data_3R1A # _model_server_result.job_id db_xhYlvuIe2-sAHxHW42w _model_server_result.datetime_utc '2024-11-29 10:28:36' _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 3r1a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":500}' # _entry.id 3R1A # _exptl.entry_id 3R1A _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 8 _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 3R1A _cell.length_a 134.381 _cell.length_b 144.549 _cell.length_c 229.275 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3R1A _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 PISA monomeric 1 author_and_software_defined_assembly 4 PISA monomeric 1 author_and_software_defined_assembly 5 PISA monomeric 1 author_and_software_defined_assembly 6 PISA monomeric 1 author_and_software_defined_assembly 7 PISA monomeric 1 author_and_software_defined_assembly 8 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,I,J,Y 1 1 B,K,L,Z 2 1 C,M,N,AA 3 1 D,O,P,BA 4 1 E,Q,R,CA 5 1 F,S,T,DA 6 1 G,U,V,EA 7 1 H,W,X,FA 8 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 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q N N ? 2 S N N ? 2 U N N ? 2 W 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 A OG1 THR 283 A THR 302 1_555 J C1 TB2 . A TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.27 ? covale ? covale2 B OG1 THR 283 B THR 302 1_555 L C1 TB2 . B TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 C OG1 THR 283 C THR 302 1_555 N C1 TB2 . C TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.278 ? covale ? covale4 D OG1 THR 283 D THR 302 1_555 P C1 TB2 . D TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale5 E OG1 THR 283 E THR 302 1_555 R C1 TB2 . E TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale6 F OG1 THR 283 F THR 302 1_555 T C1 TB2 . F TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.271 ? covale ? covale7 G OG1 THR 283 G THR 302 1_555 V C1 TB2 . G TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale8 H OG1 THR 283 H THR 302 1_555 X C1 TB2 . H TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? metalc ? metalc1 A SG CYS 417 A CYS 436 1_555 I FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc2 B SG CYS 417 B CYS 436 1_555 K FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc3 C SG CYS 417 C CYS 436 1_555 M FE HEM . C HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc4 D SG CYS 417 D CYS 436 1_555 O FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc5 CA O HOH . E HOH 5 1_555 Q FE HEM . E HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc6 E SG CYS 417 E CYS 436 1_555 Q FE HEM . E HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc7 F SG CYS 417 F CYS 436 1_555 S FE HEM . F HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc8 G SG CYS 417 G CYS 436 1_555 U FE HEM . G HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? # _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 3R1A _atom_sites.fract_transf_matrix[1][1] 0.007442 _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] 0.006918 _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] 0.004362 _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 I 2 HEM A 1 500 500 HEM HEM . J 3 TB2 A 1 501 501 TB2 TB2 . K 2 HEM B 1 500 500 HEM HEM . L 3 TB2 B 1 501 501 TB2 TB2 . M 2 HEM C 1 500 500 HEM HEM . N 3 TB2 C 1 501 501 TB2 TB2 . O 2 HEM D 1 500 500 HEM HEM . P 3 TB2 D 1 501 501 TB2 TB2 . Q 2 HEM E 1 500 500 HEM HEM . R 3 TB2 E 1 501 501 TB2 TB2 . S 2 HEM F 1 500 500 HEM HEM . T 3 TB2 F 1 501 501 TB2 TB2 . U 2 HEM G 1 500 500 HEM HEM . V 3 TB2 G 1 501 501 TB2 TB2 . W 2 HEM H 1 500 500 HEM HEM . X 3 TB2 H 1 501 501 TB2 TB2 . Y 4 HOH A 1 1 1 HOH HOH . Z 4 HOH B 1 2 2 HOH HOH . AA 4 HOH C 1 4 4 HOH HOH . BA 4 HOH D 1 3 3 HOH HOH . CA 4 HOH E 1 5 5 HOH HOH . DA 4 HOH F 1 6 6 HOH HOH . EA 4 HOH G 1 7 7 HOH HOH . FA 4 HOH H 1 8 8 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 . . . U 2 -102.641 81.753 -15.88 1 75.13 ? CHA HEM 500 G 1 HETATM 2 C CHB HEM . . . U 2 -100.701 79.047 -19.392 1 71.41 ? CHB HEM 500 G 1 HETATM 3 C CHC HEM . . . U 2 -97.497 82.55 -20.373 1 70.07 ? CHC HEM 500 G 1 HETATM 4 C CHD HEM . . . U 2 -99.858 85.514 -17.338 1 82.2 ? CHD HEM 500 G 1 HETATM 5 C C1A HEM . . . U 2 -102.367 80.686 -16.704 1 60.25 ? C1A HEM 500 G 1 HETATM 6 C C2A HEM . . . U 2 -102.976 79.373 -16.653 1 59.7 ? C2A HEM 500 G 1 HETATM 7 C C3A HEM . . . U 2 -102.44 78.632 -17.621 1 63.43 ? C3A HEM 500 G 1 HETATM 8 C C4A HEM . . . U 2 -101.473 79.444 -18.326 1 68.01 ? C4A HEM 500 G 1 HETATM 9 C CMA HEM . . . U 2 -102.79 77.164 -17.938 1 65.5 ? CMA HEM 500 G 1 HETATM 10 C CAA HEM . . . U 2 -104.057 78.897 -15.659 1 69.44 ? CAA HEM 500 G 1 HETATM 11 C CBA HEM . . . U 2 -105.436 79.31 -16.159 1 61.91 ? CBA HEM 500 G 1 HETATM 12 C CGA HEM . . . U 2 -106.478 78.825 -15.186 1 63.2 ? CGA HEM 500 G 1 HETATM 13 O O1A HEM . . . U 2 -107.481 79.55 -14.967 1 68.4 ? O1A HEM 500 G 1 HETATM 14 O O2A HEM . . . U 2 -106.299 77.719 -14.617 1 68.65 ? O2A HEM 500 G 1 HETATM 15 C C1B HEM . . . U 2 -99.593 79.713 -19.861 1 69.14 ? C1B HEM 500 G 1 HETATM 16 C C2B HEM . . . U 2 -98.51 79.117 -20.609 1 66.99 ? C2B HEM 500 G 1 HETATM 17 C C3B HEM . . . U 2 -97.621 80.078 -20.885 1 68.57 ? C3B HEM 500 G 1 HETATM 18 C C4B HEM . . . U 2 -98.116 81.319 -20.316 1 68.76 ? C4B HEM 500 G 1 HETATM 19 C CMB HEM . . . U 2 -98.439 77.624 -20.999 1 70.86 ? CMB HEM 500 G 1 HETATM 20 C CAB HEM . . . U 2 -96.296 79.926 -21.667 1 70.32 ? CAB HEM 500 G 1 HETATM 21 C CBB HEM . . . U 2 -95.902 78.751 -22.169 1 68.93 ? CBB HEM 500 G 1 HETATM 22 C C1C HEM . . . U 2 -97.906 83.684 -19.703 1 73.11 ? C1C HEM 500 G 1 HETATM 23 C C2C HEM . . . U 2 -97.399 85.028 -19.902 1 68.15 ? C2C HEM 500 G 1 HETATM 24 C C3C HEM . . . U 2 -98.053 85.846 -19.064 1 72.66 ? C3C HEM 500 G 1 HETATM 25 C C4C HEM . . . U 2 -98.996 85.046 -18.307 1 78.77 ? C4C HEM 500 G 1 HETATM 26 C CMC HEM . . . U 2 -96.296 85.414 -20.913 1 65.86 ? CMC HEM 500 G 1 HETATM 27 C CAC HEM . . . U 2 -97.873 87.372 -18.894 1 76.64 ? CAC HEM 500 G 1 HETATM 28 C CBC HEM . . . U 2 -96.983 88.064 -19.612 1 84.44 ? CBC HEM 500 G 1 HETATM 29 C C1D HEM . . . U 2 -100.88 84.81 -16.734 1 82.17 ? C1D HEM 500 G 1 HETATM 30 C C2D HEM . . . U 2 -101.95 85.402 -15.962 1 74.96 ? C2D HEM 500 G 1 HETATM 31 C C3D HEM . . . U 2 -102.827 84.22 -15.503 1 79.82 ? C3D HEM 500 G 1 HETATM 32 C C4D HEM . . . U 2 -102.189 83.044 -16.05 1 82.36 ? C4D HEM 500 G 1 HETATM 33 C CMD HEM . . . U 2 -102.129 86.911 -15.687 1 70.26 ? CMD HEM 500 G 1 HETATM 34 C CAD HEM . . . U 2 -104.118 84.212 -14.651 1 85.68 ? CAD HEM 500 G 1 HETATM 35 C CBD HEM . . . U 2 -104.453 85.599 -14.119 1 98.24 ? CBD HEM 500 G 1 HETATM 36 C CGD HEM . . . U 2 -105.944 85.809 -14.159 1 97.93 ? CGD HEM 500 G 1 HETATM 37 O O1D HEM . . . U 2 -106.38 86.969 -13.945 1 93.13 ? O1D HEM 500 G 1 HETATM 38 O O2D HEM . . . U 2 -106.69 84.826 -14.411 1 89.17 ? O2D HEM 500 G 1 HETATM 39 N NA HEM . . . U 2 -101.454 80.691 -17.737 1 62.28 ? NA HEM 500 G 1 HETATM 40 N NB HEM . . . U 2 -99.322 81.057 -19.694 1 69.56 ? NB HEM 500 G 1 HETATM 41 N NC HEM . . . U 2 -98.879 83.734 -18.721 1 76.67 ? NC HEM 500 G 1 HETATM 42 N ND HEM . . . U 2 -101.055 83.429 -16.76 1 82.21 ? ND HEM 500 G 1 HETATM 43 FE FE HEM . . . U 2 -100.121 82.194 -18.13 1 59.46 ? FE HEM 500 G 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #