data_2CDV # _model_server_result.job_id bNYaGl330gbQbvWRajseIg _model_server_result.datetime_utc '2024-11-22 09:26:28' _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 2cdv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":108}' # _entry.id 2CDV # _exptl.entry_id 2CDV _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 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 2CDV _cell.length_a 52.9 _cell.length_b 68.1 _cell.length_c 34.9 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2CDV _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 B N N ? 2 C N N ? 2 D N N ? 2 E 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 covale ? covale1 A SG CYS 30 A CYS 30 1_555 D CAB HEC . A HEC 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? covale ? covale2 A SG CYS 33 A CYS 33 1_555 D CAC HEC . A HEC 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.85 ? covale ? covale3 A SG CYS 46 A CYS 46 1_555 C CAB HEC . A HEC 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.843 ? covale ? covale4 A SG CYS 51 A CYS 51 1_555 C CAC HEC . A HEC 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.864 ? covale ? covale5 A SG CYS 79 A CYS 79 1_555 E CAB HEC . A HEC 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? covale ? covale6 A SG CYS 82 A CYS 82 1_555 E CAC HEC . A HEC 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.8 ? covale ? covale7 A SG CYS 100 A CYS 100 1_555 B CAB HEC . A HEC 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? covale ? covale8 A SG CYS 105 A CYS 105 1_555 B CAC HEC . A HEC 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.779 ? metalc ? metalc1 A NE2 HIS 22 A HIS 22 1_555 D FE HEC . A HEC 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc2 A NE2 HIS 25 A HIS 25 1_555 E FE HEC . A HEC 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc3 A NE2 HIS 34 A HIS 34 1_555 D FE HEC . A HEC 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? metalc ? metalc4 A NE2 HIS 35 A HIS 35 1_555 C FE HEC . A HEC 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc5 A NE2 HIS 52 A HIS 52 1_555 C FE HEC . A HEC 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc6 A NE2 HIS 70 A HIS 70 1_555 B FE HEC . A HEC 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? metalc ? metalc7 A NE2 HIS 83 A HIS 83 1_555 E FE HEC . A HEC 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc8 A NE2 HIS 106 A HIS 106 1_555 B FE HEC . A HEC 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? # _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 103 n n FE NB HEC sing 104 n n FE NC HEC sing 105 n n FE ND HEC sing 106 n n CHA C1A HEC doub 107 n n CHA C4D HEC sing 108 n n CHA HHA HEC sing 109 n n CHB C4A HEC doub 110 n n CHB C1B HEC sing 111 n n CHB HHB HEC sing 112 n n CHC C4B HEC doub 113 n n CHC C1C HEC sing 114 n n CHC HHC HEC sing 115 n n CHD C4C HEC doub 116 n n CHD C1D HEC sing 117 n n CHD HHD HEC sing 118 n n NA C1A HEC sing 119 n y NA C4A HEC sing 120 n y C1A C2A HEC sing 121 n y C2A C3A HEC doub 122 n y C2A CAA HEC sing 123 n n C3A C4A HEC sing 124 n y C3A CMA HEC sing 125 n n CMA HMA1 HEC sing 126 n n CMA HMA2 HEC sing 127 n n CMA HMA3 HEC sing 128 n n CAA CBA HEC sing 129 n n CAA HAA1 HEC sing 130 n n CAA HAA2 HEC sing 131 n n CBA CGA HEC sing 132 n n CBA HBA1 HEC sing 133 n n CBA HBA2 HEC sing 134 n n CGA O1A HEC doub 135 n n CGA O2A HEC sing 136 n n O2A H2A HEC sing 137 n n NB C1B HEC sing 138 n y NB C4B HEC sing 139 n y C1B C2B HEC doub 140 n y C2B C3B HEC sing 141 n y C2B CMB HEC sing 142 n n C3B C4B HEC sing 143 n y C3B CAB HEC doub 144 e n CMB HMB1 HEC sing 145 n n CMB HMB2 HEC sing 146 n n CMB HMB3 HEC sing 147 n n CAB CBB HEC sing 148 n n CAB HAB HEC sing 149 n n CBB HBB1 HEC sing 150 n n CBB HBB2 HEC sing 151 n n CBB HBB3 HEC sing 152 n n NC C1C HEC sing 153 n y NC C4C HEC sing 154 n y C1C C2C HEC doub 155 n y C2C C3C HEC sing 156 n y C2C CMC HEC sing 157 n n C3C C4C HEC sing 158 n y C3C CAC HEC doub 159 e n CMC HMC1 HEC sing 160 n n CMC HMC2 HEC sing 161 n n CMC HMC3 HEC sing 162 n n CAC CBC HEC sing 163 n n CAC HAC HEC sing 164 n n CBC HBC1 HEC sing 165 n n CBC HBC2 HEC sing 166 n n CBC HBC3 HEC sing 167 n n ND C1D HEC sing 168 n y ND C4D HEC sing 169 n y C1D C2D HEC doub 170 n y C2D C3D HEC sing 171 n y C2D CMD HEC sing 172 n n C3D C4D HEC doub 173 n y C3D CAD HEC sing 174 n n CMD HMD1 HEC sing 175 n n CMD HMD2 HEC sing 176 n n CMD HMD3 HEC sing 177 n n CAD CBD HEC sing 178 n n CAD HAD1 HEC sing 179 n n CAD HAD2 HEC sing 180 n n CBD CGD HEC sing 181 n n CBD HBD1 HEC sing 182 n n CBD HBD2 HEC sing 183 n n CGD O1D HEC doub 184 n n CGD O2D HEC sing 185 n n O2D H2D HEC sing 186 n n # _atom_sites.entry_id 2CDV _atom_sites.fract_transf_matrix[1][1] 0.018904 _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] 0.014684 _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] 0.028653 _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 1 108 1 HEC HEM . C 2 HEC A 1 109 2 HEC HEM . D 2 HEC A 1 110 3 HEC HEM . E 2 HEC A 1 111 4 HEC HEM . F 3 HOH A 1 112 5 HOH HOH . F 3 HOH A 2 113 6 HOH HOH . F 3 HOH A 3 114 7 HOH HOH . F 3 HOH A 4 115 8 HOH HOH . F 3 HOH A 5 116 9 HOH HOH . F 3 HOH A 6 117 10 HOH HOH . F 3 HOH A 7 118 11 HOH HOH . F 3 HOH A 8 119 12 HOH HOH . F 3 HOH A 9 120 13 HOH HOH . F 3 HOH A 10 121 14 HOH HOH . F 3 HOH A 11 122 15 HOH HOH . F 3 HOH A 12 123 16 HOH HOH . F 3 HOH A 13 124 17 HOH HOH . F 3 HOH A 14 125 18 HOH HOH . F 3 HOH A 15 126 19 HOH HOH . F 3 HOH A 16 127 20 HOH HOH . F 3 HOH A 17 128 21 HOH HOH . F 3 HOH A 18 129 22 HOH HOH . F 3 HOH A 19 130 23 HOH HOH . F 3 HOH A 20 131 24 HOH HOH . F 3 HOH A 21 132 25 HOH HOH . F 3 HOH A 22 133 26 HOH HOH . F 3 HOH A 23 134 27 HOH HOH . F 3 HOH A 24 135 28 HOH HOH . F 3 HOH A 25 136 29 HOH HOH . F 3 HOH A 26 137 30 HOH HOH . F 3 HOH A 27 138 31 HOH HOH . F 3 HOH A 28 139 32 HOH HOH . F 3 HOH A 29 140 33 HOH HOH . F 3 HOH A 30 141 34 HOH HOH . F 3 HOH A 31 142 35 HOH HOH . F 3 HOH A 32 143 36 HOH HOH . F 3 HOH A 33 144 37 HOH HOH . F 3 HOH A 34 145 38 HOH HOH . F 3 HOH A 35 146 39 HOH HOH . F 3 HOH A 36 147 40 HOH HOH . F 3 HOH A 37 148 41 HOH HOH . F 3 HOH A 38 149 42 HOH HOH . F 3 HOH A 39 150 43 HOH HOH . F 3 HOH A 40 151 44 HOH HOH . F 3 HOH A 41 152 45 HOH HOH . F 3 HOH A 42 153 46 HOH HOH . F 3 HOH A 43 154 47 HOH HOH . F 3 HOH A 44 155 48 HOH HOH . F 3 HOH A 45 156 49 HOH HOH . F 3 HOH A 46 157 50 HOH HOH . F 3 HOH A 47 158 51 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 24.191 39.364 26.12 1 5.98 ? FE HEC 108 A 1 HETATM 2 C CHA HEC . . . B 2 22.15 42.086 25.629 1 6.19 ? CHA HEC 108 A 1 HETATM 3 C CHB HEC . . . B 2 21.94 37.409 24.391 1 6.66 ? CHB HEC 108 A 1 HETATM 4 C CHC HEC . . . B 2 25.995 36.619 26.892 1 6.97 ? CHC HEC 108 A 1 HETATM 5 C CHD HEC . . . B 2 26.563 41.383 27.535 1 5.03 ? CHD HEC 108 A 1 HETATM 6 N NA HEC . . . B 2 22.418 39.682 25.174 1 6.54 ? NA HEC 108 A 1 HETATM 7 C C1A HEC . . . B 2 21.682 40.867 25.13 1 6.78 ? C1A HEC 108 A 1 HETATM 8 C C2A HEC . . . B 2 20.398 40.605 24.518 1 7.19 ? C2A HEC 108 A 1 HETATM 9 C C3A HEC . . . B 2 20.39 39.35 24.103 1 7.17 ? C3A HEC 108 A 1 HETATM 10 C C4A HEC . . . B 2 21.6 38.721 24.615 1 6.66 ? C4A HEC 108 A 1 HETATM 11 C CMA HEC . . . B 2 19.284 38.548 23.377 1 6.75 ? CMA HEC 108 A 1 HETATM 12 C CAA HEC . . . B 2 19.357 41.704 24.144 1 8.18 ? CAA HEC 108 A 1 HETATM 13 C CBA HEC . . . B 2 19.297 41.934 22.595 1 9.02 ? CBA HEC 108 A 1 HETATM 14 C CGA HEC . . . B 2 18.16 42.823 22.137 1 9.39 ? CGA HEC 108 A 1 HETATM 15 O O1A HEC . . . B 2 17.009 42.493 22.507 1 10.1 ? O1A HEC 108 A 1 HETATM 16 O O2A HEC . . . B 2 18.465 43.888 21.567 1 10.63 ? O2A HEC 108 A 1 HETATM 17 N NB HEC . . . B 2 24 37.426 25.728 1 6.48 ? NB HEC 108 A 1 HETATM 18 C C1B HEC . . . B 2 23.079 36.821 24.891 1 6.68 ? C1B HEC 108 A 1 HETATM 19 C C2B HEC . . . B 2 23.527 35.48 24.539 1 6.31 ? C2B HEC 108 A 1 HETATM 20 C C3B HEC . . . B 2 24.656 35.268 25.223 1 6.61 ? C3B HEC 108 A 1 HETATM 21 C C4B HEC . . . B 2 24.923 36.42 26.022 1 6.6 ? C4B HEC 108 A 1 HETATM 22 C CMB HEC . . . B 2 22.756 34.534 23.614 1 5.4 ? CMB HEC 108 A 1 HETATM 23 C CAB HEC . . . B 2 25.54 33.99 25.202 1 6.94 ? CAB HEC 108 A 1 HETATM 24 C CBB HEC . . . B 2 26.234 33.828 24.044 1 7.11 ? CBB HEC 108 A 1 HETATM 25 N NC HEC . . . B 2 25.942 39.083 27.012 1 5.58 ? NC HEC 108 A 1 HETATM 26 C C1C HEC . . . B 2 26.495 37.845 27.354 1 6.05 ? C1C HEC 108 A 1 HETATM 27 C C2C HEC . . . B 2 27.452 38.03 28.396 1 5.65 ? C2C HEC 108 A 1 HETATM 28 C C3C HEC . . . B 2 27.684 39.36 28.503 1 6.04 ? C3C HEC 108 A 1 HETATM 29 C C4C HEC . . . B 2 26.671 40.027 27.698 1 5.2 ? C4C HEC 108 A 1 HETATM 30 C CMC HEC . . . B 2 28.273 36.877 29.009 1 6.35 ? CMC HEC 108 A 1 HETATM 31 C CAC HEC . . . B 2 28.676 40.098 29.441 1 5.57 ? CAC HEC 108 A 1 HETATM 32 C CBC HEC . . . B 2 30.031 39.908 29.319 1 5.02 ? CBC HEC 108 A 1 HETATM 33 N ND HEC . . . B 2 24.32 41.331 26.518 1 5.62 ? ND HEC 108 A 1 HETATM 34 C C1D HEC . . . B 2 25.431 41.988 27.029 1 5.09 ? C1D HEC 108 A 1 HETATM 35 C C2D HEC . . . B 2 25.231 43.432 26.946 1 5.04 ? C2D HEC 108 A 1 HETATM 36 C C3D HEC . . . B 2 24.03 43.63 26.395 1 5.62 ? C3D HEC 108 A 1 HETATM 37 C C4D HEC . . . B 2 23.424 42.322 26.163 1 6.07 ? C4D HEC 108 A 1 HETATM 38 C CMD HEC . . . B 2 26.278 44.484 27.358 1 3.83 ? CMD HEC 108 A 1 HETATM 39 C CAD HEC . . . B 2 23.286 44.956 26.165 1 5.39 ? CAD HEC 108 A 1 HETATM 40 C CBD HEC . . . B 2 22.71 45.509 27.496 1 5.24 ? CBD HEC 108 A 1 HETATM 41 C CGD HEC . . . B 2 21.707 46.614 27.272 1 6.74 ? CGD HEC 108 A 1 HETATM 42 O O1D HEC . . . B 2 22.163 47.721 26.905 1 7.2 ? O1D HEC 108 A 1 HETATM 43 O O2D HEC . . . B 2 20.506 46.32 27.303 1 6.33 ? O2D HEC 108 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #