data_3NLT # _model_server_result.job_id 8Vov28DVSCPmAXfuQLzLbw _model_server_result.datetime_utc '2025-01-25 10:29:03' _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 3nlt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":500}' # _entry.id 3NLT # _exptl.entry_id 3NLT _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 3NLT _cell.length_a 57.91 _cell.length_b 106.905 _cell.length_c 157.024 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NLT _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 C N N ? 2 I 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 58 A CYS 96 1_555 H ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc2 A SG CYS 63 A CYS 101 1_555 H ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc3 A SG CYS 148 A CYS 186 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc4 H ZN ZN . A ZN 900 1_555 B SG CYS 58 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc5 H ZN ZN . A ZN 900 1_555 B SG CYS 63 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc6 B SG CYS 148 B CYS 186 1_555 I FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? # _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 249 n n CHA C4D HEM doub 250 n n CHA HHA HEM sing 251 n n CHB C4A HEM sing 252 n n CHB C1B HEM doub 253 n n CHB HHB HEM sing 254 n n CHC C4B HEM sing 255 n n CHC C1C HEM doub 256 n n CHC HHC HEM sing 257 n n CHD C4C HEM doub 258 n n CHD C1D HEM sing 259 n n CHD HHD HEM sing 260 n n C1A C2A HEM doub 261 n y C1A NA HEM sing 262 n y C2A C3A HEM sing 263 n y C2A CAA HEM sing 264 n n C3A C4A HEM doub 265 n y C3A CMA HEM sing 266 n n C4A NA HEM sing 267 n y CMA HMA HEM sing 268 n n CMA HMAA HEM sing 269 n n CMA HMAB HEM sing 270 n n CAA CBA HEM sing 271 n n CAA HAA HEM sing 272 n n CAA HAAA HEM sing 273 n n CBA CGA HEM sing 274 n n CBA HBA HEM sing 275 n n CBA HBAA HEM sing 276 n n CGA O1A HEM doub 277 n n CGA O2A HEM sing 278 n n C1B C2B HEM sing 279 n n C1B NB HEM sing 280 n n C2B C3B HEM doub 281 n n C2B CMB HEM sing 282 n n C3B C4B HEM sing 283 n n C3B CAB HEM sing 284 n n C4B NB HEM doub 285 n n CMB HMB HEM sing 286 n n CMB HMBA HEM sing 287 n n CMB HMBB HEM sing 288 n n CAB CBB HEM doub 289 n n CAB HAB HEM sing 290 n n CBB HBB HEM sing 291 n n CBB HBBA HEM sing 292 n n C1C C2C HEM sing 293 n y C1C NC HEM sing 294 n y C2C C3C HEM doub 295 n y C2C CMC HEM sing 296 n n C3C C4C HEM sing 297 n y C3C CAC HEM sing 298 n n C4C NC HEM sing 299 n y CMC HMC HEM sing 300 n n CMC HMCA HEM sing 301 n n CMC HMCB HEM sing 302 n n CAC CBC HEM doub 303 n n CAC HAC HEM sing 304 n n CBC HBC HEM sing 305 n n CBC HBCA HEM sing 306 n n C1D C2D HEM sing 307 n n C1D ND HEM doub 308 n n C2D C3D HEM doub 309 n n C2D CMD HEM sing 310 n n C3D C4D HEM sing 311 n n C3D CAD HEM sing 312 n n C4D ND HEM sing 313 n n CMD HMD HEM sing 314 n n CMD HMDA HEM sing 315 n n CMD HMDB HEM sing 316 n n CAD CBD HEM sing 317 n n CAD HAD HEM sing 318 n n CAD HADA HEM sing 319 n n CBD CGD HEM sing 320 n n CBD HBD HEM sing 321 n n CBD HBDA HEM sing 322 n n CGD O1D HEM doub 323 n n CGD O2D HEM sing 324 n n O2A H2A HEM sing 325 n n O2D H2D HEM sing 326 n n FE NA HEM sing 327 n n FE NB HEM sing 328 n n FE NC HEM sing 329 n n FE ND HEM sing 330 n n # _atom_sites.entry_id 3NLT _atom_sites.fract_transf_matrix[1][1] 0.017268 _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] 0.009354 _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] 0.006368 _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 C 2 HEM A 1 500 500 HEM HEM . D 3 H4B A 1 600 600 H4B H4B . E 4 GOL A 1 880 880 GOL GOL . F 5 3XF A 1 800 800 3XF 3XF . G 6 CAD A 1 950 950 CAD CAD . H 7 ZN A 1 900 900 ZN ZN . I 2 HEM B 1 500 500 HEM HEM . J 3 H4B B 1 600 600 H4B H4B . K 4 GOL B 1 880 880 GOL GOL . L 5 3XF B 1 800 800 3XF 3XF . M 6 CAD B 1 950 950 CAD CAD . N 8 HOH A 1 1001 1001 HOH HOH . N 8 HOH A 2 1002 1002 HOH HOH . N 8 HOH A 3 1003 1003 HOH HOH . N 8 HOH A 4 1004 1004 HOH HOH . N 8 HOH A 5 1005 1005 HOH HOH . N 8 HOH A 6 1006 1006 HOH HOH . N 8 HOH A 7 1007 1007 HOH HOH . N 8 HOH A 8 1008 1008 HOH HOH . N 8 HOH A 9 1009 1009 HOH HOH . N 8 HOH A 10 1010 1010 HOH HOH . N 8 HOH A 11 1011 1011 HOH HOH . N 8 HOH A 12 1012 1012 HOH HOH . N 8 HOH A 13 1013 1013 HOH HOH . N 8 HOH A 14 1014 1014 HOH HOH . N 8 HOH A 15 1015 1015 HOH HOH . N 8 HOH A 16 1016 1016 HOH HOH . N 8 HOH A 17 1017 1017 HOH HOH . N 8 HOH A 18 1018 1018 HOH HOH . N 8 HOH A 19 1019 1019 HOH HOH . N 8 HOH A 20 1020 1020 HOH HOH . N 8 HOH A 21 1021 1021 HOH HOH . N 8 HOH A 22 1022 1022 HOH HOH . N 8 HOH A 23 1023 1023 HOH HOH . N 8 HOH A 24 1024 1024 HOH HOH . N 8 HOH A 25 1025 1025 HOH HOH . N 8 HOH A 26 1026 1026 HOH HOH . N 8 HOH A 27 1027 1027 HOH HOH . N 8 HOH A 28 1028 1028 HOH HOH . N 8 HOH A 29 1029 1029 HOH HOH . N 8 HOH A 30 1030 1030 HOH HOH . N 8 HOH A 31 1031 1031 HOH HOH . N 8 HOH A 32 1032 1032 HOH HOH . O 8 HOH B 1 1001 1001 HOH HOH . O 8 HOH B 2 1002 1002 HOH HOH . O 8 HOH B 3 1003 1003 HOH HOH . O 8 HOH B 4 1004 1004 HOH HOH . O 8 HOH B 5 1005 1005 HOH HOH . O 8 HOH B 6 1006 1006 HOH HOH . O 8 HOH B 7 1007 1007 HOH HOH . O 8 HOH B 8 1008 1008 HOH HOH . O 8 HOH B 9 1009 1009 HOH HOH . O 8 HOH B 10 1010 1010 HOH HOH . O 8 HOH B 11 1011 1011 HOH HOH . O 8 HOH B 12 1012 1012 HOH HOH . O 8 HOH B 13 1013 1013 HOH HOH . O 8 HOH B 14 1014 1014 HOH HOH . O 8 HOH B 15 1015 1015 HOH HOH . O 8 HOH B 16 1016 1016 HOH HOH . O 8 HOH B 17 1017 1017 HOH HOH . O 8 HOH B 18 1018 1018 HOH HOH . O 8 HOH B 19 1019 1019 HOH HOH . O 8 HOH B 20 1020 1020 HOH HOH . O 8 HOH B 21 1021 1021 HOH HOH . O 8 HOH B 22 1022 1022 HOH HOH . O 8 HOH B 23 1023 1023 HOH HOH . O 8 HOH B 24 1024 1024 HOH HOH . O 8 HOH B 25 1025 1025 HOH HOH . O 8 HOH B 26 1026 1026 HOH HOH . O 8 HOH B 27 1027 1027 HOH HOH . O 8 HOH B 28 1028 1028 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 4.287 7.769 64.487 1 32.06 ? CHA HEM 500 B 1 HETATM 2 C CHB HEM . . . I 2 2.839 12.328 64.993 1 29.93 ? CHB HEM 500 B 1 HETATM 3 C CHC HEM . . . I 2 3.845 12.108 69.718 1 30.82 ? CHC HEM 500 B 1 HETATM 4 C CHD HEM . . . I 2 6.262 8.082 68.937 1 31.88 ? CHD HEM 500 B 1 HETATM 5 C C1A HEM . . . I 2 3.679 8.955 64.223 1 30.46 ? C1A HEM 500 B 1 HETATM 6 C C2A HEM . . . I 2 2.964 9.323 63.017 1 31.64 ? C2A HEM 500 B 1 HETATM 7 C C3A HEM . . . I 2 2.571 10.589 63.174 1 30.56 ? C3A HEM 500 B 1 HETATM 8 C C4A HEM . . . I 2 3.027 11.067 64.464 1 30.21 ? C4A HEM 500 B 1 HETATM 9 C CMA HEM . . . I 2 1.762 11.412 62.164 1 30.44 ? CMA HEM 500 B 1 HETATM 10 C CAA HEM . . . I 2 2.666 8.428 61.792 1 32.31 ? CAA HEM 500 B 1 HETATM 11 C CBA HEM . . . I 2 1.751 7.341 62.336 1 35.45 ? CBA HEM 500 B 1 HETATM 12 C CGA HEM . . . I 2 0.676 6.755 61.439 1 37.06 ? CGA HEM 500 B 1 HETATM 13 O O1A HEM . . . I 2 0.299 7.344 60.38 1 36.07 ? O1A HEM 500 B 1 HETATM 14 O O2A HEM . . . I 2 0.173 5.655 61.843 1 38.08 ? O2A HEM 500 B 1 HETATM 15 C C1B HEM . . . I 2 2.939 12.676 66.323 1 29.01 ? C1B HEM 500 B 1 HETATM 16 C C2B HEM . . . I 2 2.499 13.914 66.958 1 29.54 ? C2B HEM 500 B 1 HETATM 17 C C3B HEM . . . I 2 2.772 13.826 68.26 1 30.49 ? C3B HEM 500 B 1 HETATM 18 C C4B HEM . . . I 2 3.4 12.549 68.489 1 31.24 ? C4B HEM 500 B 1 HETATM 19 C CMB HEM . . . I 2 1.824 15.124 66.278 1 26.69 ? CMB HEM 500 B 1 HETATM 20 C CAB HEM . . . I 2 2.5 14.874 69.366 1 30.44 ? CAB HEM 500 B 1 HETATM 21 C CBB HEM . . . I 2 3.167 14.799 70.525 1 29.21 ? CBB HEM 500 B 1 HETATM 22 C C1C HEM . . . I 2 4.57 10.972 69.928 1 29.61 ? C1C HEM 500 B 1 HETATM 23 C C2C HEM . . . I 2 4.976 10.464 71.212 1 30.68 ? C2C HEM 500 B 1 HETATM 24 C C3C HEM . . . I 2 5.645 9.341 70.977 1 31.33 ? C3C HEM 500 B 1 HETATM 25 C C4C HEM . . . I 2 5.671 9.129 69.558 1 30 ? C4C HEM 500 B 1 HETATM 26 C CMC HEM . . . I 2 4.678 11.087 72.604 1 30.14 ? CMC HEM 500 B 1 HETATM 27 C CAC HEM . . . I 2 6.295 8.424 72.03 1 31.54 ? CAC HEM 500 B 1 HETATM 28 C CBC HEM . . . I 2 6.265 8.771 73.316 1 31.69 ? CBC HEM 500 B 1 HETATM 29 C C1D HEM . . . I 2 5.904 7.554 67.72 1 32.03 ? C1D HEM 500 B 1 HETATM 30 C C2D HEM . . . I 2 6.267 6.24 67.237 1 30.69 ? C2D HEM 500 B 1 HETATM 31 C C3D HEM . . . I 2 5.649 6.153 65.852 1 31.34 ? C3D HEM 500 B 1 HETATM 32 C C4D HEM . . . I 2 4.992 7.426 65.628 1 32.47 ? C4D HEM 500 B 1 HETATM 33 C CMD HEM . . . I 2 7.092 5.159 67.952 1 28.36 ? CMD HEM 500 B 1 HETATM 34 C CAD HEM . . . I 2 5.762 4.951 64.9 1 33.24 ? CAD HEM 500 B 1 HETATM 35 C CBD HEM . . . I 2 4.45 4.223 64.613 1 35.11 ? CBD HEM 500 B 1 HETATM 36 C CGD HEM . . . I 2 4.796 2.927 63.912 1 38.33 ? CGD HEM 500 B 1 HETATM 37 O O1D HEM . . . I 2 6.036 2.575 63.767 1 41.03 ? O1D HEM 500 B 1 HETATM 38 O O2D HEM . . . I 2 3.813 2.24 63.505 1 38.66 ? O2D HEM 500 B 1 HETATM 39 N NA HEM . . . I 2 3.722 10.038 65.07 1 30.11 ? NA HEM 500 B 1 HETATM 40 N NB HEM . . . I 2 3.513 11.887 67.281 1 29.36 ? NB HEM 500 B 1 HETATM 41 N NC HEM . . . I 2 5.014 10.137 68.938 1 29.11 ? NC HEM 500 B 1 HETATM 42 N ND HEM . . . I 2 5.189 8.231 66.744 1 31.79 ? ND HEM 500 B 1 HETATM 43 FE FE HEM . . . I 2 4.408 10.1 67.009 1 30.75 ? FE HEM 500 B 1 # _model_server_stats.io_time_ms 87 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #