data_4M06 # _model_server_result.job_id uLnBKnTYwOrcAvzUj-oDrQ _model_server_result.datetime_utc '2024-11-27 08:17:09' _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 4m06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":301}' # _entry.id 4M06 # _exptl.entry_id 4M06 _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 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 117.94 _cell.angle_gamma 90 _cell.entry_id 4M06 _cell.length_a 136.21 _cell.length_b 113.42 _cell.length_c 118.84 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M06 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,Q,R,S,T,U _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 F N N ? 2 I N N ? 2 K N N ? 2 N N N ? 2 P 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 182 A HIS 160 1_555 F FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc2 B NE2 HIS 182 B HIS 160 1_555 I FE HEM . B HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc3 C NE2 HIS 182 C HIS 160 1_555 K FE HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc4 D NE2 HIS 182 D HIS 160 1_555 N FE HEM . D HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc5 E NE2 HIS 182 E HIS 160 1_555 P FE HEM . E HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? # _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 139 n n CHA C4D HEM doub 140 n n CHA HHA HEM sing 141 n n CHB C4A HEM sing 142 n n CHB C1B HEM doub 143 n n CHB HHB HEM sing 144 n n CHC C4B HEM sing 145 n n CHC C1C HEM doub 146 n n CHC HHC HEM sing 147 n n CHD C4C HEM doub 148 n n CHD C1D HEM sing 149 n n CHD HHD HEM sing 150 n n C1A C2A HEM doub 151 n y C1A NA HEM sing 152 n y C2A C3A HEM sing 153 n y C2A CAA HEM sing 154 n n C3A C4A HEM doub 155 n y C3A CMA HEM sing 156 n n C4A NA HEM sing 157 n y CMA HMA HEM sing 158 n n CMA HMAA HEM sing 159 n n CMA HMAB HEM sing 160 n n CAA CBA HEM sing 161 n n CAA HAA HEM sing 162 n n CAA HAAA HEM sing 163 n n CBA CGA HEM sing 164 n n CBA HBA HEM sing 165 n n CBA HBAA HEM sing 166 n n CGA O1A HEM doub 167 n n CGA O2A HEM sing 168 n n C1B C2B HEM sing 169 n n C1B NB HEM sing 170 n n C2B C3B HEM doub 171 n n C2B CMB HEM sing 172 n n C3B C4B HEM sing 173 n n C3B CAB HEM sing 174 n n C4B NB HEM doub 175 n n CMB HMB HEM sing 176 n n CMB HMBA HEM sing 177 n n CMB HMBB HEM sing 178 n n CAB CBB HEM doub 179 n n CAB HAB HEM sing 180 n n CBB HBB HEM sing 181 n n CBB HBBA HEM sing 182 n n C1C C2C HEM sing 183 n y C1C NC HEM sing 184 n y C2C C3C HEM doub 185 n y C2C CMC HEM sing 186 n n C3C C4C HEM sing 187 n y C3C CAC HEM sing 188 n n C4C NC HEM sing 189 n y CMC HMC HEM sing 190 n n CMC HMCA HEM sing 191 n n CMC HMCB HEM sing 192 n n CAC CBC HEM doub 193 n n CAC HAC HEM sing 194 n n CBC HBC HEM sing 195 n n CBC HBCA HEM sing 196 n n C1D C2D HEM sing 197 n n C1D ND HEM doub 198 n n C2D C3D HEM doub 199 n n C2D CMD HEM sing 200 n n C3D C4D HEM sing 201 n n C3D CAD HEM sing 202 n n C4D ND HEM sing 203 n n CMD HMD HEM sing 204 n n CMD HMDA HEM sing 205 n n CMD HMDB HEM sing 206 n n CAD CBD HEM sing 207 n n CAD HAD HEM sing 208 n n CAD HADA HEM sing 209 n n CBD CGD HEM sing 210 n n CBD HBD HEM sing 211 n n CBD HBDA HEM sing 212 n n CGD O1D HEM doub 213 n n CGD O2D HEM sing 214 n n O2A H2A HEM sing 215 n n O2D H2D HEM sing 216 n n FE NA HEM sing 217 n n FE NB HEM sing 218 n n FE NC HEM sing 219 n n FE ND HEM sing 220 n n # _atom_sites.entry_id 4M06 _atom_sites.fract_transf_matrix[1][1] 0.007342 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003894 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008817 _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] 0.009525 _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 F 2 HEM A 1 301 239 HEM HEM . G 3 GOL A 1 302 1 GOL GOL . H 4 CYN A 1 303 1 CYN CYN . I 2 HEM B 1 301 239 HEM HEM . J 4 CYN B 1 302 1 CYN CYN . K 2 HEM C 1 301 239 HEM HEM . L 4 CYN C 1 302 1 CYN CYN . M 5 EDO C 1 303 1 EDO EDO . N 2 HEM D 1 301 239 HEM HEM . O 4 CYN D 1 302 1 CYN CYN . P 2 HEM E 1 301 239 HEM HEM . Q 4 CYN E 1 302 1 CYN CYN . R 5 EDO E 1 303 1 EDO EDO . S 6 HOH A 1 401 1 HOH HOH . T 6 HOH C 1 401 2 HOH HOH . T 6 HOH C 2 402 3 HOH HOH . T 6 HOH C 3 403 5 HOH HOH . U 6 HOH E 1 401 4 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 2 -12.004 -25.327 -13.111 1 65.81 ? CHA HEM 301 B 1 HETATM 2 C CHB HEM . . . I 2 -16.327 -26.917 -11.546 1 70.45 ? CHB HEM 301 B 1 HETATM 3 C CHC HEM . . . I 2 -18.454 -23.193 -13.784 1 59.46 ? CHC HEM 301 B 1 HETATM 4 C CHD HEM . . . I 2 -14.127 -21.258 -14.87 1 52.83 ? CHD HEM 301 B 1 HETATM 5 C C1A HEM . . . I 2 -12.988 -26.079 -12.499 1 67.29 ? C1A HEM 301 B 1 HETATM 6 C C2A HEM . . . I 2 -12.774 -27.302 -11.743 1 64.55 ? C2A HEM 301 B 1 HETATM 7 C C3A HEM . . . I 2 -13.957 -27.74 -11.309 1 69.12 ? C3A HEM 301 B 1 HETATM 8 C C4A HEM . . . I 2 -14.972 -26.816 -11.775 1 72.61 ? C4A HEM 301 B 1 HETATM 9 C CMA HEM . . . I 2 -14.198 -29.009 -10.464 1 71.35 ? CMA HEM 301 B 1 HETATM 10 C CAA HEM . . . I 2 -11.411 -27.975 -11.488 1 61.05 ? CAA HEM 301 B 1 HETATM 11 C CBA HEM . . . I 2 -11.13 -28.979 -12.601 1 67.3 ? CBA HEM 301 B 1 HETATM 12 C CGA HEM . . . I 2 -9.643 -29.125 -12.804 1 78.3 ? CGA HEM 301 B 1 HETATM 13 O O1A HEM . . . I 2 -9.053 -30.054 -12.2 1 85.24 ? O1A HEM 301 B 1 HETATM 14 O O2A HEM . . . I 2 -9.043 -28.319 -13.565 1 79.86 ? O2A HEM 301 B 1 HETATM 15 C C1B HEM . . . I 2 -17.284 -26.103 -12.118 1 66.66 ? C1B HEM 301 B 1 HETATM 16 C C2B HEM . . . I 2 -18.705 -26.385 -12.187 1 71.4 ? C2B HEM 301 B 1 HETATM 17 C C3B HEM . . . I 2 -19.298 -25.344 -12.807 1 68.32 ? C3B HEM 301 B 1 HETATM 18 C C4B HEM . . . I 2 -18.257 -24.392 -13.141 1 58.79 ? C4B HEM 301 B 1 HETATM 19 C CMB HEM . . . I 2 -19.319 -27.68 -11.607 1 71.72 ? CMB HEM 301 B 1 HETATM 20 C CAB HEM . . . I 2 -20.779 -25.068 -13.18 1 71.7 ? CAB HEM 301 B 1 HETATM 21 C CBB HEM . . . I 2 -21.788 -25.943 -13.069 1 77.79 ? CBB HEM 301 B 1 HETATM 22 C C1C HEM . . . I 2 -17.472 -22.331 -14.211 1 60.87 ? C1C HEM 301 B 1 HETATM 23 C C2C HEM . . . I 2 -17.724 -21.024 -14.768 1 59.85 ? C2C HEM 301 B 1 HETATM 24 C C3C HEM . . . I 2 -16.533 -20.473 -15.069 1 65.36 ? C3C HEM 301 B 1 HETATM 25 C C4C HEM . . . I 2 -15.494 -21.431 -14.716 1 61.87 ? C4C HEM 301 B 1 HETATM 26 C CMC HEM . . . I 2 -19.162 -20.477 -14.926 1 55.46 ? CMC HEM 301 B 1 HETATM 27 C CAC HEM . . . I 2 -16.196 -19.102 -15.702 1 68.25 ? CAC HEM 301 B 1 HETATM 28 C CBC HEM . . . I 2 -17.084 -18.321 -16.328 1 61.14 ? CBC HEM 301 B 1 HETATM 29 C C1D HEM . . . I 2 -13.141 -22.177 -14.545 1 53.19 ? C1D HEM 301 B 1 HETATM 30 C C2D HEM . . . I 2 -11.72 -22.03 -14.809 1 61.13 ? C2D HEM 301 B 1 HETATM 31 C C3D HEM . . . I 2 -11.063 -23.295 -14.249 1 65.78 ? C3D HEM 301 B 1 HETATM 32 C C4D HEM . . . I 2 -12.15 -24.091 -13.713 1 58.89 ? C4D HEM 301 B 1 HETATM 33 C CMD HEM . . . I 2 -10.985 -20.858 -15.5 1 65.93 ? CMD HEM 301 B 1 HETATM 34 C CAD HEM . . . I 2 -9.557 -23.647 -14.299 1 79.23 ? CAD HEM 301 B 1 HETATM 35 C CBD HEM . . . I 2 -8.848 -23.447 -12.962 1 77.69 ? CBD HEM 301 B 1 HETATM 36 C CGD HEM . . . I 2 -7.472 -24.064 -13.072 1 81.03 ? CGD HEM 301 B 1 HETATM 37 O O1D HEM . . . I 2 -7.361 -25.243 -13.508 1 84.07 ? O1D HEM 301 B 1 HETATM 38 O O2D HEM . . . I 2 -6.475 -23.383 -12.724 1 82.2 ? O2D HEM 301 B 1 HETATM 39 N NA HEM . . . I 2 -14.345 -25.813 -12.501 1 66.51 ? NA HEM 301 B 1 HETATM 40 N NB HEM . . . I 2 -17.046 -24.879 -12.715 1 51.83 ? NB HEM 301 B 1 HETATM 41 N NC HEM . . . I 2 -16.11 -22.55 -14.187 1 57.89 ? NC HEM 301 B 1 HETATM 42 N ND HEM . . . I 2 -13.347 -23.399 -13.9 1 53.51 ? ND HEM 301 B 1 HETATM 43 FE FE HEM . . . I 2 -15.243 -24.164 -13.414 1 64.41 ? FE HEM 301 B 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #