data_2OYU # _model_server_result.job_id DjyIvLDgW7JyraO_WqjY_g _model_server_result.datetime_utc '2024-10-30 08:18:03' _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 2oyu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":601}' # _entry.id 2OYU # _exptl.entry_id 2OYU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 6 _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 2OYU _cell.length_a 181.41 _cell.length_b 181.41 _cell.length_c 103.398 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2OYU _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 7_555 y,x,-z+2/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 68.932 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG 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 NAG 1 A 1 NAG S 661 NAG 2 n B NAG 2 A 2 NAG S 662 NAG 3 n C NAG 1 B 1 NAG S 671 NAG 3 n C NAG 2 B 2 NAG S 672 NAG 3 n C BMA 3 B 3 BMA S 673 BMA 2 n D NAG 1 C 1 NAG S 681 NAG 2 n D NAG 2 C 2 NAG S 682 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 36 P CYS 36 1_555 A SG CYS 47 P CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf2 A SG CYS 37 P CYS 37 1_555 A SG CYS 159 P CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf3 A SG CYS 41 P CYS 41 1_555 A SG CYS 57 P CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 A SG CYS 59 P CYS 59 1_555 A SG CYS 69 P CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf5 A SG CYS 569 P CYS 569 1_555 A SG CYS 575 P CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? covale ? covale1 A ND2 ASN 68 P ASN 68 1_555 B C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 A ND2 ASN 144 P ASN 144 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale3 A ND2 ASN 410 P ASN 410 1_555 D C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale4 B O4 NAG . A NAG 1 1_555 B C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale6 C O4 NAG . B NAG 2 1_555 C C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale7 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? metalc ? metalc1 A NE2 HIS 388 P HIS 388 1_555 H FE HEM . P HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? # _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 201 n n CHA C4D HEM doub 202 n n CHA HHA HEM sing 203 n n CHB C4A HEM sing 204 n n CHB C1B HEM doub 205 n n CHB HHB HEM sing 206 n n CHC C4B HEM sing 207 n n CHC C1C HEM doub 208 n n CHC HHC HEM sing 209 n n CHD C4C HEM doub 210 n n CHD C1D HEM sing 211 n n CHD HHD HEM sing 212 n n C1A C2A HEM doub 213 n y C1A NA HEM sing 214 n y C2A C3A HEM sing 215 n y C2A CAA HEM sing 216 n n C3A C4A HEM doub 217 n y C3A CMA HEM sing 218 n n C4A NA HEM sing 219 n y CMA HMA HEM sing 220 n n CMA HMAA HEM sing 221 n n CMA HMAB HEM sing 222 n n CAA CBA HEM sing 223 n n CAA HAA HEM sing 224 n n CAA HAAA HEM sing 225 n n CBA CGA HEM sing 226 n n CBA HBA HEM sing 227 n n CBA HBAA HEM sing 228 n n CGA O1A HEM doub 229 n n CGA O2A HEM sing 230 n n C1B C2B HEM sing 231 n n C1B NB HEM sing 232 n n C2B C3B HEM doub 233 n n C2B CMB HEM sing 234 n n C3B C4B HEM sing 235 n n C3B CAB HEM sing 236 n n C4B NB HEM doub 237 n n CMB HMB HEM sing 238 n n CMB HMBA HEM sing 239 n n CMB HMBB HEM sing 240 n n CAB CBB HEM doub 241 n n CAB HAB HEM sing 242 n n CBB HBB HEM sing 243 n n CBB HBBA HEM sing 244 n n C1C C2C HEM sing 245 n y C1C NC HEM sing 246 n y C2C C3C HEM doub 247 n y C2C CMC HEM sing 248 n n C3C C4C HEM sing 249 n y C3C CAC HEM sing 250 n n C4C NC HEM sing 251 n y CMC HMC HEM sing 252 n n CMC HMCA HEM sing 253 n n CMC HMCB HEM sing 254 n n CAC CBC HEM doub 255 n n CAC HAC HEM sing 256 n n CBC HBC HEM sing 257 n n CBC HBCA HEM sing 258 n n C1D C2D HEM sing 259 n n C1D ND HEM doub 260 n n C2D C3D HEM doub 261 n n C2D CMD HEM sing 262 n n C3D C4D HEM sing 263 n n C3D CAD HEM sing 264 n n C4D ND HEM sing 265 n n CMD HMD HEM sing 266 n n CMD HMDA HEM sing 267 n n CMD HMDB HEM sing 268 n n CAD CBD HEM sing 269 n n CAD HAD HEM sing 270 n n CAD HADA HEM sing 271 n n CBD CGD HEM sing 272 n n CBD HBD HEM sing 273 n n CBD HBDA HEM sing 274 n n CGD O1D HEM doub 275 n n CGD O2D HEM sing 276 n n O2A H2A HEM sing 277 n n O2D H2D HEM sing 278 n n FE NA HEM sing 279 n n FE NB HEM sing 280 n n FE NC HEM sing 281 n n FE ND HEM sing 282 n n # _atom_sites.entry_id 2OYU _atom_sites.fract_transf_matrix[1][1] 0.005512 _atom_sites.fract_transf_matrix[1][2] 0.003183 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006365 _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] 0.009671 _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 4 BOG P 1 750 750 BOG BOG . F 4 BOG P 1 751 751 BOG BOG . G 5 IMS P 1 700 700 IMS IMS . H 6 HEM P 1 601 601 HEM HEM . I 7 HOH P 1 752 1 HOH HOH . I 7 HOH P 2 753 2 HOH HOH . I 7 HOH P 3 754 3 HOH HOH . I 7 HOH P 4 755 4 HOH HOH . I 7 HOH P 5 756 5 HOH HOH . I 7 HOH P 6 757 6 HOH HOH . I 7 HOH P 7 758 7 HOH HOH . I 7 HOH P 8 759 8 HOH HOH . I 7 HOH P 9 760 9 HOH HOH . I 7 HOH P 10 761 10 HOH HOH . I 7 HOH P 11 762 11 HOH HOH . I 7 HOH P 12 763 12 HOH HOH . I 7 HOH P 13 764 13 HOH HOH . I 7 HOH P 14 765 14 HOH HOH . I 7 HOH P 15 766 15 HOH HOH . I 7 HOH P 16 767 16 HOH HOH . I 7 HOH P 17 768 17 HOH HOH . I 7 HOH P 18 769 18 HOH HOH . I 7 HOH P 19 770 19 HOH HOH . I 7 HOH P 20 771 20 HOH HOH . I 7 HOH P 21 772 21 HOH HOH . I 7 HOH P 22 773 22 HOH HOH . I 7 HOH P 23 774 23 HOH HOH . I 7 HOH P 24 775 24 HOH HOH . I 7 HOH P 25 776 25 HOH HOH . I 7 HOH P 26 777 26 HOH HOH . I 7 HOH P 27 778 27 HOH HOH . I 7 HOH P 28 779 28 HOH HOH . I 7 HOH P 29 780 29 HOH HOH . I 7 HOH P 30 781 30 HOH HOH . I 7 HOH P 31 782 31 HOH HOH . I 7 HOH P 32 783 32 HOH HOH . I 7 HOH P 33 784 33 HOH HOH . I 7 HOH P 34 785 34 HOH HOH . I 7 HOH P 35 786 35 HOH HOH . I 7 HOH P 36 787 36 HOH HOH . I 7 HOH P 37 788 37 HOH HOH . I 7 HOH P 38 789 38 HOH HOH . I 7 HOH P 39 790 39 HOH HOH . I 7 HOH P 40 791 40 HOH HOH . I 7 HOH P 41 792 41 HOH HOH . I 7 HOH P 42 793 42 HOH HOH . I 7 HOH P 43 794 43 HOH HOH . I 7 HOH P 44 795 44 HOH HOH . I 7 HOH P 45 796 45 HOH HOH . I 7 HOH P 46 797 46 HOH HOH . I 7 HOH P 47 798 47 HOH HOH . I 7 HOH P 48 799 48 HOH HOH . I 7 HOH P 49 800 49 HOH HOH . I 7 HOH P 50 801 50 HOH HOH . I 7 HOH P 51 802 51 HOH HOH . I 7 HOH P 52 803 52 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 6 32.956 65.997 10.286 1 49.7 ? CHA HEM 601 P 1 HETATM 2 C CHB HEM . . . H 6 30.919 69.138 7.267 1 50.61 ? CHB HEM 601 P 1 HETATM 3 C CHC HEM . . . H 6 26.622 66.863 7.478 1 50.26 ? CHC HEM 601 P 1 HETATM 4 C CHD HEM . . . H 6 28.588 63.861 10.714 1 48.54 ? CHD HEM 601 P 1 HETATM 5 C C1A HEM . . . H 6 32.749 67.11 9.526 1 50.76 ? C1A HEM 601 P 1 HETATM 6 C C2A HEM . . . H 6 33.648 68.241 9.404 1 51.23 ? C2A HEM 601 P 1 HETATM 7 C C3A HEM . . . H 6 33.073 69.114 8.569 1 51.79 ? C3A HEM 601 P 1 HETATM 8 C C4A HEM . . . H 6 31.802 68.555 8.138 1 51.2 ? C4A HEM 601 P 1 HETATM 9 C CMA HEM . . . H 6 33.644 70.484 8.114 1 51.04 ? CMA HEM 601 P 1 HETATM 10 C CAA HEM . . . H 6 35.003 68.405 10.126 1 51.16 ? CAA HEM 601 P 1 HETATM 11 C CBA HEM . . . H 6 36.153 68.004 9.211 1 53.47 ? CBA HEM 601 P 1 HETATM 12 C CGA HEM . . . H 6 37.375 67.679 10.042 1 55.76 ? CGA HEM 601 P 1 HETATM 13 O O1A HEM . . . H 6 38.342 67.055 9.514 1 56.38 ? O1A HEM 601 P 1 HETATM 14 O O2A HEM . . . H 6 37.391 68.046 11.251 1 57.17 ? O2A HEM 601 P 1 HETATM 15 C C1B HEM . . . H 6 29.592 68.826 7.137 1 50.9 ? C1B HEM 601 P 1 HETATM 16 C C2B HEM . . . H 6 28.618 69.674 6.497 1 51.74 ? C2B HEM 601 P 1 HETATM 17 C C3B HEM . . . H 6 27.427 69.065 6.55 1 51.45 ? C3B HEM 601 P 1 HETATM 18 C C4B HEM . . . H 6 27.609 67.795 7.224 1 51.04 ? C4B HEM 601 P 1 HETATM 19 C CMB HEM . . . H 6 28.937 71.055 5.884 1 51.66 ? CMB HEM 601 P 1 HETATM 20 C CAB HEM . . . H 6 26.079 69.598 6.006 1 51.29 ? CAB HEM 601 P 1 HETATM 21 C CBB HEM . . . H 6 25.997 70.392 4.936 1 51.16 ? CBB HEM 601 P 1 HETATM 22 C C1C HEM . . . H 6 26.793 65.775 8.303 1 50.12 ? C1C HEM 601 P 1 HETATM 23 C C2C HEM . . . H 6 25.903 64.645 8.47 1 49.4 ? C2C HEM 601 P 1 HETATM 24 C C3C HEM . . . H 6 26.461 63.815 9.367 1 49.43 ? C3C HEM 601 P 1 HETATM 25 C C4C HEM . . . H 6 27.72 64.392 9.793 1 49.38 ? C4C HEM 601 P 1 HETATM 26 C CMC HEM . . . H 6 24.562 64.45 7.726 1 48.28 ? CMC HEM 601 P 1 HETATM 27 C CAC HEM . . . H 6 25.892 62.461 9.864 1 50.11 ? CAC HEM 601 P 1 HETATM 28 C CBC HEM . . . H 6 25.428 62.295 11.105 1 49.72 ? CBC HEM 601 P 1 HETATM 29 C C1D HEM . . . H 6 29.894 64.223 10.961 1 49.04 ? C1D HEM 601 P 1 HETATM 30 C C2D HEM . . . H 6 30.692 63.698 12.05 1 48.91 ? C2D HEM 601 P 1 HETATM 31 C C3D HEM . . . H 6 32.069 64.365 11.927 1 47.82 ? C3D HEM 601 P 1 HETATM 32 C C4D HEM . . . H 6 31.95 65.216 10.767 1 48.75 ? C4D HEM 601 P 1 HETATM 33 C CMD HEM . . . H 6 30.224 62.678 13.109 1 49.36 ? CMD HEM 601 P 1 HETATM 34 C CAD HEM . . . H 6 33.317 64.177 12.825 1 45.25 ? CAD HEM 601 P 1 HETATM 35 C CBD HEM . . . H 6 33.126 64.932 14.135 1 41.55 ? CBD HEM 601 P 1 HETATM 36 C CGD HEM . . . H 6 34.302 64.811 15.082 1 40.35 ? CGD HEM 601 P 1 HETATM 37 O O1D HEM . . . H 6 34.268 65.558 16.09 1 39.9 ? O1D HEM 601 P 1 HETATM 38 O O2D HEM . . . H 6 35.256 64.003 14.873 1 38.35 ? O2D HEM 601 P 1 HETATM 39 N NA HEM . . . H 6 31.632 67.326 8.741 1 50.8 ? NA HEM 601 P 1 HETATM 40 N NB HEM . . . H 6 28.946 67.685 7.566 1 50.43 ? NB HEM 601 P 1 HETATM 41 N NC HEM . . . H 6 27.889 65.585 9.125 1 50.29 ? NC HEM 601 P 1 HETATM 42 N ND HEM . . . H 6 30.668 65.117 10.228 1 49.46 ? ND HEM 601 P 1 HETATM 43 FE FE HEM . . . H 6 29.74 66.277 8.687 1 49.9 ? FE HEM 601 P 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #