data_4Y8W # _model_server_result.job_id 7_zLeLXhm1nBZwSDspyk5g _model_server_result.datetime_utc '2024-12-02 20:18:16' _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 4y8w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":602}' # _entry.id 4Y8W # _exptl.entry_id 4Y8W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.11 _cell.angle_gamma 90 _cell.entry_id 4Y8W _cell.length_a 150.383 _cell.length_b 86.86 _cell.length_c 108.923 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y8W _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,N 1 1 B,H,I,J,O 2 1 C,K,L,M,P 3 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 ? 3 F N N ? 3 I N N ? 3 L N N # 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 D S SO4 . A SO4 601 1_555 E O2 SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 D S SO4 . A SO4 601 1_555 E O4 SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.568 ? covale ? covale3 D S SO4 . A SO4 601 1_555 E O3 SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.66 ? covale ? covale4 D O2 SO4 . A SO4 601 1_555 E S SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale5 D O3 SO4 . A SO4 601 1_555 E S SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.668 ? covale ? covale6 D O4 SO4 . A SO4 601 1_555 E S SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.578 ? metalc ? metalc1 A SG CYS 410 A CYS 429 1_555 F FE HEM . A HEM 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc2 B SG CYS 410 B CYS 429 1_555 I FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc3 C SG CYS 410 C CYS 429 1_555 L FE HEM . C HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? # _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 4Y8W _atom_sites.fract_transf_matrix[1][1] 0.00665 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001427 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011513 _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] 0.00939 _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 D 2 SO4 A 1 601 3 SO4 SO4 . E 2 SO4 A 1 602 4 SO4 SO4 . F 3 HEM A 1 603 500 HEM HEM . G 4 STR A 1 604 501 STR STR . H 2 SO4 B 1 601 2 SO4 SO4 . I 3 HEM B 1 602 500 HEM HEM . J 4 STR B 1 603 501 STR STR . K 2 SO4 C 1 601 1 SO4 SO4 . L 3 HEM C 1 602 500 HEM HEM . M 4 STR C 1 603 501 STR STR . N 5 HOH A 1 701 39 HOH HOH . N 5 HOH A 2 702 56 HOH HOH . N 5 HOH A 3 703 73 HOH HOH . N 5 HOH A 4 704 69 HOH HOH . N 5 HOH A 5 705 70 HOH HOH . N 5 HOH A 6 706 29 HOH HOH . N 5 HOH A 7 707 45 HOH HOH . N 5 HOH A 8 708 32 HOH HOH . N 5 HOH A 9 709 55 HOH HOH . N 5 HOH A 10 710 21 HOH HOH . N 5 HOH A 11 711 2 HOH HOH . N 5 HOH A 12 712 42 HOH HOH . N 5 HOH A 13 713 72 HOH HOH . N 5 HOH A 14 714 68 HOH HOH . N 5 HOH A 15 715 4 HOH HOH . N 5 HOH A 16 716 1 HOH HOH . N 5 HOH A 17 717 81 HOH HOH . N 5 HOH A 18 718 51 HOH HOH . N 5 HOH A 19 719 71 HOH HOH . N 5 HOH A 20 720 3 HOH HOH . N 5 HOH A 21 721 40 HOH HOH . N 5 HOH A 22 722 54 HOH HOH . O 5 HOH B 1 701 37 HOH HOH . O 5 HOH B 2 702 64 HOH HOH . O 5 HOH B 3 703 67 HOH HOH . O 5 HOH B 4 704 47 HOH HOH . O 5 HOH B 5 705 65 HOH HOH . O 5 HOH B 6 706 49 HOH HOH . O 5 HOH B 7 707 36 HOH HOH . O 5 HOH B 8 708 80 HOH HOH . O 5 HOH B 9 709 50 HOH HOH . O 5 HOH B 10 710 22 HOH HOH . O 5 HOH B 11 711 44 HOH HOH . O 5 HOH B 12 712 43 HOH HOH . O 5 HOH B 13 713 62 HOH HOH . O 5 HOH B 14 714 79 HOH HOH . O 5 HOH B 15 715 31 HOH HOH . O 5 HOH B 16 716 66 HOH HOH . O 5 HOH B 17 717 20 HOH HOH . O 5 HOH B 18 718 24 HOH HOH . O 5 HOH B 19 719 25 HOH HOH . O 5 HOH B 20 720 19 HOH HOH . O 5 HOH B 21 721 61 HOH HOH . O 5 HOH B 22 722 26 HOH HOH . O 5 HOH B 23 723 38 HOH HOH . O 5 HOH B 24 724 63 HOH HOH . O 5 HOH B 25 725 30 HOH HOH . P 5 HOH C 1 701 60 HOH HOH . P 5 HOH C 2 702 52 HOH HOH . P 5 HOH C 3 703 11 HOH HOH . P 5 HOH C 4 704 59 HOH HOH . P 5 HOH C 5 705 7 HOH HOH . P 5 HOH C 6 706 77 HOH HOH . P 5 HOH C 7 707 34 HOH HOH . P 5 HOH C 8 708 41 HOH HOH . P 5 HOH C 9 709 5 HOH HOH . P 5 HOH C 10 710 74 HOH HOH . P 5 HOH C 11 711 6 HOH HOH . P 5 HOH C 12 712 9 HOH HOH . P 5 HOH C 13 713 14 HOH HOH . P 5 HOH C 14 714 28 HOH HOH . P 5 HOH C 15 715 8 HOH HOH . P 5 HOH C 16 716 78 HOH HOH . P 5 HOH C 17 717 15 HOH HOH . P 5 HOH C 18 718 53 HOH HOH . P 5 HOH C 19 719 13 HOH HOH . P 5 HOH C 20 720 12 HOH HOH . P 5 HOH C 21 721 27 HOH HOH . P 5 HOH C 22 722 75 HOH HOH . P 5 HOH C 23 723 17 HOH HOH . P 5 HOH C 24 724 18 HOH HOH . P 5 HOH C 25 725 58 HOH HOH . P 5 HOH C 26 726 16 HOH HOH . P 5 HOH C 27 727 57 HOH HOH . P 5 HOH C 28 728 46 HOH HOH . P 5 HOH C 29 729 76 HOH HOH . P 5 HOH C 30 730 48 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 . . . I 3 -36.378 50.79 30.996 1 27.61 ? CHA HEM 602 B 1 HETATM 2 C CHB HEM . . . I 3 -32.806 48.648 28.557 1 27.19 ? CHB HEM 602 B 1 HETATM 3 C CHC HEM . . . I 3 -34.481 50.586 24.409 1 27.96 ? CHC HEM 602 B 1 HETATM 4 C CHD HEM . . . I 3 -38.002 52.812 26.893 1 27.63 ? CHD HEM 602 B 1 HETATM 5 C C1A HEM . . . I 3 -35.269 50.048 30.683 1 27.39 ? C1A HEM 602 B 1 HETATM 6 C C2A HEM . . . I 3 -34.471 49.364 31.632 1 27.56 ? C2A HEM 602 B 1 HETATM 7 C C3A HEM . . . I 3 -33.46 48.763 30.939 1 27.22 ? C3A HEM 602 B 1 HETATM 8 C C4A HEM . . . I 3 -33.642 49.066 29.572 1 27.15 ? C4A HEM 602 B 1 HETATM 9 C CMA HEM . . . I 3 -32.355 47.909 31.511 1 26.63 ? CMA HEM 602 B 1 HETATM 10 C CAA HEM . . . I 3 -34.691 49.332 33.135 1 27.71 ? CAA HEM 602 B 1 HETATM 11 C CBA HEM . . . I 3 -35.317 48.037 33.659 1 28.24 ? CBA HEM 602 B 1 HETATM 12 C CGA HEM . . . I 3 -35.545 48.105 35.154 1 28.66 ? CGA HEM 602 B 1 HETATM 13 O O1A HEM . . . I 3 -35.62 49.206 35.757 1 29.11 ? O1A HEM 602 B 1 HETATM 14 O O2A HEM . . . I 3 -35.668 47.043 35.805 1 28.42 ? O2A HEM 602 B 1 HETATM 15 C C1B HEM . . . I 3 -32.968 49 27.212 1 27.72 ? C1B HEM 602 B 1 HETATM 16 C C2B HEM . . . I 3 -32.091 48.517 26.192 1 28.19 ? C2B HEM 602 B 1 HETATM 17 C C3B HEM . . . I 3 -32.538 49.052 25.003 1 28.39 ? C3B HEM 602 B 1 HETATM 18 C C4B HEM . . . I 3 -33.726 49.879 25.353 1 28.33 ? C4B HEM 602 B 1 HETATM 19 C CMB HEM . . . I 3 -30.905 47.595 26.423 1 27.71 ? CMB HEM 602 B 1 HETATM 20 C CAB HEM . . . I 3 -32.007 48.889 23.627 1 29.03 ? CAB HEM 602 B 1 HETATM 21 C CBB HEM . . . I 3 -31.306 47.831 23.215 1 29.98 ? CBB HEM 602 B 1 HETATM 22 C C1C HEM . . . I 3 -35.636 51.319 24.697 1 27.75 ? C1C HEM 602 B 1 HETATM 23 C C2C HEM . . . I 3 -36.516 51.886 23.747 1 27.87 ? C2C HEM 602 B 1 HETATM 24 C C3C HEM . . . I 3 -37.535 52.531 24.465 1 27.55 ? C3C HEM 602 B 1 HETATM 25 C C4C HEM . . . I 3 -37.246 52.336 25.85 1 27.6 ? C4C HEM 602 B 1 HETATM 26 C CMC HEM . . . I 3 -36.346 51.792 22.239 1 27.49 ? CMC HEM 602 B 1 HETATM 27 C CAC HEM . . . I 3 -38.702 53.301 23.957 1 27.44 ? CAC HEM 602 B 1 HETATM 28 C CBC HEM . . . I 3 -39.428 52.965 22.893 1 27.3 ? CBC HEM 602 B 1 HETATM 29 C C1D HEM . . . I 3 -37.818 52.402 28.218 1 27.53 ? C1D HEM 602 B 1 HETATM 30 C C2D HEM . . . I 3 -38.731 52.847 29.286 1 27.53 ? C2D HEM 602 B 1 HETATM 31 C C3D HEM . . . I 3 -38.282 52.282 30.428 1 27.47 ? C3D HEM 602 B 1 HETATM 32 C C4D HEM . . . I 3 -37.095 51.5 30.042 1 27.49 ? C4D HEM 602 B 1 HETATM 33 C CMD HEM . . . I 3 -39.927 53.762 29.123 1 27.57 ? CMD HEM 602 B 1 HETATM 34 C CAD HEM . . . I 3 -38.86 52.421 31.823 1 27.59 ? CAD HEM 602 B 1 HETATM 35 C CBD HEM . . . I 3 -39.898 51.321 32.094 1 28.34 ? CBD HEM 602 B 1 HETATM 36 C CGD HEM . . . I 3 -40.419 51.3 33.525 1 29.27 ? CGD HEM 602 B 1 HETATM 37 O O1D HEM . . . I 3 -39.931 52.015 34.436 1 29.7 ? O1D HEM 602 B 1 HETATM 38 O O2D HEM . . . I 3 -41.37 50.541 33.825 1 29.69 ? O2D HEM 602 B 1 HETATM 39 N NA HEM . . . I 3 -34.723 49.899 29.432 1 27.51 ? NA HEM 602 B 1 HETATM 40 N NB HEM . . . I 3 -33.907 49.801 26.684 1 28.12 ? NB HEM 602 B 1 HETATM 41 N NC HEM . . . I 3 -36.096 51.601 25.959 1 27.51 ? NC HEM 602 B 1 HETATM 42 N ND HEM . . . I 3 -36.853 51.606 28.719 1 27.41 ? ND HEM 602 B 1 HETATM 43 FE FE HEM . . . I 3 -35.452 50.764 27.768 1 27.3 ? FE HEM 602 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #