data_3RUK # _model_server_result.job_id 07ZegPX8tdyPZR-yiyje5A _model_server_result.datetime_utc '2024-10-12 08:22:08' _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 3ruk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":600}' # _entry.id 3RUK # _exptl.entry_id 3RUK _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 90 _cell.angle_gamma 90 _cell.entry_id 3RUK _cell.length_a 85.813 _cell.length_b 152.098 _cell.length_c 172.882 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RUK _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,M 1 1 B,G,H,N 2 1 C,I,J,O 3 1 D,K,L,P 4 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 K 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 424 A CYS 442 1_555 E FE HEM . A HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc2 E FE HEM . A HEM 600 1_555 F N22 AER . A AER 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc3 B SG CYS 424 B CYS 442 1_555 G FE HEM . B HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc4 G FE HEM . B HEM 600 1_555 H N22 AER . B AER 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc5 C SG CYS 424 C CYS 442 1_555 I FE HEM . C HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc6 I FE HEM . C HEM 600 1_555 J N22 AER . C AER 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc7 D SG CYS 424 D CYS 442 1_555 K FE HEM . D HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc8 K FE HEM . D HEM 600 1_555 L N22 AER . D AER 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? # _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 190 n n CHA C4D HEM doub 191 n n CHA HHA HEM sing 192 n n CHB C4A HEM sing 193 n n CHB C1B HEM doub 194 n n CHB HHB HEM sing 195 n n CHC C4B HEM sing 196 n n CHC C1C HEM doub 197 n n CHC HHC HEM sing 198 n n CHD C4C HEM doub 199 n n CHD C1D HEM sing 200 n n CHD HHD HEM sing 201 n n C1A C2A HEM doub 202 n y C1A NA HEM sing 203 n y C2A C3A HEM sing 204 n y C2A CAA HEM sing 205 n n C3A C4A HEM doub 206 n y C3A CMA HEM sing 207 n n C4A NA HEM sing 208 n y CMA HMA HEM sing 209 n n CMA HMAA HEM sing 210 n n CMA HMAB HEM sing 211 n n CAA CBA HEM sing 212 n n CAA HAA HEM sing 213 n n CAA HAAA HEM sing 214 n n CBA CGA HEM sing 215 n n CBA HBA HEM sing 216 n n CBA HBAA HEM sing 217 n n CGA O1A HEM doub 218 n n CGA O2A HEM sing 219 n n C1B C2B HEM sing 220 n n C1B NB HEM sing 221 n n C2B C3B HEM doub 222 n n C2B CMB HEM sing 223 n n C3B C4B HEM sing 224 n n C3B CAB HEM sing 225 n n C4B NB HEM doub 226 n n CMB HMB HEM sing 227 n n CMB HMBA HEM sing 228 n n CMB HMBB HEM sing 229 n n CAB CBB HEM doub 230 n n CAB HAB HEM sing 231 n n CBB HBB HEM sing 232 n n CBB HBBA HEM sing 233 n n C1C C2C HEM sing 234 n y C1C NC HEM sing 235 n y C2C C3C HEM doub 236 n y C2C CMC HEM sing 237 n n C3C C4C HEM sing 238 n y C3C CAC HEM sing 239 n n C4C NC HEM sing 240 n y CMC HMC HEM sing 241 n n CMC HMCA HEM sing 242 n n CMC HMCB HEM sing 243 n n CAC CBC HEM doub 244 n n CAC HAC HEM sing 245 n n CBC HBC HEM sing 246 n n CBC HBCA HEM sing 247 n n C1D C2D HEM sing 248 n n C1D ND HEM doub 249 n n C2D C3D HEM doub 250 n n C2D CMD HEM sing 251 n n C3D C4D HEM sing 252 n n C3D CAD HEM sing 253 n n C4D ND HEM sing 254 n n CMD HMD HEM sing 255 n n CMD HMDA HEM sing 256 n n CMD HMDB HEM sing 257 n n CAD CBD HEM sing 258 n n CAD HAD HEM sing 259 n n CAD HADA HEM sing 260 n n CBD CGD HEM sing 261 n n CBD HBD HEM sing 262 n n CBD HBDA HEM sing 263 n n CGD O1D HEM doub 264 n n CGD O2D HEM sing 265 n n O2A H2A HEM sing 266 n n O2D H2D HEM sing 267 n n FE NA HEM sing 268 n n FE NB HEM sing 269 n n FE NC HEM sing 270 n n FE ND HEM sing 271 n n # _atom_sites.entry_id 3RUK _atom_sites.fract_transf_matrix[1][1] 0.011653 _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] 0.006575 _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] 0.005784 _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 1 600 600 HEM HEM . F 3 AER A 1 601 601 AER AER . G 2 HEM B 1 600 600 HEM HEM . H 3 AER B 1 601 601 AER AER . I 2 HEM C 1 600 600 HEM HEM . J 3 AER C 1 601 601 AER AER . K 2 HEM D 1 600 600 HEM HEM . L 3 AER D 1 601 601 AER AER . M 4 HOH A 1 3 3 HOH HOH . M 4 HOH A 2 5 5 HOH HOH . M 4 HOH A 3 8 8 HOH HOH . M 4 HOH A 4 9 9 HOH HOH . M 4 HOH A 5 18 18 HOH HOH . M 4 HOH A 6 513 19 HOH HOH . M 4 HOH A 7 514 21 HOH HOH . M 4 HOH A 8 515 23 HOH HOH . M 4 HOH A 9 516 32 HOH HOH . M 4 HOH A 10 517 34 HOH HOH . M 4 HOH A 11 518 35 HOH HOH . M 4 HOH A 12 519 36 HOH HOH . M 4 HOH A 13 520 41 HOH HOH . M 4 HOH A 14 521 46 HOH HOH . M 4 HOH A 15 522 49 HOH HOH . M 4 HOH A 16 523 53 HOH HOH . M 4 HOH A 17 524 54 HOH HOH . M 4 HOH A 18 525 55 HOH HOH . M 4 HOH A 19 526 57 HOH HOH . M 4 HOH A 20 527 58 HOH HOH . M 4 HOH A 21 528 60 HOH HOH . M 4 HOH A 22 529 63 HOH HOH . M 4 HOH A 23 530 65 HOH HOH . M 4 HOH A 24 531 68 HOH HOH . M 4 HOH A 25 532 73 HOH HOH . M 4 HOH A 26 533 75 HOH HOH . M 4 HOH A 27 534 76 HOH HOH . M 4 HOH A 28 535 77 HOH HOH . M 4 HOH A 29 536 80 HOH HOH . M 4 HOH A 30 537 83 HOH HOH . M 4 HOH A 31 538 84 HOH HOH . M 4 HOH A 32 539 86 HOH HOH . M 4 HOH A 33 540 89 HOH HOH . M 4 HOH A 34 541 91 HOH HOH . M 4 HOH A 35 542 92 HOH HOH . M 4 HOH A 36 543 94 HOH HOH . M 4 HOH A 37 544 100 HOH HOH . M 4 HOH A 38 545 101 HOH HOH . M 4 HOH A 39 546 103 HOH HOH . M 4 HOH A 40 547 111 HOH HOH . M 4 HOH A 41 548 112 HOH HOH . M 4 HOH A 42 549 113 HOH HOH . M 4 HOH A 43 550 118 HOH HOH . N 4 HOH B 1 1 1 HOH HOH . N 4 HOH B 2 2 2 HOH HOH . N 4 HOH B 3 4 4 HOH HOH . N 4 HOH B 4 12 12 HOH HOH . N 4 HOH B 5 15 15 HOH HOH . N 4 HOH B 6 513 20 HOH HOH . N 4 HOH B 7 514 25 HOH HOH . N 4 HOH B 8 515 26 HOH HOH . N 4 HOH B 9 516 31 HOH HOH . N 4 HOH B 10 517 39 HOH HOH . N 4 HOH B 11 518 42 HOH HOH . N 4 HOH B 12 519 43 HOH HOH . N 4 HOH B 13 520 44 HOH HOH . N 4 HOH B 14 521 52 HOH HOH . N 4 HOH B 15 522 67 HOH HOH . N 4 HOH B 16 523 71 HOH HOH . N 4 HOH B 17 524 81 HOH HOH . N 4 HOH B 18 525 85 HOH HOH . N 4 HOH B 19 526 90 HOH HOH . N 4 HOH B 20 527 105 HOH HOH . N 4 HOH B 21 528 110 HOH HOH . N 4 HOH B 22 529 114 HOH HOH . O 4 HOH C 1 11 11 HOH HOH . O 4 HOH C 2 14 14 HOH HOH . O 4 HOH C 3 16 16 HOH HOH . O 4 HOH C 4 17 17 HOH HOH . O 4 HOH C 5 513 22 HOH HOH . O 4 HOH C 6 514 28 HOH HOH . O 4 HOH C 7 515 29 HOH HOH . O 4 HOH C 8 516 30 HOH HOH . O 4 HOH C 9 517 33 HOH HOH . O 4 HOH C 10 518 50 HOH HOH . O 4 HOH C 11 519 64 HOH HOH . O 4 HOH C 12 520 69 HOH HOH . O 4 HOH C 13 521 70 HOH HOH . O 4 HOH C 14 522 78 HOH HOH . O 4 HOH C 15 523 79 HOH HOH . O 4 HOH C 16 524 87 HOH HOH . O 4 HOH C 17 525 88 HOH HOH . O 4 HOH C 18 526 95 HOH HOH . O 4 HOH C 19 527 96 HOH HOH . O 4 HOH C 20 528 97 HOH HOH . O 4 HOH C 21 529 99 HOH HOH . O 4 HOH C 22 530 107 HOH HOH . O 4 HOH C 23 531 115 HOH HOH . P 4 HOH D 1 6 6 HOH HOH . P 4 HOH D 2 7 7 HOH HOH . P 4 HOH D 3 10 10 HOH HOH . P 4 HOH D 4 13 13 HOH HOH . P 4 HOH D 5 513 24 HOH HOH . P 4 HOH D 6 514 27 HOH HOH . P 4 HOH D 7 515 37 HOH HOH . P 4 HOH D 8 516 38 HOH HOH . P 4 HOH D 9 517 40 HOH HOH . P 4 HOH D 10 518 45 HOH HOH . P 4 HOH D 11 519 47 HOH HOH . P 4 HOH D 12 520 48 HOH HOH . P 4 HOH D 13 521 51 HOH HOH . P 4 HOH D 14 522 56 HOH HOH . P 4 HOH D 15 523 59 HOH HOH . P 4 HOH D 16 524 61 HOH HOH . P 4 HOH D 17 525 62 HOH HOH . P 4 HOH D 18 526 66 HOH HOH . P 4 HOH D 19 527 72 HOH HOH . P 4 HOH D 20 528 74 HOH HOH . P 4 HOH D 21 529 82 HOH HOH . P 4 HOH D 22 530 93 HOH HOH . P 4 HOH D 23 531 98 HOH HOH . P 4 HOH D 24 532 102 HOH HOH . P 4 HOH D 25 533 104 HOH HOH . P 4 HOH D 26 534 106 HOH HOH . P 4 HOH D 27 535 108 HOH HOH . P 4 HOH D 28 536 109 HOH HOH . P 4 HOH D 29 537 116 HOH HOH . P 4 HOH D 30 538 117 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 . . . K 2 -13.947 12.273 64.69 1 27.34 ? CHA HEM 600 D 1 HETATM 2 C CHB HEM . . . K 2 -13.048 11.367 69.346 1 25.7 ? CHB HEM 600 D 1 HETATM 3 C CHC HEM . . . K 2 -11.803 6.793 68.35 1 26.5 ? CHC HEM 600 D 1 HETATM 4 C CHD HEM . . . K 2 -13.311 7.593 63.799 1 27.38 ? CHD HEM 600 D 1 HETATM 5 C C1A HEM . . . K 2 -13.699 12.429 66.021 1 27.37 ? C1A HEM 600 D 1 HETATM 6 C C2A HEM . . . K 2 -13.69 13.689 66.731 1 28.53 ? C2A HEM 600 D 1 HETATM 7 C C3A HEM . . . K 2 -13.442 13.454 68.036 1 28.62 ? C3A HEM 600 D 1 HETATM 8 C C4A HEM . . . K 2 -13.305 12.021 68.171 1 27.7 ? C4A HEM 600 D 1 HETATM 9 C CMA HEM . . . K 2 -13.328 14.504 69.179 1 24.42 ? CMA HEM 600 D 1 HETATM 10 C CAA HEM . . . K 2 -13.879 15.061 66.07 1 28.19 ? CAA HEM 600 D 1 HETATM 11 C CBA HEM . . . K 2 -15.316 15.409 65.88 1 31.87 ? CBA HEM 600 D 1 HETATM 12 C CGA HEM . . . K 2 -15.274 16.825 65.413 1 34.82 ? CGA HEM 600 D 1 HETATM 13 O O1A HEM . . . K 2 -15.973 17.626 66.087 1 41.36 ? O1A HEM 600 D 1 HETATM 14 O O2A HEM . . . K 2 -14.577 17.15 64.412 1 33.7 ? O2A HEM 600 D 1 HETATM 15 C C1B HEM . . . K 2 -12.596 10.081 69.515 1 25.78 ? C1B HEM 600 D 1 HETATM 16 C C2B HEM . . . K 2 -12.161 9.493 70.762 1 28.61 ? C2B HEM 600 D 1 HETATM 17 C C3B HEM . . . K 2 -11.803 8.23 70.485 1 28.07 ? C3B HEM 600 D 1 HETATM 18 C C4B HEM . . . K 2 -12.028 7.964 69.076 1 26.42 ? C4B HEM 600 D 1 HETATM 19 C CMB HEM . . . K 2 -12.112 10.191 72.164 1 21.16 ? CMB HEM 600 D 1 HETATM 20 C CAB HEM . . . K 2 -11.3 7.258 71.577 1 29.12 ? CAB HEM 600 D 1 HETATM 21 C CBB HEM . . . K 2 -10.1 6.704 71.584 1 29.92 ? CBB HEM 600 D 1 HETATM 22 C C1C HEM . . . K 2 -12.221 6.555 67.044 1 25.82 ? C1C HEM 600 D 1 HETATM 23 C C2C HEM . . . K 2 -12.398 5.278 66.374 1 25.55 ? C2C HEM 600 D 1 HETATM 24 C C3C HEM . . . K 2 -12.814 5.541 65.117 1 26.46 ? C3C HEM 600 D 1 HETATM 25 C C4C HEM . . . K 2 -12.924 6.971 64.969 1 26.82 ? C4C HEM 600 D 1 HETATM 26 C CMC HEM . . . K 2 -12.167 3.884 67.011 1 22.93 ? CMC HEM 600 D 1 HETATM 27 C CAC HEM . . . K 2 -13.212 4.606 63.942 1 24.6 ? CAC HEM 600 D 1 HETATM 28 C CBC HEM . . . K 2 -12.648 3.445 63.709 1 23.37 ? CBC HEM 600 D 1 HETATM 29 C C1D HEM . . . K 2 -13.54 8.92 63.573 1 27.95 ? C1D HEM 600 D 1 HETATM 30 C C2D HEM . . . K 2 -13.799 9.514 62.285 1 29.14 ? C2D HEM 600 D 1 HETATM 31 C C3D HEM . . . K 2 -14.029 10.991 62.579 1 29.54 ? C3D HEM 600 D 1 HETATM 32 C C4D HEM . . . K 2 -13.865 11.11 64.001 1 27.6 ? C4D HEM 600 D 1 HETATM 33 C CMD HEM . . . K 2 -13.855 8.809 60.914 1 30.39 ? CMD HEM 600 D 1 HETATM 34 C CAD HEM . . . K 2 -14.356 12.144 61.596 1 30.4 ? CAD HEM 600 D 1 HETATM 35 C CBD HEM . . . K 2 -15.868 12.199 61.332 1 30.4 ? CBD HEM 600 D 1 HETATM 36 C CGD HEM . . . K 2 -16.218 13.31 60.363 1 30.49 ? CGD HEM 600 D 1 HETATM 37 O O1D HEM . . . K 2 -17.384 13.428 59.906 1 29.13 ? O1D HEM 600 D 1 HETATM 38 O O2D HEM . . . K 2 -15.314 14.113 60.048 1 34.15 ? O2D HEM 600 D 1 HETATM 39 N NA HEM . . . K 2 -13.448 11.426 66.911 1 27.8 ? NA HEM 600 D 1 HETATM 40 N NB HEM . . . K 2 -12.491 9.133 68.53 1 26.95 ? NB HEM 600 D 1 HETATM 41 N NC HEM . . . K 2 -12.566 7.561 66.151 1 26.87 ? NC HEM 600 D 1 HETATM 42 N ND HEM . . . K 2 -13.583 9.89 64.551 1 28.17 ? ND HEM 600 D 1 HETATM 43 FE FE HEM . . . K 2 -13.002 9.536 66.524 1 28.1 ? FE HEM 600 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #