data_6VDP # _model_server_result.job_id zyeZm-4GlyfcvL9WGvOhhQ _model_server_result.datetime_utc '2024-11-14 20:33:20' _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 6vdp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6VDP # _exptl.entry_id 6VDP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _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 120 _cell.entry_id 6VDP _cell.length_a 59.863 _cell.length_b 59.863 _cell.length_c 155.848 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VDP _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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 covale ? covale1 A SG CYS 317 A CYS 317 1_555 B CAC HEC . A HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? metalc ? metalc1 A NE2 HIS 274 A HIS 274 1_555 B FE HEC . A HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc2 A NE2 HIS 313 A HIS 313 1_555 B FE HEC . A HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 FE NA HEC sing 129 n n FE NB HEC sing 130 n n FE NC HEC sing 131 n n FE ND HEC sing 132 n n CHA C1A HEC doub 133 n n CHA C4D HEC sing 134 n n CHA HHA HEC sing 135 n n CHB C4A HEC doub 136 n n CHB C1B HEC sing 137 n n CHB HHB HEC sing 138 n n CHC C4B HEC doub 139 n n CHC C1C HEC sing 140 n n CHC HHC HEC sing 141 n n CHD C4C HEC doub 142 n n CHD C1D HEC sing 143 n n CHD HHD HEC sing 144 n n NA C1A HEC sing 145 n y NA C4A HEC sing 146 n y C1A C2A HEC sing 147 n y C2A C3A HEC doub 148 n y C2A CAA HEC sing 149 n n C3A C4A HEC sing 150 n y C3A CMA HEC sing 151 n n CMA HMA1 HEC sing 152 n n CMA HMA2 HEC sing 153 n n CMA HMA3 HEC sing 154 n n CAA CBA HEC sing 155 n n CAA HAA1 HEC sing 156 n n CAA HAA2 HEC sing 157 n n CBA CGA HEC sing 158 n n CBA HBA1 HEC sing 159 n n CBA HBA2 HEC sing 160 n n CGA O1A HEC doub 161 n n CGA O2A HEC sing 162 n n O2A H2A HEC sing 163 n n NB C1B HEC sing 164 n y NB C4B HEC sing 165 n y C1B C2B HEC doub 166 n y C2B C3B HEC sing 167 n y C2B CMB HEC sing 168 n n C3B C4B HEC sing 169 n y C3B CAB HEC doub 170 e n CMB HMB1 HEC sing 171 n n CMB HMB2 HEC sing 172 n n CMB HMB3 HEC sing 173 n n CAB CBB HEC sing 174 n n CAB HAB HEC sing 175 n n CBB HBB1 HEC sing 176 n n CBB HBB2 HEC sing 177 n n CBB HBB3 HEC sing 178 n n NC C1C HEC sing 179 n y NC C4C HEC sing 180 n y C1C C2C HEC doub 181 n y C2C C3C HEC sing 182 n y C2C CMC HEC sing 183 n n C3C C4C HEC sing 184 n y C3C CAC HEC doub 185 e n CMC HMC1 HEC sing 186 n n CMC HMC2 HEC sing 187 n n CMC HMC3 HEC sing 188 n n CAC CBC HEC sing 189 n n CAC HAC HEC sing 190 n n CBC HBC1 HEC sing 191 n n CBC HBC2 HEC sing 192 n n CBC HBC3 HEC sing 193 n n ND C1D HEC sing 194 n y ND C4D HEC sing 195 n y C1D C2D HEC doub 196 n y C2D C3D HEC sing 197 n y C2D CMD HEC sing 198 n n C3D C4D HEC doub 199 n y C3D CAD HEC sing 200 n n CMD HMD1 HEC sing 201 n n CMD HMD2 HEC sing 202 n n CMD HMD3 HEC sing 203 n n CAD CBD HEC sing 204 n n CAD HAD1 HEC sing 205 n n CAD HAD2 HEC sing 206 n n CBD CGD HEC sing 207 n n CBD HBD1 HEC sing 208 n n CBD HBD2 HEC sing 209 n n CGD O1D HEC doub 210 n n CGD O2D HEC sing 211 n n O2D H2D HEC sing 212 n n # _atom_sites.entry_id 6VDP _atom_sites.fract_transf_matrix[1][1] 0.016705 _atom_sites.fract_transf_matrix[1][2] 0.009645 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019289 _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] 0.006417 _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 HEC A 1 401 1 HEC HEC . C 3 HOH A 1 501 75 HOH HOH . C 3 HOH A 2 502 52 HOH HOH . C 3 HOH A 3 503 65 HOH HOH . C 3 HOH A 4 504 8 HOH HOH . C 3 HOH A 5 505 22 HOH HOH . C 3 HOH A 6 506 46 HOH HOH . C 3 HOH A 7 507 37 HOH HOH . C 3 HOH A 8 508 26 HOH HOH . C 3 HOH A 9 509 58 HOH HOH . C 3 HOH A 10 510 51 HOH HOH . C 3 HOH A 11 511 41 HOH HOH . C 3 HOH A 12 512 33 HOH HOH . C 3 HOH A 13 513 53 HOH HOH . C 3 HOH A 14 514 1 HOH HOH . C 3 HOH A 15 515 11 HOH HOH . C 3 HOH A 16 516 76 HOH HOH . C 3 HOH A 17 517 24 HOH HOH . C 3 HOH A 18 518 77 HOH HOH . C 3 HOH A 19 519 19 HOH HOH . C 3 HOH A 20 520 63 HOH HOH . C 3 HOH A 21 521 36 HOH HOH . C 3 HOH A 22 522 5 HOH HOH . C 3 HOH A 23 523 73 HOH HOH . C 3 HOH A 24 524 34 HOH HOH . C 3 HOH A 25 525 44 HOH HOH . C 3 HOH A 26 526 10 HOH HOH . C 3 HOH A 27 527 13 HOH HOH . C 3 HOH A 28 528 17 HOH HOH . C 3 HOH A 29 529 50 HOH HOH . C 3 HOH A 30 530 45 HOH HOH . C 3 HOH A 31 531 21 HOH HOH . C 3 HOH A 32 532 55 HOH HOH . C 3 HOH A 33 533 32 HOH HOH . C 3 HOH A 34 534 9 HOH HOH . C 3 HOH A 35 535 23 HOH HOH . C 3 HOH A 36 536 56 HOH HOH . C 3 HOH A 37 537 67 HOH HOH . C 3 HOH A 38 538 54 HOH HOH . C 3 HOH A 39 539 20 HOH HOH . C 3 HOH A 40 540 14 HOH HOH . C 3 HOH A 41 541 3 HOH HOH . C 3 HOH A 42 542 61 HOH HOH . C 3 HOH A 43 543 59 HOH HOH . C 3 HOH A 44 544 66 HOH HOH . C 3 HOH A 45 545 30 HOH HOH . C 3 HOH A 46 546 31 HOH HOH . C 3 HOH A 47 547 42 HOH HOH . C 3 HOH A 48 548 49 HOH HOH . C 3 HOH A 49 549 70 HOH HOH . C 3 HOH A 50 550 62 HOH HOH . C 3 HOH A 51 551 7 HOH HOH . C 3 HOH A 52 552 47 HOH HOH . C 3 HOH A 53 553 57 HOH HOH . C 3 HOH A 54 554 25 HOH HOH . C 3 HOH A 55 555 39 HOH HOH . C 3 HOH A 56 556 2 HOH HOH . C 3 HOH A 57 557 74 HOH HOH . C 3 HOH A 58 558 64 HOH HOH . C 3 HOH A 59 559 38 HOH HOH . C 3 HOH A 60 560 43 HOH HOH . C 3 HOH A 61 561 18 HOH HOH . C 3 HOH A 62 562 27 HOH HOH . C 3 HOH A 63 563 4 HOH HOH . C 3 HOH A 64 564 40 HOH HOH . C 3 HOH A 65 565 48 HOH HOH . C 3 HOH A 66 566 78 HOH HOH . C 3 HOH A 67 567 69 HOH HOH . C 3 HOH A 68 568 6 HOH HOH . C 3 HOH A 69 569 71 HOH HOH . C 3 HOH A 70 570 16 HOH HOH . C 3 HOH A 71 571 12 HOH HOH . C 3 HOH A 72 572 68 HOH HOH . C 3 HOH A 73 573 15 HOH HOH . C 3 HOH A 74 574 72 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 FE FE HEC . . . B 2 36.928 24.513 69.044 1 37.93 ? FE HEC 401 A 1 HETATM 2 C CHA HEC . . . B 2 38.479 27.587 69.253 1 36.77 ? CHA HEC 401 A 1 HETATM 3 C CHB HEC . . . B 2 34.831 25.767 66.697 1 42.68 ? CHB HEC 401 A 1 HETATM 4 C CHC HEC . . . B 2 35.079 21.741 69.321 1 34.67 ? CHC HEC 401 A 1 HETATM 5 C CHD HEC . . . B 2 39.446 23.103 70.914 1 35.57 ? CHD HEC 401 A 1 HETATM 6 N NA HEC . . . B 2 36.709 26.321 68.147 1 37.29 ? NA HEC 401 A 1 HETATM 7 C C1A HEC . . . B 2 37.426 27.475 68.385 1 37.89 ? C1A HEC 401 A 1 HETATM 8 C C2A HEC . . . B 2 36.858 28.538 67.572 1 42.17 ? C2A HEC 401 A 1 HETATM 9 C C3A HEC . . . B 2 35.853 28.014 66.873 1 43.1 ? C3A HEC 401 A 1 HETATM 10 C C4A HEC . . . B 2 35.75 26.627 67.218 1 37.9 ? C4A HEC 401 A 1 HETATM 11 C CMA HEC . . . B 2 34.922 28.724 65.873 1 43.67 ? CMA HEC 401 A 1 HETATM 12 C CAA HEC . . . B 2 37.318 30.01 67.501 1 45.11 ? CAA HEC 401 A 1 HETATM 13 C CBA HEC . . . B 2 38.144 30.227 66.231 1 47.12 ? CBA HEC 401 A 1 HETATM 14 C CGA HEC . . . B 2 38.338 31.709 65.988 1 52.13 ? CGA HEC 401 A 1 HETATM 15 O O1A HEC . . . B 2 38.816 32.107 64.899 1 47.81 ? O1A HEC 401 A 1 HETATM 16 O O2A HEC . . . B 2 37.986 32.503 66.887 1 50.79 ? O2A HEC 401 A 1 HETATM 17 N NB HEC . . . B 2 35.273 23.884 68.2 1 36.4 ? NB HEC 401 A 1 HETATM 18 C C1B HEC . . . B 2 34.569 24.541 67.228 1 37.58 ? C1B HEC 401 A 1 HETATM 19 C C2B HEC . . . B 2 33.459 23.759 66.841 1 37.76 ? C2B HEC 401 A 1 HETATM 20 C C3B HEC . . . B 2 33.5 22.607 67.541 1 39.46 ? C3B HEC 401 A 1 HETATM 21 C C4B HEC . . . B 2 34.653 22.685 68.423 1 36.55 ? C4B HEC 401 A 1 HETATM 22 C CMB HEC . . . B 2 32.541 24.304 65.725 1 41.4 ? CMB HEC 401 A 1 HETATM 23 C CAB HEC . . . B 2 32.525 21.407 67.527 1 38.05 ? CAB HEC 401 A 1 HETATM 24 C CBB HEC . . . B 2 32.17 20.98 66.084 1 47.35 ? CBB HEC 401 A 1 HETATM 25 N NC HEC . . . B 2 37.255 22.725 69.869 1 35.75 ? NC HEC 401 A 1 HETATM 26 C C1C HEC . . . B 2 36.274 21.765 70.006 1 36.16 ? C1C HEC 401 A 1 HETATM 27 C C2C HEC . . . B 2 36.784 20.74 70.896 1 38.18 ? C2C HEC 401 A 1 HETATM 28 C C3C HEC . . . B 2 37.933 21.187 71.415 1 39.18 ? C3C HEC 401 A 1 HETATM 29 C C4C HEC . . . B 2 38.289 22.396 70.726 1 36.76 ? C4C HEC 401 A 1 HETATM 30 C CMC HEC . . . B 2 35.97 19.537 71.426 1 44.14 ? CMC HEC 401 A 1 HETATM 31 C CAC HEC . . . B 2 38.853 20.489 72.441 1 43.12 ? CAC HEC 401 A 1 HETATM 32 C CBC HEC . . . B 2 39.882 19.685 71.615 1 47.53 ? CBC HEC 401 A 1 HETATM 33 N ND HEC . . . B 2 38.679 25.252 69.974 1 40.61 ? ND HEC 401 A 1 HETATM 34 C C1D HEC . . . B 2 39.597 24.442 70.633 1 40.26 ? C1D HEC 401 A 1 HETATM 35 C C2D HEC . . . B 2 40.76 25.227 70.971 1 40.36 ? C2D HEC 401 A 1 HETATM 36 C C3D HEC . . . B 2 40.474 26.635 70.463 1 41.94 ? C3D HEC 401 A 1 HETATM 37 C C4D HEC . . . B 2 39.158 26.559 69.855 1 39.48 ? C4D HEC 401 A 1 HETATM 38 C CMD HEC . . . B 2 42.029 24.735 71.698 1 45.3 ? CMD HEC 401 A 1 HETATM 39 C CAD HEC . . . B 2 41.458 27.827 70.6 1 47.5 ? CAD HEC 401 A 1 HETATM 40 C CBD HEC . . . B 2 40.797 29.047 71.226 1 57.46 ? CBD HEC 401 A 1 HETATM 41 C CGD HEC . . . B 2 41.827 30.13 71.468 1 67.98 ? CGD HEC 401 A 1 HETATM 42 O O1D HEC . . . B 2 43.06 29.841 71.427 1 72.76 ? O1D HEC 401 A 1 HETATM 43 O O2D HEC . . . B 2 41.403 31.289 71.712 1 64.77 ? O2D HEC 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 215 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 43 #