data_4NVJ # _model_server_result.job_id HaWUWMcp0e3Kf3m1JyvcpQ _model_server_result.datetime_utc '2024-11-25 08:58:09' _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 4nvj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4NVJ # _exptl.entry_id 4NVJ _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 1 _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 4NVJ _cell.length_a 51.3 _cell.length_b 73.08 _cell.length_c 104.03 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NVJ _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 172 B HIS 175 1_555 B FE HEM . B HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc2 B FE HEM . B HEM 301 1_555 E O HOH . B HOH 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? # _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 156 n n CHA C4D HEM doub 157 n n CHA HHA HEM sing 158 n n CHB C4A HEM sing 159 n n CHB C1B HEM doub 160 n n CHB HHB HEM sing 161 n n CHC C4B HEM sing 162 n n CHC C1C HEM doub 163 n n CHC HHC HEM sing 164 n n CHD C4C HEM doub 165 n n CHD C1D HEM sing 166 n n CHD HHD HEM sing 167 n n C1A C2A HEM doub 168 n y C1A NA HEM sing 169 n y C2A C3A HEM sing 170 n y C2A CAA HEM sing 171 n n C3A C4A HEM doub 172 n y C3A CMA HEM sing 173 n n C4A NA HEM sing 174 n y CMA HMA HEM sing 175 n n CMA HMAA HEM sing 176 n n CMA HMAB HEM sing 177 n n CAA CBA HEM sing 178 n n CAA HAA HEM sing 179 n n CAA HAAA HEM sing 180 n n CBA CGA HEM sing 181 n n CBA HBA HEM sing 182 n n CBA HBAA HEM sing 183 n n CGA O1A HEM doub 184 n n CGA O2A HEM sing 185 n n C1B C2B HEM sing 186 n n C1B NB HEM sing 187 n n C2B C3B HEM doub 188 n n C2B CMB HEM sing 189 n n C3B C4B HEM sing 190 n n C3B CAB HEM sing 191 n n C4B NB HEM doub 192 n n CMB HMB HEM sing 193 n n CMB HMBA HEM sing 194 n n CMB HMBB HEM sing 195 n n CAB CBB HEM doub 196 n n CAB HAB HEM sing 197 n n CBB HBB HEM sing 198 n n CBB HBBA HEM sing 199 n n C1C C2C HEM sing 200 n y C1C NC HEM sing 201 n y C2C C3C HEM doub 202 n y C2C CMC HEM sing 203 n n C3C C4C HEM sing 204 n y C3C CAC HEM sing 205 n n C4C NC HEM sing 206 n y CMC HMC HEM sing 207 n n CMC HMCA HEM sing 208 n n CMC HMCB HEM sing 209 n n CAC CBC HEM doub 210 n n CAC HAC HEM sing 211 n n CBC HBC HEM sing 212 n n CBC HBCA HEM sing 213 n n C1D C2D HEM sing 214 n n C1D ND HEM doub 215 n n C2D C3D HEM doub 216 n n C2D CMD HEM sing 217 n n C3D C4D HEM sing 218 n n C3D CAD HEM sing 219 n n C4D ND HEM sing 220 n n CMD HMD HEM sing 221 n n CMD HMDA HEM sing 222 n n CMD HMDB HEM sing 223 n n CAD CBD HEM sing 224 n n CAD HAD HEM sing 225 n n CAD HADA HEM sing 226 n n CBD CGD HEM sing 227 n n CBD HBD HEM sing 228 n n CBD HBDA HEM sing 229 n n CGD O1D HEM doub 230 n n CGD O2D HEM sing 231 n n O2A H2A HEM sing 232 n n O2D H2D HEM sing 233 n n FE NA HEM sing 234 n n FE NB HEM sing 235 n n FE NC HEM sing 236 n n FE ND HEM sing 237 n n # _atom_sites.entry_id 4NVJ _atom_sites.fract_transf_matrix[1][1] 0.019493 _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] 0.013684 _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] 0.009613 _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 B 2 HEM B 1 301 1 HEM HEM . C 3 2NX B 1 302 1 2NX DRG . D 4 MES B 1 303 1 MES MES . E 5 HOH B 1 401 1 HOH HOH . E 5 HOH B 2 402 2 HOH HOH . E 5 HOH B 3 403 3 HOH HOH . E 5 HOH B 4 404 4 HOH HOH . E 5 HOH B 5 405 5 HOH HOH . E 5 HOH B 6 406 6 HOH HOH . E 5 HOH B 7 407 7 HOH HOH . E 5 HOH B 8 408 8 HOH HOH . E 5 HOH B 9 409 9 HOH HOH . E 5 HOH B 10 410 10 HOH HOH . E 5 HOH B 11 411 11 HOH HOH . E 5 HOH B 12 412 13 HOH HOH . E 5 HOH B 13 413 14 HOH HOH . E 5 HOH B 14 414 15 HOH HOH . E 5 HOH B 15 415 16 HOH HOH . E 5 HOH B 16 416 17 HOH HOH . E 5 HOH B 17 417 18 HOH HOH . E 5 HOH B 18 418 19 HOH HOH . E 5 HOH B 19 419 20 HOH HOH . E 5 HOH B 20 420 21 HOH HOH . E 5 HOH B 21 421 22 HOH HOH . E 5 HOH B 22 422 23 HOH HOH . E 5 HOH B 23 423 24 HOH HOH . E 5 HOH B 24 424 25 HOH HOH . E 5 HOH B 25 425 26 HOH HOH . E 5 HOH B 26 426 27 HOH HOH . E 5 HOH B 27 427 28 HOH HOH . E 5 HOH B 28 428 29 HOH HOH . E 5 HOH B 29 429 30 HOH HOH . E 5 HOH B 30 430 31 HOH HOH . E 5 HOH B 31 431 32 HOH HOH . E 5 HOH B 32 432 33 HOH HOH . E 5 HOH B 33 433 34 HOH HOH . E 5 HOH B 34 434 35 HOH HOH . E 5 HOH B 35 435 36 HOH HOH . E 5 HOH B 36 436 37 HOH HOH . E 5 HOH B 37 437 38 HOH HOH . E 5 HOH B 38 438 39 HOH HOH . E 5 HOH B 39 439 40 HOH HOH . E 5 HOH B 40 440 41 HOH HOH . E 5 HOH B 41 441 42 HOH HOH . E 5 HOH B 42 442 43 HOH HOH . E 5 HOH B 43 443 44 HOH HOH . E 5 HOH B 44 444 45 HOH HOH . E 5 HOH B 45 445 46 HOH HOH . E 5 HOH B 46 446 47 HOH HOH . E 5 HOH B 47 447 48 HOH HOH . E 5 HOH B 48 448 49 HOH HOH . E 5 HOH B 49 449 50 HOH HOH . E 5 HOH B 50 450 51 HOH HOH . E 5 HOH B 51 451 52 HOH HOH . E 5 HOH B 52 452 53 HOH HOH . E 5 HOH B 53 453 54 HOH HOH . E 5 HOH B 54 454 55 HOH HOH . E 5 HOH B 55 455 56 HOH HOH . E 5 HOH B 56 456 57 HOH HOH . E 5 HOH B 57 457 58 HOH HOH . E 5 HOH B 58 458 59 HOH HOH . E 5 HOH B 59 459 60 HOH HOH . E 5 HOH B 60 460 61 HOH HOH . E 5 HOH B 61 461 62 HOH HOH . E 5 HOH B 62 462 63 HOH HOH . E 5 HOH B 63 463 64 HOH HOH . E 5 HOH B 64 464 65 HOH HOH . E 5 HOH B 65 465 66 HOH HOH . E 5 HOH B 66 466 67 HOH HOH . E 5 HOH B 67 467 68 HOH HOH . E 5 HOH B 68 468 69 HOH HOH . E 5 HOH B 69 469 70 HOH HOH . E 5 HOH B 70 470 71 HOH HOH . E 5 HOH B 71 471 72 HOH HOH . E 5 HOH B 72 472 73 HOH HOH . E 5 HOH B 73 473 74 HOH HOH . E 5 HOH B 74 474 75 HOH HOH . E 5 HOH B 75 475 76 HOH HOH . E 5 HOH B 76 476 77 HOH HOH . E 5 HOH B 77 477 78 HOH HOH . E 5 HOH B 78 478 79 HOH HOH . E 5 HOH B 79 479 80 HOH HOH . E 5 HOH B 80 480 81 HOH HOH . E 5 HOH B 81 481 82 HOH HOH . E 5 HOH B 82 482 83 HOH HOH . E 5 HOH B 83 483 84 HOH HOH . E 5 HOH B 84 484 85 HOH HOH . E 5 HOH B 85 485 86 HOH HOH . E 5 HOH B 86 486 87 HOH HOH . E 5 HOH B 87 487 88 HOH HOH . E 5 HOH B 88 488 90 HOH HOH . E 5 HOH B 89 489 91 HOH HOH . E 5 HOH B 90 490 92 HOH HOH . E 5 HOH B 91 491 93 HOH HOH . E 5 HOH B 92 492 94 HOH HOH . E 5 HOH B 93 493 95 HOH HOH . E 5 HOH B 94 494 96 HOH HOH . E 5 HOH B 95 495 97 HOH HOH . E 5 HOH B 96 496 98 HOH HOH . E 5 HOH B 97 497 99 HOH HOH . E 5 HOH B 98 498 100 HOH HOH . E 5 HOH B 99 499 101 HOH HOH . E 5 HOH B 100 500 102 HOH HOH . E 5 HOH B 101 501 103 HOH HOH . E 5 HOH B 102 502 104 HOH HOH . E 5 HOH B 103 503 105 HOH HOH . E 5 HOH B 104 504 106 HOH HOH . E 5 HOH B 105 505 107 HOH HOH . E 5 HOH B 106 506 108 HOH HOH . E 5 HOH B 107 507 109 HOH HOH . E 5 HOH B 108 508 110 HOH HOH . E 5 HOH B 109 509 111 HOH HOH . E 5 HOH B 110 510 112 HOH HOH . E 5 HOH B 111 511 113 HOH HOH . E 5 HOH B 112 512 114 HOH HOH . E 5 HOH B 113 513 115 HOH HOH . E 5 HOH B 114 514 117 HOH HOH . E 5 HOH B 115 515 118 HOH HOH . E 5 HOH B 116 516 120 HOH HOH . E 5 HOH B 117 517 121 HOH HOH . E 5 HOH B 118 518 122 HOH HOH . E 5 HOH B 119 519 123 HOH HOH . E 5 HOH B 120 520 124 HOH HOH . E 5 HOH B 121 521 125 HOH HOH . E 5 HOH B 122 522 126 HOH HOH . E 5 HOH B 123 523 127 HOH HOH . E 5 HOH B 124 524 128 HOH HOH . E 5 HOH B 125 525 129 HOH HOH . E 5 HOH B 126 526 130 HOH HOH . E 5 HOH B 127 527 131 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 . . . B 2 15.414 -0.181 1.807 1 18.12 ? CHA HEM 301 B 1 HETATM 2 C CHB HEM . . . B 2 11.191 -0.695 -0.511 1 17.05 ? CHB HEM 301 B 1 HETATM 3 C CHC HEM . . . B 2 9.924 3.793 0.954 1 16.43 ? CHC HEM 301 B 1 HETATM 4 C CHD HEM . . . B 2 13.887 3.999 3.798 1 13.63 ? CHD HEM 301 B 1 HETATM 5 C C1A HEM . . . B 2 14.374 -0.73 1.08 1 20.54 ? C1A HEM 301 B 1 HETATM 6 C C2A HEM . . . B 2 14.4 -2.014 0.418 1 16.72 ? C2A HEM 301 B 1 HETATM 7 C C3A HEM . . . B 2 13.228 -2.18 -0.237 1 19.12 ? C3A HEM 301 B 1 HETATM 8 C C4A HEM . . . B 2 12.436 -0.971 -0.025 1 16.64 ? C4A HEM 301 B 1 HETATM 9 C CMA HEM . . . B 2 12.764 -3.4 -1.079 1 18.19 ? CMA HEM 301 B 1 HETATM 10 C CAA HEM . . . B 2 15.59 -3.023 0.564 1 20.54 ? CAA HEM 301 B 1 HETATM 11 C CBA HEM . . . B 2 15.321 -3.838 1.87 1 22.45 ? CBA HEM 301 B 1 HETATM 12 C CGA HEM . . . B 2 16.499 -4.777 2.072 1 27.87 ? CGA HEM 301 B 1 HETATM 13 O O1A HEM . . . B 2 16.719 -5.557 1.117 1 27.01 ? O1A HEM 301 B 1 HETATM 14 O O2A HEM . . . B 2 17.233 -4.746 3.114 1 23.72 ? O2A HEM 301 B 1 HETATM 15 C C1B HEM . . . B 2 10.524 0.505 -0.32 1 17.24 ? C1B HEM 301 B 1 HETATM 16 C C2B HEM . . . B 2 9.284 0.836 -0.969 1 18.36 ? C2B HEM 301 B 1 HETATM 17 C C3B HEM . . . B 2 8.933 2.056 -0.582 1 16.69 ? C3B HEM 301 B 1 HETATM 18 C C4B HEM . . . B 2 9.94 2.547 0.334 1 15.07 ? C4B HEM 301 B 1 HETATM 19 C CMB HEM . . . B 2 8.51 -0.128 -1.909 1 16.14 ? CMB HEM 301 B 1 HETATM 20 C CAB HEM . . . B 2 7.667 2.87 -0.971 1 16.28 ? CAB HEM 301 B 1 HETATM 21 C CBB HEM . . . B 2 7.177 2.83 -2.222 1 20.55 ? CBB HEM 301 B 1 HETATM 22 C C1C HEM . . . B 2 10.833 4.194 1.924 1 13.26 ? C1C HEM 301 B 1 HETATM 23 C C2C HEM . . . B 2 10.733 5.343 2.783 1 16.19 ? C2C HEM 301 B 1 HETATM 24 C C3C HEM . . . B 2 11.833 5.374 3.575 1 15.04 ? C3C HEM 301 B 1 HETATM 25 C C4C HEM . . . B 2 12.643 4.25 3.249 1 14.09 ? C4C HEM 301 B 1 HETATM 26 C CMC HEM . . . B 2 9.536 6.305 2.768 1 15.29 ? CMC HEM 301 B 1 HETATM 27 C CAC HEM . . . B 2 12.208 6.324 4.707 1 15.07 ? CAC HEM 301 B 1 HETATM 28 C CBC HEM . . . B 2 11.828 7.619 4.757 1 19 ? CBC HEM 301 B 1 HETATM 29 C C1D HEM . . . B 2 14.693 2.944 3.433 1 16.29 ? C1D HEM 301 B 1 HETATM 30 C C2D HEM . . . B 2 16.064 2.794 3.858 1 15.96 ? C2D HEM 301 B 1 HETATM 31 C C3D HEM . . . B 2 16.531 1.517 3.246 1 15.89 ? C3D HEM 301 B 1 HETATM 32 C C4D HEM . . . B 2 15.425 1.007 2.504 1 16.87 ? C4D HEM 301 B 1 HETATM 33 C CMD HEM . . . B 2 16.868 3.781 4.746 1 17.35 ? CMD HEM 301 B 1 HETATM 34 C CAD HEM . . . B 2 17.958 0.93 3.408 1 17.27 ? CAD HEM 301 B 1 HETATM 35 C CBD HEM . . . B 2 17.915 0.043 4.685 1 18.45 ? CBD HEM 301 B 1 HETATM 36 C CGD HEM . . . B 2 19.206 -0.76 4.88 1 19.73 ? CGD HEM 301 B 1 HETATM 37 O O1D HEM . . . B 2 20.235 -0.364 4.28 1 19.76 ? O1D HEM 301 B 1 HETATM 38 O O2D HEM . . . B 2 19.155 -1.756 5.687 1 21.61 ? O2D HEM 301 B 1 HETATM 39 N NA HEM . . . B 2 13.171 -0.131 0.752 1 16 ? NA HEM 301 B 1 HETATM 40 N NB HEM . . . B 2 10.925 1.583 0.444 1 15.87 ? NB HEM 301 B 1 HETATM 41 N NC HEM . . . B 2 12.045 3.58 2.224 1 16.67 ? NC HEM 301 B 1 HETATM 42 N ND HEM . . . B 2 14.356 1.889 2.63 1 17.65 ? ND HEM 301 B 1 HETATM 43 FE FE HEM . . . B 2 12.648 1.759 1.456 1 16.43 ? FE HEM 301 B 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #