 30 C C2D HEM . . . K 4 69.407 33.882 184.475 1 18.81 ? C2D HEM 601 B 1 HETATM 31 C C3D HEM . . . K 4 69.123 35.036 183.89 1 16.5 ? C3D HEM 601 B 1 HETATM 32 C C4D HEM . . . K 4 69.901 35.067 182.657 1 18.04 ? C4D HEM 601 B 1 HETATM 33 C CMD HEM . . . K 4 68.839 33.476 185.801 1 14.04 ? CMD HEM 601 B 1 HETATM 34 C CAD HEM . . . K 4 68.221 36.132 184.421 1 20.83 ? CAD HEM 601 B 1 HETATM 35 C CBD HEM . . . K 4 66.946 36.18 183.592 1 21.57 ? CBD HEM 601 B 1 HETATM 36 C CGD HEM . . . K 4 66.208 37.519 183.666 1 17.57 ? CGD HEM 601 B 1 HETATM 37 O O1D HEM . . . K 4 66.815 38.486 184.201 1 21.95 ? O1D HEM 601 B 1 HETATM 38 O O2D HEM . . . K 4 65.042 37.596 183.176 1 30.25 ? O2D HEM 601 B 1 HETATM 39 N NA HEM . . . K 4 71.794 35.243 180.541 1 12.42 ? NA HEM 601 B 1 HETATM 40 N NB HEM . . . K 4 73.133 32.951 179.605 1 14.29 ? NB HEM 601 B 1 HETATM 41 N NC HEM . . . K 4 71.896 31.627 181.637 1 17.66 ? NC HEM 601 B 1 HETATM 42 N ND HEM . . . K 4 70.624 33.883 182.423 1 18.56 ? ND HEM 601 B 1 HETATM 43 FE FE HEM . . . K 4 71.852 33.382 180.943 1 16.44 ? FE HEM 601 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #