data_6VDT # _model_server_result.job_id CRCM_GRqxRB63JN_MbKohg _model_server_result.datetime_utc '2025-01-09 12:51:27' _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 6vdt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":202}' # _entry.id 6VDT # _exptl.entry_id 6VDT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 564.413 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FE(III) DEUTEROPORPHYRIN IX' _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 6VDT _cell.length_a 58.7 _cell.length_b 67.66 _cell.length_c 67.73 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VDT _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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,K 1 1 B,I,J,L 2 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 J N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id NE2 _struct_conn.ptnr1_label_comp_id HIS _struct_conn.ptnr1_label_seq_id 89 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id HIS _struct_conn.ptnr1_auth_seq_id 89 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id J _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id FDE _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id FDE _struct_conn.ptnr2_auth_seq_id 202 _struct_conn.ptnr2_symmetry 1_555 _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 2.739 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C30 H28 Fe N4 O4' _chem_comp.formula_weight 564.413 _chem_comp.id FDE _chem_comp.mon_nstd_flag . _chem_comp.name 'FE(III) DEUTEROPORPHYRIN IX' _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 CHA C1A FDE sing 92 n n CHA C4D FDE doub 93 n n CHA HHA FDE sing 94 n n C1A C2A FDE sing 95 n n C1A NA FDE doub 96 n n C2A CAA FDE sing 97 n n C2A C3A FDE doub 98 n n CAA CBA FDE sing 99 n n CAA HAA1 FDE sing 100 n n CAA HAA2 FDE sing 101 n n CBA CGA FDE sing 102 n n CBA HBA1 FDE sing 103 n n CBA HBA2 FDE sing 104 n n CGA O1A FDE sing 105 n n CGA O2A FDE doub 106 n n O1A H1A FDE sing 107 n n C3A CMA FDE sing 108 n n C3A C4A FDE sing 109 n n CMA HMA1 FDE sing 110 n n CMA HMA2 FDE sing 111 n n CMA HMA3 FDE sing 112 n n C4A NA FDE sing 113 n n C4A CHB FDE doub 114 n n NA FE FDE sing 115 n n CHB C1B FDE sing 116 n n CHB HHB FDE sing 117 n n C1B C2B FDE doub 118 n y C1B NB FDE sing 119 n y C2B C3B FDE sing 120 n y C2B H2B FDE sing 121 n n C3B CME FDE sing 122 n n C3B C4B FDE doub 123 n y CME HME1 FDE sing 124 n n CME HME2 FDE sing 125 n n CME HME3 FDE sing 126 n n C4B NB FDE sing 127 n y C4B CHC FDE sing 128 n n NB FE FDE sing 129 n n CHC C1C FDE doub 130 n n CHC HHC FDE sing 131 n n C1C C2C FDE sing 132 n n C1C NC FDE sing 133 n n C2C C3C FDE doub 134 n n C2C H2C FDE sing 135 n n C3C CMF FDE sing 136 n n C3C C4C FDE sing 137 n n CMF HMF1 FDE sing 138 n n CMF HMF2 FDE sing 139 n n CMF HMF3 FDE sing 140 n n C4C NC FDE doub 141 n n C4C CHD FDE sing 142 n n NC FE FDE sing 143 n n CHD C1D FDE doub 144 n n CHD HHD FDE sing 145 n n C1D C2D FDE sing 146 n n C1D ND FDE sing 147 n n C2D CMD FDE sing 148 n n C2D C3D FDE doub 149 n n CMD HMD1 FDE sing 150 n n CMD HMD2 FDE sing 151 n n CMD HMD3 FDE sing 152 n n C3D CAD FDE sing 153 n n C3D C4D FDE sing 154 n n CAD CBD FDE sing 155 n n CAD HAD1 FDE sing 156 n n CAD HAD2 FDE sing 157 n n CBD CGD FDE sing 158 n n CBD HBD1 FDE sing 159 n n CBD HBD2 FDE sing 160 n n CGD O1D FDE sing 161 n n CGD O2D FDE doub 162 n n O1D H1D FDE sing 163 n n C4D ND FDE sing 164 n n ND FE FDE sing 165 n n # _atom_sites.entry_id 6VDT _atom_sites.fract_transf_matrix[1][1] 0.017036 _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] 0.01478 _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] 0.014765 _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 FDE A 1 201 201 FDE FDE . D 3 EDO A 1 202 301 EDO EDO . E 4 NPO A 1 203 401 NPO NPO . F 5 PEG A 1 204 501 PEG PEG . G 6 SO4 A 1 205 1 SO4 SO4 . H 6 SO4 A 1 206 2 SO4 SO4 . I 3 EDO B 1 201 201 EDO EDO . J 2 FDE B 1 202 301 FDE FDE . K 7 HOH A 1 301 112 HOH HOH . K 7 HOH A 2 302 6 HOH HOH . K 7 HOH A 3 303 126 HOH HOH . K 7 HOH A 4 304 14 HOH HOH . K 7 HOH A 5 305 114 HOH HOH . K 7 HOH A 6 306 13 HOH HOH . K 7 HOH A 7 307 4 HOH HOH . K 7 HOH A 8 308 34 HOH HOH . K 7 HOH A 9 309 2 HOH HOH . K 7 HOH A 10 310 23 HOH HOH . K 7 HOH A 11 311 38 HOH HOH . K 7 HOH A 12 312 85 HOH HOH . K 7 HOH A 13 313 68 HOH HOH . K 7 HOH A 14 314 97 HOH HOH . K 7 HOH A 15 315 108 HOH HOH . K 7 HOH A 16 316 31 HOH HOH . K 7 HOH A 17 317 19 HOH HOH . K 7 HOH A 18 318 67 HOH HOH . K 7 HOH A 19 319 24 HOH HOH . K 7 HOH A 20 320 121 HOH HOH . K 7 HOH A 21 321 74 HOH HOH . K 7 HOH A 22 322 5 HOH HOH . K 7 HOH A 23 323 26 HOH HOH . K 7 HOH A 24 324 123 HOH HOH . K 7 HOH A 25 325 18 HOH HOH . K 7 HOH A 26 326 125 HOH HOH . K 7 HOH A 27 327 16 HOH HOH . K 7 HOH A 28 328 48 HOH HOH . K 7 HOH A 29 329 29 HOH HOH . K 7 HOH A 30 330 53 HOH HOH . K 7 HOH A 31 331 70 HOH HOH . K 7 HOH A 32 332 42 HOH HOH . K 7 HOH A 33 333 47 HOH HOH . K 7 HOH A 34 334 102 HOH HOH . K 7 HOH A 35 335 113 HOH HOH . K 7 HOH A 36 336 25 HOH HOH . K 7 HOH A 37 337 120 HOH HOH . K 7 HOH A 38 338 66 HOH HOH . K 7 HOH A 39 339 124 HOH HOH . K 7 HOH A 40 340 21 HOH HOH . K 7 HOH A 41 341 3 HOH HOH . K 7 HOH A 42 342 39 HOH HOH . K 7 HOH A 43 343 54 HOH HOH . K 7 HOH A 44 344 88 HOH HOH . K 7 HOH A 45 345 98 HOH HOH . K 7 HOH A 46 346 101 HOH HOH . K 7 HOH A 47 347 103 HOH HOH . K 7 HOH A 48 348 100 HOH HOH . K 7 HOH A 49 349 61 HOH HOH . K 7 HOH A 50 350 45 HOH HOH . K 7 HOH A 51 351 20 HOH HOH . K 7 HOH A 52 352 99 HOH HOH . K 7 HOH A 53 353 111 HOH HOH . K 7 HOH A 54 354 122 HOH HOH . K 7 HOH A 55 355 96 HOH HOH . K 7 HOH A 56 356 1 HOH HOH . K 7 HOH A 57 357 78 HOH HOH . K 7 HOH A 58 358 50 HOH HOH . K 7 HOH A 59 359 109 HOH HOH . K 7 HOH A 60 360 127 HOH HOH . K 7 HOH A 61 361 17 HOH HOH . K 7 HOH A 62 362 72 HOH HOH . L 7 HOH B 1 301 134 HOH HOH . L 7 HOH B 2 302 128 HOH HOH . L 7 HOH B 3 303 106 HOH HOH . L 7 HOH B 4 304 115 HOH HOH . L 7 HOH B 5 305 95 HOH HOH . L 7 HOH B 6 306 59 HOH HOH . L 7 HOH B 7 307 33 HOH HOH . L 7 HOH B 8 308 130 HOH HOH . L 7 HOH B 9 309 92 HOH HOH . L 7 HOH B 10 310 86 HOH HOH . L 7 HOH B 11 311 7 HOH HOH . L 7 HOH B 12 312 51 HOH HOH . L 7 HOH B 13 313 131 HOH HOH . L 7 HOH B 14 314 46 HOH HOH . L 7 HOH B 15 315 10 HOH HOH . L 7 HOH B 16 316 62 HOH HOH . L 7 HOH B 17 317 80 HOH HOH . L 7 HOH B 18 318 116 HOH HOH . L 7 HOH B 19 319 119 HOH HOH . L 7 HOH B 20 320 69 HOH HOH . L 7 HOH B 21 321 30 HOH HOH . L 7 HOH B 22 322 52 HOH HOH . L 7 HOH B 23 323 129 HOH HOH . L 7 HOH B 24 324 75 HOH HOH . L 7 HOH B 25 325 37 HOH HOH . L 7 HOH B 26 326 84 HOH HOH . L 7 HOH B 27 327 110 HOH HOH . L 7 HOH B 28 328 91 HOH HOH . L 7 HOH B 29 329 132 HOH HOH . L 7 HOH B 30 330 36 HOH HOH . L 7 HOH B 31 331 35 HOH HOH . L 7 HOH B 32 332 93 HOH HOH . L 7 HOH B 33 333 43 HOH HOH . L 7 HOH B 34 334 40 HOH HOH . L 7 HOH B 35 335 63 HOH HOH . L 7 HOH B 36 336 15 HOH HOH . L 7 HOH B 37 337 104 HOH HOH . L 7 HOH B 38 338 28 HOH HOH . L 7 HOH B 39 339 81 HOH HOH . L 7 HOH B 40 340 107 HOH HOH . L 7 HOH B 41 341 94 HOH HOH . L 7 HOH B 42 342 9 HOH HOH . L 7 HOH B 43 343 90 HOH HOH . L 7 HOH B 44 344 117 HOH HOH . L 7 HOH B 45 345 56 HOH HOH . L 7 HOH B 46 346 118 HOH HOH . L 7 HOH B 47 347 133 HOH HOH . L 7 HOH B 48 348 105 HOH HOH . L 7 HOH B 49 349 44 HOH HOH . L 7 HOH B 50 350 89 HOH HOH . L 7 HOH B 51 351 65 HOH HOH . L 7 HOH B 52 352 87 HOH HOH . L 7 HOH B 53 353 136 HOH HOH . L 7 HOH B 54 354 12 HOH HOH . L 7 HOH B 55 355 82 HOH HOH . L 7 HOH B 56 356 60 HOH HOH . L 7 HOH B 57 357 27 HOH HOH . L 7 HOH B 58 358 73 HOH HOH . L 7 HOH B 59 359 135 HOH HOH . L 7 HOH B 60 360 32 HOH HOH . L 7 HOH B 61 361 77 HOH HOH . L 7 HOH B 62 362 79 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 FDE . . . J 2 -21.285 -6.31 -22.413 0.8 58.09 ? CHA FDE 202 B 1 HETATM 2 C C1A FDE . . . J 2 -20.339 -5.422 -23.091 0.8 51.53 ? C1A FDE 202 B 1 HETATM 3 C C2A FDE . . . J 2 -18.95 -5.781 -23.527 0.8 55.12 ? C2A FDE 202 B 1 HETATM 4 C CAA FDE . . . J 2 -18.192 -7.092 -23.407 0.8 53.28 ? CAA FDE 202 B 1 HETATM 5 C CBA FDE . . . J 2 -19.095 -8.239 -22.975 0.8 51.07 ? CBA FDE 202 B 1 HETATM 6 C CGA FDE . . . J 2 -18.369 -9.553 -22.904 0.8 52.16 ? CGA FDE 202 B 1 HETATM 7 O O1A FDE . . . J 2 -17.321 -9.725 -23.558 0.8 53.6 ? O1A FDE 202 B 1 HETATM 8 O O2A FDE . . . J 2 -18.877 -10.424 -22.18 0.8 51.27 ? O2A FDE 202 B 1 HETATM 9 C C3A FDE . . . J 2 -18.389 -4.548 -24.13 0.8 54.27 ? C3A FDE 202 B 1 HETATM 10 C CMA FDE . . . J 2 -17.026 -4.326 -24.72 0.8 56.72 ? CMA FDE 202 B 1 HETATM 11 C C4A FDE . . . J 2 -19.463 -3.542 -24.031 0.8 59.29 ? C4A FDE 202 B 1 HETATM 12 N NA FDE . . . J 2 -20.733 -4.07 -23.497 0.8 61.65 ? NA FDE 202 B 1 HETATM 13 C CHB FDE . . . J 2 -19.274 -2.174 -24.489 0.8 58.86 ? CHB FDE 202 B 1 HETATM 14 C C1B FDE . . . J 2 -20.091 -1.089 -23.963 0.8 61.19 ? C1B FDE 202 B 1 HETATM 15 C C2B FDE . . . J 2 -19.679 0.186 -24.278 0.8 58.04 ? C2B FDE 202 B 1 HETATM 16 C C3B FDE . . . J 2 -20.617 0.927 -23.639 0.8 56.91 ? C3B FDE 202 B 1 HETATM 17 C CME FDE . . . J 2 -20.499 2.378 -23.771 0.8 56.6 ? CME FDE 202 B 1 HETATM 18 C C4B FDE . . . J 2 -21.529 0.031 -22.934 0.8 62.04 ? C4B FDE 202 B 1 HETATM 19 N NB FDE . . . J 2 -21.162 -1.234 -23.163 0.8 62.26 ? NB FDE 202 B 1 HETATM 20 C CHC FDE . . . J 2 -22.677 0.47 -22.119 0.8 62.21 ? CHC FDE 202 B 1 HETATM 21 C C1C FDE . . . J 2 -23.611 -0.449 -21.454 0.8 65.7 ? C1C FDE 202 B 1 HETATM 22 C C2C FDE . . . J 2 -24.671 0.121 -20.749 0.8 65.81 ? C2C FDE 202 B 1 HETATM 23 C C3C FDE . . . J 2 -25.329 -0.986 -20.279 0.8 63.35 ? C3C FDE 202 B 1 HETATM 24 C CMF FDE . . . J 2 -26.551 -0.738 -19.437 0.8 61.84 ? CMF FDE 202 B 1 HETATM 25 C C4C FDE . . . J 2 -24.564 -2.168 -20.769 0.8 65.43 ? C4C FDE 202 B 1 HETATM 26 N NC FDE . . . J 2 -23.493 -1.798 -21.495 0.8 65.92 ? NC FDE 202 B 1 HETATM 27 C CHD FDE . . . J 2 -24.901 -3.586 -20.51 0.8 62.25 ? CHD FDE 202 B 1 HETATM 28 C C1D FDE . . . J 2 -24.072 -4.755 -20.884 0.8 61.22 ? C1D FDE 202 B 1 HETATM 29 C C2D FDE . . . J 2 -24.407 -6.132 -20.431 0.8 58.64 ? C2D FDE 202 B 1 HETATM 30 C CMD FDE . . . J 2 -25.574 -6.602 -19.611 0.8 61.03 ? CMD FDE 202 B 1 HETATM 31 C C3D FDE . . . J 2 -23.315 -6.947 -20.978 0.8 59.78 ? C3D FDE 202 B 1 HETATM 32 C CAD FDE . . . J 2 -23.078 -8.441 -20.857 0.8 60.39 ? CAD FDE 202 B 1 HETATM 33 C CBD FDE . . . J 2 -21.688 -8.691 -20.254 0.8 58.52 ? CBD FDE 202 B 1 HETATM 34 C CGD FDE . . . J 2 -21.699 -9.129 -18.812 0.8 59.08 ? CGD FDE 202 B 1 HETATM 35 O O1D FDE . . . J 2 -21.7 -10.361 -18.567 0.8 63.29 ? O1D FDE 202 B 1 HETATM 36 O O2D FDE . . . J 2 -21.648 -8.242 -17.923 0.8 50.74 ? O2D FDE 202 B 1 HETATM 37 C C4D FDE . . . J 2 -22.499 -5.932 -21.689 0.8 60.15 ? C4D FDE 202 B 1 HETATM 38 N ND FDE . . . J 2 -22.935 -4.671 -21.614 0.8 60.78 ? ND FDE 202 B 1 HETATM 39 FE FE FDE . . . J 2 -22.03 -2.99 -22.463 0.8 70.06 ? FE FDE 202 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 523 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #