data_6VBN # _model_server_result.job_id CnIY0d8QVYFRulXAPcmwpQ _model_server_result.datetime_utc '2025-01-03 00:16:42' _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 6vbn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 6VBN # _exptl.entry_id 6VBN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 4 _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 6VBN _cell.length_a 78.475 _cell.length_b 143.044 _cell.length_c 147.236 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VBN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,P _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 ? 2 E N N ? 2 G N N ? 2 I N N ? 2 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 metalc ? metalc1 A NE2 HIS 314 A HIS 328 1_555 E FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc2 E FE HEM . A HEM 401 1_555 F N9 QVY . A QVY 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc3 B NE2 HIS 314 B HIS 328 1_555 G FE HEM . B HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc4 G FE HEM . B HEM 401 1_555 H N9 QVY . B QVY 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc5 C NE2 HIS 314 C HIS 328 1_555 I FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc6 I FE HEM . C HEM 401 1_555 K N9 QVY . C QVY 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc7 J N9 QVY . C QVY 402 1_555 L FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc8 D NE2 HIS 314 D HIS 328 1_555 L FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _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 6VBN _atom_sites.fract_transf_matrix[1][1] 0.012743 _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] 0.006991 _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] 0.006792 _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 2 HEM A 1 401 401 HEM HEM . F 3 QVY A 1 402 1 QVY DRG . G 2 HEM B 1 401 401 HEM HEM . H 3 QVY B 1 402 1 QVY DRG . I 2 HEM C 1 401 401 HEM HEM . J 3 QVY C 1 402 1 QVY DRG . K 3 QVY C 1 403 1 QVY DRG . L 2 HEM D 1 401 401 HEM HEM . M 4 HOH A 1 501 49 HOH HOH . M 4 HOH A 2 502 48 HOH HOH . M 4 HOH A 3 503 50 HOH HOH . M 4 HOH A 4 504 1 HOH HOH . M 4 HOH A 5 505 55 HOH HOH . M 4 HOH A 6 506 54 HOH HOH . M 4 HOH A 7 507 3 HOH HOH . M 4 HOH A 8 508 16 HOH HOH . M 4 HOH A 9 509 21 HOH HOH . M 4 HOH A 10 510 40 HOH HOH . M 4 HOH A 11 511 43 HOH HOH . M 4 HOH A 12 512 38 HOH HOH . M 4 HOH A 13 513 58 HOH HOH . N 4 HOH B 1 501 33 HOH HOH . N 4 HOH B 2 502 28 HOH HOH . N 4 HOH B 3 503 25 HOH HOH . N 4 HOH B 4 504 51 HOH HOH . N 4 HOH B 5 505 47 HOH HOH . N 4 HOH B 6 506 7 HOH HOH . N 4 HOH B 7 507 45 HOH HOH . N 4 HOH B 8 508 57 HOH HOH . N 4 HOH B 9 509 24 HOH HOH . N 4 HOH B 10 510 56 HOH HOH . N 4 HOH B 11 511 60 HOH HOH . N 4 HOH B 12 512 59 HOH HOH . O 4 HOH C 1 501 5 HOH HOH . O 4 HOH C 2 502 22 HOH HOH . O 4 HOH C 3 503 27 HOH HOH . O 4 HOH C 4 504 46 HOH HOH . P 4 HOH D 1 501 6 HOH HOH . P 4 HOH D 2 502 44 HOH HOH . P 4 HOH D 3 503 53 HOH HOH . P 4 HOH D 4 504 52 HOH HOH . P 4 HOH D 5 505 4 HOH HOH . P 4 HOH D 6 506 20 HOH HOH . P 4 HOH D 7 507 12 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 . . . E 2 13.613 -16.115 -2.744 1 99.39 ? CHA HEM 401 A 1 HETATM 2 C CHB HEM . . . E 2 18.032 -15.265 -1.05 1 98.88 ? CHB HEM 401 A 1 HETATM 3 C CHC HEM . . . E 2 17.726 -10.748 -2.579 1 98.7 ? CHC HEM 401 A 1 HETATM 4 C CHD HEM . . . E 2 13.147 -11.477 -3.801 1 99.24 ? CHD HEM 401 A 1 HETATM 5 C C1A HEM . . . E 2 14.874 -16.279 -2.185 1 98.83 ? C1A HEM 401 A 1 HETATM 6 C C2A HEM . . . E 2 15.396 -17.502 -1.658 1 99.22 ? C2A HEM 401 A 1 HETATM 7 C C3A HEM . . . E 2 16.613 -17.256 -1.143 1 99.12 ? C3A HEM 401 A 1 HETATM 8 C C4A HEM . . . E 2 16.876 -15.892 -1.396 1 98.61 ? C4A HEM 401 A 1 HETATM 9 C CMA HEM . . . E 2 17.536 -18.25 -0.538 1 100.08 ? CMA HEM 401 A 1 HETATM 10 C CAA HEM . . . E 2 14.667 -18.799 -1.626 1 100.62 ? CAA HEM 401 A 1 HETATM 11 C CBA HEM . . . E 2 13.557 -18.668 -0.576 1 101.82 ? CBA HEM 401 A 1 HETATM 12 C CGA HEM . . . E 2 14.033 -18.212 0.807 1 103.28 ? CGA HEM 401 A 1 HETATM 13 O O1A HEM . . . E 2 13.853 -17.07 1.104 1 104.72 ? O1A HEM 401 A 1 HETATM 14 O O2A HEM . . . E 2 14.632 -19.027 1.702 1 104.1 ? O2A HEM 401 A 1 HETATM 15 C C1B HEM . . . E 2 18.306 -13.939 -1.334 1 98.42 ? C1B HEM 401 A 1 HETATM 16 C C2B HEM . . . E 2 19.599 -13.391 -1.062 1 98.54 ? C2B HEM 401 A 1 HETATM 17 C C3B HEM . . . E 2 19.549 -12.114 -1.498 1 98.69 ? C3B HEM 401 A 1 HETATM 18 C C4B HEM . . . E 2 18.167 -11.926 -2.034 1 98.18 ? C4B HEM 401 A 1 HETATM 19 C CMB HEM . . . E 2 20.755 -14.137 -0.436 1 100.16 ? CMB HEM 401 A 1 HETATM 20 C CAB HEM . . . E 2 20.604 -11.1 -1.466 1 99.79 ? CAB HEM 401 A 1 HETATM 21 C CBB HEM . . . E 2 21.224 -10.824 -0.331 1 99.2 ? CBB HEM 401 A 1 HETATM 22 C C1C HEM . . . E 2 16.453 -10.569 -3.051 1 97.95 ? C1C HEM 401 A 1 HETATM 23 C C2C HEM . . . E 2 15.938 -9.312 -3.463 1 98.68 ? C2C HEM 401 A 1 HETATM 24 C C3C HEM . . . E 2 14.623 -9.498 -3.793 1 98.78 ? C3C HEM 401 A 1 HETATM 25 C C4C HEM . . . E 2 14.363 -10.893 -3.572 1 98.43 ? C4C HEM 401 A 1 HETATM 26 C CMC HEM . . . E 2 16.702 -8.02 -3.522 1 100.02 ? CMC HEM 401 A 1 HETATM 27 C CAC HEM . . . E 2 13.664 -8.496 -4.305 1 99.74 ? CAC HEM 401 A 1 HETATM 28 C CBC HEM . . . E 2 12.586 -8.18 -3.576 1 101.63 ? CBC HEM 401 A 1 HETATM 29 C C1D HEM . . . E 2 12.907 -12.827 -3.613 1 98.78 ? C1D HEM 401 A 1 HETATM 30 C C2D HEM . . . E 2 11.624 -13.451 -4.013 1 99.16 ? C2D HEM 401 A 1 HETATM 31 C C3D HEM . . . E 2 11.778 -14.765 -3.836 1 99.27 ? C3D HEM 401 A 1 HETATM 32 C C4D HEM . . . E 2 13.145 -14.918 -3.266 1 98.81 ? C4D HEM 401 A 1 HETATM 33 C CMD HEM . . . E 2 10.45 -12.735 -4.582 1 100.67 ? CMD HEM 401 A 1 HETATM 34 C CAD HEM . . . E 2 10.824 -15.884 -4.156 1 100.2 ? CAD HEM 401 A 1 HETATM 35 C CBD HEM . . . E 2 11.291 -16.349 -5.568 1 101.61 ? CBD HEM 401 A 1 HETATM 36 C CGD HEM . . . E 2 10.518 -17.488 -6.23 1 103.27 ? CGD HEM 401 A 1 HETATM 37 O O1D HEM . . . E 2 10.512 -17.613 -7.465 1 103.73 ? O1D HEM 401 A 1 HETATM 38 O O2D HEM . . . E 2 9.835 -18.363 -5.455 1 104.07 ? O2D HEM 401 A 1 HETATM 39 N NA HEM . . . E 2 15.798 -15.263 -2.023 1 98.59 ? NA HEM 401 A 1 HETATM 40 N NB HEM . . . E 2 17.442 -13.068 -1.924 1 98.01 ? NB HEM 401 A 1 HETATM 41 N NC HEM . . . E 2 15.478 -11.546 -3.079 1 98.17 ? NC HEM 401 A 1 HETATM 42 N ND HEM . . . E 2 13.786 -13.733 -3.175 1 98.51 ? ND HEM 401 A 1 HETATM 43 FE FE HEM . . . E 2 15.573 -13.404 -2.472 1 98.36 ? FE HEM 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #