data_3L4D # _model_server_result.job_id ypHTGSFP69rVMjm48wkyYw _model_server_result.datetime_utc '2024-12-26 11:54:33' _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 3l4d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":481}' # _entry.id 3L4D # _exptl.entry_id 3L4D _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 104.82 _cell.angle_gamma 90 _cell.entry_id 3L4D _cell.length_a 84.891 _cell.length_b 118.509 _cell.length_c 100.96 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L4D _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,Q _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 SG CYS 395 A CYS 422 1_555 E FE HEM . A HEM 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc2 E FE HEM . A HEM 481 1_555 F N5 TPF . A TPF 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc3 B SG CYS 395 B CYS 422 1_555 G FE HEM . B HEM 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc4 G FE HEM . B HEM 481 1_555 H N5 TPF . B TPF 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc5 C SG CYS 395 C CYS 422 1_555 I FE HEM . C HEM 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc6 I FE HEM . C HEM 481 1_555 J N5 TPF . C TPF 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? metalc ? metalc7 D SG CYS 395 D CYS 422 1_555 L FE HEM . D HEM 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc8 L FE HEM . D HEM 481 1_555 M N5 TPF . D TPF 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? # _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 3L4D _atom_sites.fract_transf_matrix[1][1] 0.01178 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003117 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008438 _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] 0.010246 _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 1 481 481 HEM HEM . F 3 TPF A 1 490 490 TPF TPF . G 2 HEM B 1 481 481 HEM HEM . H 3 TPF B 1 490 490 TPF TPF . I 2 HEM C 1 481 481 HEM HEM . J 3 TPF C 1 490 490 TPF TPF . K 4 N8E C 1 1 1 N8E N8E . L 2 HEM D 1 481 481 HEM HEM . M 3 TPF D 1 490 490 TPF TPF . N 5 HOH A 1 3 3 HOH HOH . N 5 HOH A 2 4 4 HOH HOH . N 5 HOH A 3 8 8 HOH HOH . N 5 HOH A 4 15 15 HOH HOH . N 5 HOH A 5 18 18 HOH HOH . N 5 HOH A 6 20 20 HOH HOH . N 5 HOH A 7 21 21 HOH HOH . N 5 HOH A 8 22 22 HOH HOH . N 5 HOH A 9 482 482 HOH HOH . N 5 HOH A 10 483 483 HOH HOH . N 5 HOH A 11 484 484 HOH HOH . N 5 HOH A 12 485 485 HOH HOH . N 5 HOH A 13 486 486 HOH HOH . N 5 HOH A 14 487 487 HOH HOH . N 5 HOH A 15 488 488 HOH HOH . N 5 HOH A 16 489 489 HOH HOH . O 5 HOH B 1 1 1 HOH HOH . O 5 HOH B 2 5 5 HOH HOH . O 5 HOH B 3 6 6 HOH HOH . O 5 HOH B 4 9 9 HOH HOH . O 5 HOH B 5 11 11 HOH HOH . O 5 HOH B 6 19 19 HOH HOH . O 5 HOH B 7 482 482 HOH HOH . O 5 HOH B 8 483 483 HOH HOH . O 5 HOH B 9 484 484 HOH HOH . O 5 HOH B 10 485 485 HOH HOH . O 5 HOH B 11 486 486 HOH HOH . P 5 HOH C 1 2 2 HOH HOH . P 5 HOH C 2 7 7 HOH HOH . P 5 HOH C 3 12 12 HOH HOH . P 5 HOH C 4 16 16 HOH HOH . P 5 HOH C 5 17 17 HOH HOH . P 5 HOH C 6 26 26 HOH HOH . P 5 HOH C 7 27 27 HOH HOH . P 5 HOH C 8 482 482 HOH HOH . P 5 HOH C 9 483 483 HOH HOH . P 5 HOH C 10 484 484 HOH HOH . P 5 HOH C 11 485 485 HOH HOH . P 5 HOH C 12 486 486 HOH HOH . P 5 HOH C 13 487 487 HOH HOH . P 5 HOH C 14 488 488 HOH HOH . P 5 HOH C 15 489 489 HOH HOH . P 5 HOH C 16 491 491 HOH HOH . Q 5 HOH D 1 10 10 HOH HOH . Q 5 HOH D 2 13 13 HOH HOH . Q 5 HOH D 3 14 14 HOH HOH . Q 5 HOH D 4 23 23 HOH HOH . Q 5 HOH D 5 24 24 HOH HOH . Q 5 HOH D 6 25 25 HOH HOH . Q 5 HOH D 7 482 482 HOH HOH . Q 5 HOH D 8 483 483 HOH HOH . Q 5 HOH D 9 484 484 HOH HOH . Q 5 HOH D 10 485 485 HOH HOH . Q 5 HOH D 11 486 486 HOH HOH . Q 5 HOH D 12 487 487 HOH HOH . Q 5 HOH D 13 488 488 HOH HOH . Q 5 HOH D 14 489 489 HOH HOH . Q 5 HOH D 15 491 491 HOH HOH . Q 5 HOH D 16 492 492 HOH HOH . Q 5 HOH D 17 493 493 HOH HOH . Q 5 HOH D 18 494 494 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 . . . L 2 8.504 -44.161 -34.019 1 64.11 ? CHA HEM 481 D 1 HETATM 2 C CHB HEM . . . L 2 10.612 -47.835 -36.378 1 58.14 ? CHB HEM 481 D 1 HETATM 3 C CHC HEM . . . L 2 8.742 -46.096 -40.504 1 57.63 ? CHC HEM 481 D 1 HETATM 4 C CHD HEM . . . L 2 7.691 -41.918 -38.29 1 58.01 ? CHD HEM 481 D 1 HETATM 5 C C1A HEM . . . L 2 9.195 -45.322 -34.278 1 61.77 ? C1A HEM 481 D 1 HETATM 6 C C2A HEM . . . L 2 9.784 -46.205 -33.291 1 61.63 ? C2A HEM 481 D 1 HETATM 7 C C3A HEM . . . L 2 10.366 -47.217 -33.938 1 61 ? C3A HEM 481 D 1 HETATM 8 C C4A HEM . . . L 2 10.167 -47.018 -35.361 1 60.84 ? C4A HEM 481 D 1 HETATM 9 C CMA HEM . . . L 2 11.12 -48.393 -33.281 1 60.36 ? CMA HEM 481 D 1 HETATM 10 C CAA HEM . . . L 2 9.754 -46.006 -31.759 1 58.55 ? CAA HEM 481 D 1 HETATM 11 C CBA HEM . . . L 2 10.938 -45.126 -31.371 1 59.55 ? CBA HEM 481 D 1 HETATM 12 C CGA HEM . . . L 2 11.088 -45.053 -29.874 1 62.21 ? CGA HEM 481 D 1 HETATM 13 O O1A HEM . . . L 2 10.658 -46.005 -29.173 1 60.69 ? O1A HEM 481 D 1 HETATM 14 O O2A HEM . . . L 2 11.645 -44.037 -29.381 1 64.75 ? O2A HEM 481 D 1 HETATM 15 C C1B HEM . . . L 2 10.242 -47.721 -37.7 1 59.2 ? C1B HEM 481 D 1 HETATM 16 C C2B HEM . . . L 2 10.481 -48.69 -38.754 1 59.73 ? C2B HEM 481 D 1 HETATM 17 C C3B HEM . . . L 2 9.964 -48.206 -39.885 1 56.65 ? C3B HEM 481 D 1 HETATM 18 C C4B HEM . . . L 2 9.377 -46.915 -39.597 1 56.49 ? C4B HEM 481 D 1 HETATM 19 C CMB HEM . . . L 2 11.206 -50.047 -38.601 1 58.2 ? CMB HEM 481 D 1 HETATM 20 C CAB HEM . . . L 2 9.988 -48.897 -41.264 1 52.26 ? CAB HEM 481 D 1 HETATM 21 C CBB HEM . . . L 2 9.163 -49.916 -41.516 1 52.26 ? CBB HEM 481 D 1 HETATM 22 C C1C HEM . . . L 2 8.293 -44.815 -40.269 1 56.32 ? C1C HEM 481 D 1 HETATM 23 C C2C HEM . . . L 2 7.673 -43.937 -41.24 1 54.5 ? C2C HEM 481 D 1 HETATM 24 C C3C HEM . . . L 2 7.383 -42.785 -40.632 1 54.26 ? C3C HEM 481 D 1 HETATM 25 C C4C HEM . . . L 2 7.807 -42.891 -39.253 1 53.6 ? C4C HEM 481 D 1 HETATM 26 C CMC HEM . . . L 2 7.399 -44.278 -42.72 1 51.41 ? CMC HEM 481 D 1 HETATM 27 C CAC HEM . . . L 2 6.714 -41.553 -41.279 1 54.08 ? CAC HEM 481 D 1 HETATM 28 C CBC HEM . . . L 2 6.626 -41.464 -42.611 1 55.68 ? CBC HEM 481 D 1 HETATM 29 C C1D HEM . . . L 2 7.762 -42.129 -36.934 1 60.1 ? C1D HEM 481 D 1 HETATM 30 C C2D HEM . . . L 2 7.39 -41.169 -35.921 1 61.92 ? C2D HEM 481 D 1 HETATM 31 C C3D HEM . . . L 2 7.645 -41.876 -34.584 1 64.82 ? C3D HEM 481 D 1 HETATM 32 C C4D HEM . . . L 2 8.146 -43.189 -34.928 1 63.65 ? C4D HEM 481 D 1 HETATM 33 C CMD HEM . . . L 2 6.851 -39.74 -36.143 1 63.09 ? CMD HEM 481 D 1 HETATM 34 C CAD HEM . . . L 2 7.423 -41.305 -33.166 1 64.55 ? CAD HEM 481 D 1 HETATM 35 C CBD HEM . . . L 2 5.999 -41.573 -32.692 1 62.05 ? CBD HEM 481 D 1 HETATM 36 C CGD HEM . . . L 2 5.826 -40.93 -31.341 1 60.91 ? CGD HEM 481 D 1 HETATM 37 O O1D HEM . . . L 2 6.815 -40.333 -30.839 1 60.19 ? O1D HEM 481 D 1 HETATM 38 O O2D HEM . . . L 2 4.709 -41.013 -30.767 1 57.72 ? O2D HEM 481 D 1 HETATM 39 N NA HEM . . . L 2 9.449 -45.848 -35.528 1 60.73 ? NA HEM 481 D 1 HETATM 40 N NB HEM . . . L 2 9.568 -46.649 -38.256 1 57.1 ? NB HEM 481 D 1 HETATM 41 N NC HEM . . . L 2 8.36 -44.14 -39.066 1 54.51 ? NC HEM 481 D 1 HETATM 42 N ND HEM . . . L 2 8.202 -43.296 -36.315 1 61.21 ? ND HEM 481 D 1 HETATM 43 FE FE HEM . . . L 2 8.936 -44.97 -37.299 1 58.76 ? FE HEM 481 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #