data_3GVY # _model_server_result.job_id nHydr2UbAml7qCWMVrsrgg _model_server_result.datetime_utc '2024-11-05 00:27:02' _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 3gvy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":162}' # _entry.id 3GVY # _exptl.entry_id 3GVY _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 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 3GVY _cell.length_a 160.495 _cell.length_b 160.495 _cell.length_c 116.276 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GVY _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 24-meric _pdbx_struct_assembly.oligomeric_count 24 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 116.276 6 'crystal symmetry operation' 6_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 116.276 7 'crystal symmetry operation' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 116.276 8 'crystal symmetry operation' 8_556 -y,-x,-z+1 0 -1 0 -1 0 0 0 0 -1 0 0 116.276 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 F 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 OE1 GLU 18 A GLU 18 1_555 E FE FE . A FE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc2 A OE1 GLU 51 A GLU 51 1_555 E FE FE . A FE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc3 A SD MET 52 A MET 52 1_555 D FE HEM . A HEM 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc4 A ND1 HIS 54 A HIS 54 1_555 E FE FE . A FE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc5 A OE2 GLU 127 A GLU 127 1_555 E FE FE . A FE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.83 ? metalc ? metalc6 A OE1 GLU 127 A GLU 127 1_555 E FE FE . A FE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc7 D FE HEM . A HEM 162 1_555 C SD MET 52 C MET 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc8 B OE2 GLU 18 B GLU 18 1_555 G FE FE . B FE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc9 B OE2 GLU 51 B GLU 51 1_555 G FE FE . B FE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc10 B SD MET 52 B MET 52 1_555 F FE HEM . B HEM 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.488 ? metalc ? metalc11 B ND1 HIS 54 B HIS 54 1_555 G FE FE . B FE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc12 C OE1 GLU 18 C GLU 18 1_555 H FE FE . C FE 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc13 C OE2 GLU 18 C GLU 18 1_555 H FE FE . C FE 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc14 C OE1 GLU 51 C GLU 51 1_555 H FE FE . C FE 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc15 C OE1 GLU 127 C GLU 127 1_555 H FE FE . C FE 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc16 C OE2 GLU 127 C GLU 127 1_555 H FE FE . C FE 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? # _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 3GVY _atom_sites.fract_transf_matrix[1][1] 0.006231 _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] 0.006231 _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] 0.0086 _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 HEM A 1 162 162 HEM HEM . E 3 FE A 1 163 163 FE FE . F 2 HEM B 1 162 162 HEM HEM . G 3 FE B 1 163 163 FE FE . H 3 FE C 1 162 162 FE FE . # 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 . . . D 2 -0.266 26.523 31.51 1 47.76 ? CHA HEM 162 A 1 HETATM 2 C CHB HEM . . . D 2 2.661 30.346 30.841 1 44.89 ? CHB HEM 162 A 1 HETATM 3 C CHC HEM . . . D 2 0.06 31.68 26.868 1 42.24 ? CHC HEM 162 A 1 HETATM 4 C CHD HEM . . . D 2 -2.658 27.679 27.38 1 44.64 ? CHD HEM 162 A 1 HETATM 5 C C1A HEM . . . D 2 0.806 27.399 31.648 1 46.96 ? C1A HEM 162 A 1 HETATM 6 C C2A HEM . . . D 2 1.895 27.248 32.603 1 46.68 ? C2A HEM 162 A 1 HETATM 7 C C3A HEM . . . D 2 2.708 28.314 32.398 1 46.24 ? C3A HEM 162 A 1 HETATM 8 C C4A HEM . . . D 2 2.154 29.151 31.338 1 45.34 ? C4A HEM 162 A 1 HETATM 9 C CMA HEM . . . D 2 4.021 28.68 33.134 1 47.24 ? CMA HEM 162 A 1 HETATM 10 C CAA HEM . . . D 2 1.983 26.018 33.575 1 48.46 ? CAA HEM 162 A 1 HETATM 11 C CBA HEM . . . D 2 2.778 26.151 34.884 1 51.61 ? CBA HEM 162 A 1 HETATM 12 C CGA HEM . . . D 2 3.549 24.875 35.208 1 52.84 ? CGA HEM 162 A 1 HETATM 13 O O1A HEM . . . D 2 2.886 23.853 35.534 1 55.53 ? O1A HEM 162 A 1 HETATM 14 O O2A HEM . . . D 2 4.817 24.849 35.161 1 51.62 ? O2A HEM 162 A 1 HETATM 15 C C1B HEM . . . D 2 2.193 31.048 29.731 1 44.65 ? C1B HEM 162 A 1 HETATM 16 C C2B HEM . . . D 2 2.736 32.285 29.212 1 45.51 ? C2B HEM 162 A 1 HETATM 17 C C3B HEM . . . D 2 2.029 32.643 28.119 1 45.06 ? C3B HEM 162 A 1 HETATM 18 C C4B HEM . . . D 2 0.997 31.658 27.895 1 42.91 ? C4B HEM 162 A 1 HETATM 19 C CMB HEM . . . D 2 3.938 33.038 29.823 1 46.15 ? CMB HEM 162 A 1 HETATM 20 C CAB HEM . . . D 2 2.247 33.888 27.223 1 45.83 ? CAB HEM 162 A 1 HETATM 21 C CBB HEM . . . D 2 2.806 35.004 27.717 1 47.62 ? CBB HEM 162 A 1 HETATM 22 C C1C HEM . . . D 2 -0.865 30.701 26.559 1 40.66 ? C1C HEM 162 A 1 HETATM 23 C C2C HEM . . . D 2 -1.682 30.529 25.362 1 38.67 ? C2C HEM 162 A 1 HETATM 24 C C3C HEM . . . D 2 -2.425 29.417 25.527 1 38.93 ? C3C HEM 162 A 1 HETATM 25 C C4C HEM . . . D 2 -2.121 28.842 26.825 1 41.99 ? C4C HEM 162 A 1 HETATM 26 C CMC HEM . . . D 2 -1.722 31.428 24.11 1 36 ? CMC HEM 162 A 1 HETATM 27 C CAC HEM . . . D 2 -3.44 28.834 24.527 1 36.12 ? CAC HEM 162 A 1 HETATM 28 C CBC HEM . . . D 2 -4.555 29.512 24.28 1 34.8 ? CBC HEM 162 A 1 HETATM 29 C C1D HEM . . . D 2 -2.333 27.053 28.583 1 45.75 ? C1D HEM 162 A 1 HETATM 30 C C2D HEM . . . D 2 -3.119 26.004 29.2 1 47.06 ? C2D HEM 162 A 1 HETATM 31 C C3D HEM . . . D 2 -2.373 25.624 30.512 1 47.35 ? C3D HEM 162 A 1 HETATM 32 C C4D HEM . . . D 2 -1.229 26.509 30.52 1 46.2 ? C4D HEM 162 A 1 HETATM 33 C CMD HEM . . . D 2 -4.431 25.438 28.598 1 47 ? CMD HEM 162 A 1 HETATM 34 C CAD HEM . . . D 2 -2.718 24.582 31.618 1 49.38 ? CAD HEM 162 A 1 HETATM 35 C CBD HEM . . . D 2 -2.584 23.127 31.167 1 52.92 ? CBD HEM 162 A 1 HETATM 36 C CGD HEM . . . D 2 -3.87 22.623 30.522 1 55.39 ? CGD HEM 162 A 1 HETATM 37 O O1D HEM . . . D 2 -4.95 22.728 31.17 1 57.47 ? O1D HEM 162 A 1 HETATM 38 O O2D HEM . . . D 2 -3.844 22.117 29.355 1 54.82 ? O2D HEM 162 A 1 HETATM 39 N NA HEM . . . D 2 0.99 28.558 30.906 1 45.26 ? NA HEM 162 A 1 HETATM 40 N NB HEM . . . D 2 1.127 30.714 28.896 1 42.71 ? NB HEM 162 A 1 HETATM 41 N NC HEM . . . D 2 -1.168 29.658 27.408 1 42.5 ? NC HEM 162 A 1 HETATM 42 N ND HEM . . . D 2 -1.236 27.323 29.39 1 44.4 ? ND HEM 162 A 1 HETATM 43 FE FE HEM . . . D 2 -0.26 29.213 29.152 1 44.46 ? FE HEM 162 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #