data_8DRD # _model_server_result.job_id x5Ose6g4dslMoSbF-OmILw _model_server_result.datetime_utc '2024-11-15 09:23:37' _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 8drd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 8DRD # _exptl.entry_id 8DRD _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 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 8DRD _cell.length_a 42.09 _cell.length_b 55.43 _cell.length_c 101.97 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DRD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 _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 F 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 disulf ? disulf1 A SG CYS 96 A CYS 96 1_555 B SG CYS 96 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? covale ? covale1 A SG CYS 98 A CYS 98 1_555 C CAB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.768 ? covale ? covale2 A SG CYS 101 A CYS 101 1_555 C CAC HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.773 ? covale ? covale3 B SG CYS 98 B CYS 98 1_555 F CAB HEC . B HEC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.773 ? covale ? covale4 B SG CYS 101 B CYS 101 1_555 F CAC HEC . B HEC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? metalc ? metalc1 A SD MET 7 A MET 7 1_555 C FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc2 A NE2 HIS 60 A HIS 60 1_555 D NI NI . A NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc3 A NE2 HIS 102 A HIS 102 1_555 C FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc4 A NE2 HIS 104 A HIS 104 1_555 D NI NI . A NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc5 D NI NI . A NI 202 1_555 H O HOH . A HOH 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc6 D NI NI . A NI 202 1_555 B NE2 HIS 100 B HIS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc7 D NI NI . A NI 202 1_555 B NE2 HIS 104 B HIS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc8 D NI NI . A NI 202 1_555 I O HOH . B HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc9 B OD2 ASP 2 B ASP 2 1_555 G NI NI . B NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc10 B SD MET 7 B MET 7 1_555 F FE HEC . B HEC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc11 B NE2 HIS 102 B HIS 102 1_555 F FE HEC . B HEC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? # _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 8DRD _atom_sites.fract_transf_matrix[1][1] 0.023759 _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] 0.018041 _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] 0.009807 _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 HEC A 1 201 150 HEC HEM . D 3 NI A 1 202 1 NI NI . E 4 MPD B 1 201 201 MPD MPD . F 2 HEC B 1 202 150 HEC HEM . G 3 NI B 1 203 2 NI NI . H 5 HOH A 1 301 32 HOH HOH . H 5 HOH A 2 302 11 HOH HOH . H 5 HOH A 3 303 12 HOH HOH . H 5 HOH A 4 304 60 HOH HOH . H 5 HOH A 5 305 54 HOH HOH . H 5 HOH A 6 306 41 HOH HOH . H 5 HOH A 7 307 16 HOH HOH . H 5 HOH A 8 308 38 HOH HOH . H 5 HOH A 9 309 51 HOH HOH . H 5 HOH A 10 310 30 HOH HOH . H 5 HOH A 11 311 56 HOH HOH . H 5 HOH A 12 312 17 HOH HOH . H 5 HOH A 13 313 14 HOH HOH . H 5 HOH A 14 314 39 HOH HOH . H 5 HOH A 15 315 42 HOH HOH . H 5 HOH A 16 316 59 HOH HOH . H 5 HOH A 17 317 47 HOH HOH . H 5 HOH A 18 318 3 HOH HOH . H 5 HOH A 19 319 22 HOH HOH . H 5 HOH A 20 320 18 HOH HOH . H 5 HOH A 21 321 44 HOH HOH . H 5 HOH A 22 322 65 HOH HOH . H 5 HOH A 23 323 23 HOH HOH . H 5 HOH A 24 324 71 HOH HOH . H 5 HOH A 25 325 72 HOH HOH . H 5 HOH A 26 326 34 HOH HOH . H 5 HOH A 27 327 63 HOH HOH . H 5 HOH A 28 328 28 HOH HOH . H 5 HOH A 29 329 76 HOH HOH . H 5 HOH A 30 330 50 HOH HOH . H 5 HOH A 31 331 9 HOH HOH . H 5 HOH A 32 332 45 HOH HOH . H 5 HOH A 33 333 25 HOH HOH . H 5 HOH A 34 334 5 HOH HOH . H 5 HOH A 35 335 24 HOH HOH . H 5 HOH A 36 336 4 HOH HOH . H 5 HOH A 37 337 2 HOH HOH . H 5 HOH A 38 338 57 HOH HOH . H 5 HOH A 39 339 20 HOH HOH . H 5 HOH A 40 340 13 HOH HOH . H 5 HOH A 41 341 79 HOH HOH . H 5 HOH A 42 342 37 HOH HOH . H 5 HOH A 43 343 33 HOH HOH . H 5 HOH A 44 344 46 HOH HOH . H 5 HOH A 45 345 70 HOH HOH . H 5 HOH A 46 346 43 HOH HOH . H 5 HOH A 47 347 35 HOH HOH . H 5 HOH A 48 348 61 HOH HOH . H 5 HOH A 49 349 1 HOH HOH . H 5 HOH A 50 350 36 HOH HOH . I 5 HOH B 1 301 66 HOH HOH . I 5 HOH B 2 302 55 HOH HOH . I 5 HOH B 3 303 10 HOH HOH . I 5 HOH B 4 304 48 HOH HOH . I 5 HOH B 5 305 29 HOH HOH . I 5 HOH B 6 306 31 HOH HOH . I 5 HOH B 7 307 75 HOH HOH . I 5 HOH B 8 308 68 HOH HOH . I 5 HOH B 9 309 67 HOH HOH . I 5 HOH B 10 310 15 HOH HOH . I 5 HOH B 11 311 6 HOH HOH . I 5 HOH B 12 312 74 HOH HOH . I 5 HOH B 13 313 27 HOH HOH . I 5 HOH B 14 314 73 HOH HOH . I 5 HOH B 15 315 58 HOH HOH . I 5 HOH B 16 316 49 HOH HOH . I 5 HOH B 17 317 19 HOH HOH . I 5 HOH B 18 318 40 HOH HOH . I 5 HOH B 19 319 7 HOH HOH . I 5 HOH B 20 320 21 HOH HOH . I 5 HOH B 21 321 52 HOH HOH . I 5 HOH B 22 322 78 HOH HOH . I 5 HOH B 23 323 77 HOH HOH . I 5 HOH B 24 324 8 HOH HOH . I 5 HOH B 25 325 69 HOH HOH . I 5 HOH B 26 326 53 HOH HOH . I 5 HOH B 27 327 26 HOH HOH . I 5 HOH B 28 328 62 HOH HOH . I 5 HOH B 29 329 64 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 . . . C 2 -5.518 -7.016 3.202 1 11.03 ? FE HEC 201 A 1 HETATM 2 C CHA HEC . . . C 2 -8.584 -7.401 1.714 1 12.6 ? CHA HEC 201 A 1 HETATM 3 C CHB HEC . . . C 2 -6.767 -4.443 5.143 1 11.77 ? CHB HEC 201 A 1 HETATM 4 C CHC HEC . . . C 2 -2.415 -6.452 4.408 1 10.52 ? CHC HEC 201 A 1 HETATM 5 C CHD HEC . . . C 2 -4.349 -9.762 1.495 1 11.18 ? CHD HEC 201 A 1 HETATM 6 N NA HEC . . . C 2 -7.34 -6.1 3.403 1 11.96 ? NA HEC 201 A 1 HETATM 7 C C1A HEC . . . C 2 -8.476 -6.414 2.677 1 11.42 ? C1A HEC 201 A 1 HETATM 8 C C2A HEC . . . C 2 -9.526 -5.501 3.085 1 9.73 ? C2A HEC 201 A 1 HETATM 9 C C3A HEC . . . C 2 -9.021 -4.691 4.024 1 11.52 ? C3A HEC 201 A 1 HETATM 10 C C4A HEC . . . C 2 -7.635 -5.051 4.254 1 9.64 ? C4A HEC 201 A 1 HETATM 11 C CMA HEC . . . C 2 -9.768 -3.564 4.771 1 11.07 ? CMA HEC 201 A 1 HETATM 12 C CAA HEC . . . C 2 -10.967 -5.492 2.516 1 13.05 ? CAA HEC 201 A 1 HETATM 13 C CBA HEC . . . C 2 -11.852 -6.356 3.408 1 12.45 ? CBA HEC 201 A 1 HETATM 14 C CGA HEC . . . C 2 -11.95 -7.804 2.948 1 16.65 ? CGA HEC 201 A 1 HETATM 15 O O1A HEC . . . C 2 -11.622 -8.132 1.777 1 13.59 ? O1A HEC 201 A 1 HETATM 16 O O2A HEC . . . C 2 -12.399 -8.644 3.77 1 16.09 ? O2A HEC 201 A 1 HETATM 17 N NB HEC . . . C 2 -4.749 -5.688 4.535 1 8.43 ? NB HEC 201 A 1 HETATM 18 C C1B HEC . . . C 2 -5.405 -4.675 5.199 1 8.03 ? C1B HEC 201 A 1 HETATM 19 C C2B HEC . . . C 2 -4.409 -3.911 5.932 1 9.8 ? C2B HEC 201 A 1 HETATM 20 C C3B HEC . . . C 2 -3.194 -4.462 5.724 1 8.95 ? C3B HEC 201 A 1 HETATM 21 C C4B HEC . . . C 2 -3.409 -5.62 4.861 1 9.79 ? C4B HEC 201 A 1 HETATM 22 C CMB HEC . . . C 2 -4.738 -2.658 6.771 1 10.49 ? CMB HEC 201 A 1 HETATM 23 C CAB HEC . . . C 2 -1.806 -4.046 6.266 1 10.27 ? CAB HEC 201 A 1 HETATM 24 C CBB HEC . . . C 2 -1.604 -3.525 7.495 1 11.03 ? CBB HEC 201 A 1 HETATM 25 N NC HEC . . . C 2 -3.738 -7.965 2.995 1 8.75 ? NC HEC 201 A 1 HETATM 26 C C1C HEC . . . C 2 -2.561 -7.488 3.518 1 9.6 ? C1C HEC 201 A 1 HETATM 27 C C2C HEC . . . C 2 -1.469 -8.278 3.002 1 9.23 ? C2C HEC 201 A 1 HETATM 28 C C3C HEC . . . C 2 -1.985 -9.215 2.161 1 8.62 ? C3C HEC 201 A 1 HETATM 29 C C4C HEC . . . C 2 -3.423 -9.023 2.18 1 7.99 ? C4C HEC 201 A 1 HETATM 30 C CMC HEC . . . C 2 0.006 -7.984 3.374 1 8.43 ? CMC HEC 201 A 1 HETATM 31 C CAC HEC . . . C 2 -1.269 -10.298 1.306 1 9.58 ? CAC HEC 201 A 1 HETATM 32 C CBC HEC . . . C 2 0.027 -10.626 1.489 1 10.33 ? CBC HEC 201 A 1 HETATM 33 N ND HEC . . . C 2 -6.309 -8.341 1.893 1 8.67 ? ND HEC 201 A 1 HETATM 34 C C1D HEC . . . C 2 -5.652 -9.389 1.302 1 11.21 ? C1D HEC 201 A 1 HETATM 35 C C2D HEC . . . C 2 -6.56 -10.062 0.411 1 10.67 ? C2D HEC 201 A 1 HETATM 36 C C3D HEC . . . C 2 -7.731 -9.41 0.447 1 11.85 ? C3D HEC 201 A 1 HETATM 37 C C4D HEC . . . C 2 -7.594 -8.307 1.377 1 10.95 ? C4D HEC 201 A 1 HETATM 38 C CMD HEC . . . C 2 -6.173 -11.298 -0.426 1 11.35 ? CMD HEC 201 A 1 HETATM 39 C CAD HEC . . . C 2 -9.019 -9.752 -0.353 1 10.67 ? CAD HEC 201 A 1 HETATM 40 C CBD HEC . . . C 2 -8.893 -9.138 -1.741 1 13.26 ? CBD HEC 201 A 1 HETATM 41 C CGD HEC . . . C 2 -10.14 -9.441 -2.541 1 15.66 ? CGD HEC 201 A 1 HETATM 42 O O1D HEC . . . C 2 -11.174 -8.778 -2.31 1 14.3 ? O1D HEC 201 A 1 HETATM 43 O O2D HEC . . . C 2 -10.112 -10.366 -3.389 1 18.73 ? O2D HEC 201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #