data_4JJG # _model_server_result.job_id 628-4tuNBuFRPdDrpxRI4A _model_server_result.datetime_utc '2024-11-24 13:32:11' _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 4jjg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4JJG # _exptl.entry_id 4JJG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 686.323 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'iron-guanylyl pyridinol cofactor' _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 120 _cell.entry_id 4JJG _cell.length_a 141.88 _cell.length_b 141.88 _cell.length_c 95.48 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JJG _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _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 _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 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 C O2 FE9 . A FE9 401 1_555 D C1 IC9 . A IC9 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale2 E O2 FE9 . B FE9 401 1_555 F C1 IC9 . B IC9 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? metalc ? metalc1 A SG CYS 172 A CYS 172 1_555 C FE FE9 . A FE9 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc2 C FE FE9 . A FE9 401 1_555 D N IC9 . A IC9 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc3 C FE FE9 . A FE9 401 1_555 D C1 IC9 . A IC9 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? metalc ? metalc4 B SG CYS 172 B CYS 172 1_555 E FE FE9 . B FE9 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc5 E FE FE9 . B FE9 401 1_555 F N IC9 . B IC9 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? metalc ? metalc6 E FE FE9 . B FE9 401 1_555 F C1 IC9 . B IC9 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.866 ? # _chem_comp.formula 'C21 H23 Fe N6 O13 P S 4' _chem_comp.formula_weight 686.323 _chem_comp.id FE9 _chem_comp.mon_nstd_flag . _chem_comp.name 'iron-guanylyl pyridinol cofactor' _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 O2' C2' FE9 sing 83 n n O6A C6A FE9 doub 84 n n C6A N1A FE9 sing 85 n n C6A C5A FE9 sing 86 n n N1A C2A FE9 sing 87 n n N7A C5A FE9 sing 88 n y N7A C8A FE9 doub 89 n y C5A C4A FE9 doub 90 n y C8A N9A FE9 sing 91 n y C2A N2A FE9 sing 92 n n C2A N3A FE9 doub 93 n n C2' C1' FE9 sing 94 n n C2' C3' FE9 sing 95 n n C4A N3A FE9 sing 96 n n C4A N9A FE9 sing 97 n y N9A C1' FE9 sing 98 n n O3' C3' FE9 sing 99 n n C1' O4' FE9 sing 100 n n C3' C4' FE9 sing 101 n n O4' C4' FE9 sing 102 n n C4' C5' FE9 sing 103 n n O1P P1 FE9 doub 104 n n C5' O5' FE9 sing 105 n n O5' P1 FE9 sing 106 n n P1 O2P FE9 sing 107 n n P1 O3P FE9 sing 108 n n O3P C4 FE9 sing 109 n n C3M C3 FE9 sing 110 n n C4 C3 FE9 doub 111 n n C4 C5 FE9 sing 112 n n C5M C5 FE9 sing 113 n n C3 C2 FE9 sing 114 n n C5 C6 FE9 doub 115 n n C2 O2 FE9 doub 116 n n C2 N1 FE9 sing 117 n n C6 N1 FE9 sing 118 n n C6 C7 FE9 sing 119 n n N1 FE FE9 sing 120 n n O1F C1F FE9 trip 121 n n C7 C8 FE9 sing 122 n n C1F FE FE9 sing 123 n n C8 FE FE9 sing 124 n n C8 O18 FE9 doub 125 n n FE C2F FE9 sing 126 n n C2F O2F FE9 trip 127 n n C7 H8 FE9 sing 128 n n C5M H9 FE9 sing 129 n n C5M H10 FE9 sing 130 n n C5M H11 FE9 sing 131 n n C3M H12 FE9 sing 132 n n C3M H13 FE9 sing 133 n n C3M H14 FE9 sing 134 n n O2P H15 FE9 sing 135 n n C5' H16 FE9 sing 136 n n C5' H17 FE9 sing 137 n n C4' H18 FE9 sing 138 n n C1' H19 FE9 sing 139 n n C2' H20 FE9 sing 140 n n O2' H21 FE9 sing 141 n n C3' H22 FE9 sing 142 n n O3' H23 FE9 sing 143 n n N2A H24 FE9 sing 144 n n N2A H25 FE9 sing 145 n n N1A H26 FE9 sing 146 n n C8A H27 FE9 sing 147 n n C7 H1 FE9 sing 148 n n FE O1 FE9 sing 149 n n FE S1 FE9 sing 150 n n S1 HS1 FE9 sing 151 n n O1 H2 FE9 sing 152 n n # _atom_sites.entry_id 4JJG _atom_sites.fract_transf_matrix[1][1] 0.007048 _atom_sites.fract_transf_matrix[1][2] 0.004069 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008139 _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] 0.010473 _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 FE9 A 1 401 401 FE9 FE9 . D 3 IC9 A 1 402 405 IC9 IC9 . E 2 FE9 B 1 401 401 FE9 FE9 . F 3 IC9 B 1 402 405 IC9 IC9 . G 4 HOH A 1 501 2 HOH HOH . G 4 HOH A 2 502 4 HOH HOH . G 4 HOH A 3 503 6 HOH HOH . G 4 HOH A 4 504 8 HOH HOH . G 4 HOH A 5 505 10 HOH HOH . G 4 HOH A 6 506 13 HOH HOH . G 4 HOH A 7 507 14 HOH HOH . G 4 HOH A 8 508 17 HOH HOH . G 4 HOH A 9 509 20 HOH HOH . G 4 HOH A 10 510 21 HOH HOH . G 4 HOH A 11 511 23 HOH HOH . G 4 HOH A 12 512 24 HOH HOH . G 4 HOH A 13 513 27 HOH HOH . G 4 HOH A 14 514 29 HOH HOH . H 4 HOH B 1 501 1 HOH HOH . H 4 HOH B 2 502 3 HOH HOH . H 4 HOH B 3 503 5 HOH HOH . H 4 HOH B 4 504 7 HOH HOH . H 4 HOH B 5 505 9 HOH HOH . H 4 HOH B 6 506 11 HOH HOH . H 4 HOH B 7 507 12 HOH HOH . H 4 HOH B 8 508 15 HOH HOH . H 4 HOH B 9 509 16 HOH HOH . H 4 HOH B 10 510 18 HOH HOH . H 4 HOH B 11 511 19 HOH HOH . H 4 HOH B 12 512 22 HOH HOH . H 4 HOH B 13 513 25 HOH HOH . H 4 HOH B 14 514 26 HOH HOH . H 4 HOH B 15 515 28 HOH HOH . H 4 HOH B 16 516 30 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 O O2 FE9 . . . C 2 -5.5 -22.093 -29.162 1 32.12 ? O2 FE9 401 A 1 HETATM 2 FE FE FE9 . . . C 2 -7.454 -21.465 -27.091 0.9 27.22 ? FE FE9 401 A 1 HETATM 3 C C1F FE9 . . . C 2 -8.472 -22.74 -27.937 0.9 26.49 ? C1F FE9 401 A 1 HETATM 4 O O1F FE9 . . . C 2 -9.135 -23.572 -28.469 0.9 26.04 ? O1F FE9 401 A 1 HETATM 5 C C2F FE9 . . . C 2 -7.741 -22.204 -25.416 0.9 27.59 ? C2F FE9 401 A 1 HETATM 6 O O2F FE9 . . . C 2 -7.954 -22.678 -24.33 0.9 28.25 ? O2F FE9 401 A 1 HETATM 7 C C8 FE9 . . . C 2 -8.767 -19.999 -27.337 1 25.09 ? C8 FE9 401 A 1 HETATM 8 O O18 FE9 . . . C 2 -9.575 -20.002 -26.165 1 23.32 ? O18 FE9 401 A 1 HETATM 9 C C7 FE9 . . . C 2 -8.901 -19.039 -28.461 1 24.86 ? C7 FE9 401 A 1 HETATM 10 C C6 FE9 . . . C 2 -7.809 -19.54 -29.36 1 25.95 ? C6 FE9 401 A 1 HETATM 11 N N1 FE9 . . . C 2 -7.118 -20.595 -28.934 1 27.01 ? N1 FE9 401 A 1 HETATM 12 C C5 FE9 . . . C 2 -7.575 -18.924 -30.583 1 26.36 ? C5 FE9 401 A 1 HETATM 13 C C5M FE9 . . . C 2 -8.394 -17.729 -31.023 1 25.38 ? C5M FE9 401 A 1 HETATM 14 C C4 FE9 . . . C 2 -6.568 -19.413 -31.385 1 28.29 ? C4 FE9 401 A 1 HETATM 15 C C3 FE9 . . . C 2 -5.797 -20.508 -30.928 1 29.84 ? C3 FE9 401 A 1 HETATM 16 C C3M FE9 . . . C 2 -4.672 -21.114 -31.736 1 30.58 ? C3M FE9 401 A 1 HETATM 17 C C2 FE9 . . . C 2 -6.152 -21.039 -29.683 1 29.4 ? C2 FE9 401 A 1 HETATM 18 O O3P FE9 . . . C 2 -6.327 -18.795 -32.584 1 28.99 ? O3P FE9 401 A 1 HETATM 19 P P1 FE9 . . . C 2 -6.721 -19.402 -34.019 1 29.61 ? P1 FE9 401 A 1 HETATM 20 O O1P FE9 . . . C 2 -5.601 -19.114 -35.02 1 31.39 ? O1P FE9 401 A 1 HETATM 21 O O2P FE9 . . . C 2 -7.24 -20.823 -33.863 1 29.51 ? O2P FE9 401 A 1 HETATM 22 O O5' FE9 . . . C 2 -8.018 -18.512 -34.299 1 28.66 ? O5' FE9 401 A 1 HETATM 23 C C5' FE9 . . . C 2 -7.896 -17.144 -34.708 1 28.99 ? C5' FE9 401 A 1 HETATM 24 C C4' FE9 . . . C 2 -8.85 -16.936 -35.885 1 28.82 ? C4' FE9 401 A 1 HETATM 25 O O4' FE9 . . . C 2 -9.034 -15.548 -36.125 1 29.21 ? O4' FE9 401 A 1 HETATM 26 C C1' FE9 . . . C 2 -9.271 -15.379 -37.518 1 30.28 ? C1' FE9 401 A 1 HETATM 27 C C2' FE9 . . . C 2 -8.294 -16.337 -38.152 1 31.47 ? C2' FE9 401 A 1 HETATM 28 O O2' FE9 . . . C 2 -8.782 -16.668 -39.452 1 32.47 ? O2' FE9 401 A 1 HETATM 29 C C3' FE9 . . . C 2 -8.336 -17.504 -37.188 1 30.12 ? C3' FE9 401 A 1 HETATM 30 O O3' FE9 . . . C 2 -9.345 -18.422 -37.597 1 29.67 ? O3' FE9 401 A 1 HETATM 31 N N9A FE9 . . . C 2 -9.141 -13.953 -37.915 1 31.41 ? N9A FE9 401 A 1 HETATM 32 C C4A FE9 . . . C 2 -10.179 -13.128 -38.051 1 31.39 ? C4A FE9 401 A 1 HETATM 33 N N3A FE9 . . . C 2 -11.523 -13.294 -37.92 1 30.14 ? N3A FE9 401 A 1 HETATM 34 C C2A FE9 . . . C 2 -12.391 -12.295 -38.153 1 30.83 ? C2A FE9 401 A 1 HETATM 35 N N2A FE9 . . . C 2 -13.724 -12.554 -37.998 1 30.24 ? N2A FE9 401 A 1 HETATM 36 N N1A FE9 . . . C 2 -11.937 -11.062 -38.509 1 32.5 ? N1A FE9 401 A 1 HETATM 37 C C6A FE9 . . . C 2 -10.595 -10.839 -38.647 1 33.77 ? C6A FE9 401 A 1 HETATM 38 O O6A FE9 . . . C 2 -10.117 -9.608 -38.995 1 35.75 ? O6A FE9 401 A 1 HETATM 39 C C5A FE9 . . . C 2 -9.688 -11.887 -38.426 1 33.18 ? C5A FE9 401 A 1 HETATM 40 N N7A FE9 . . . C 2 -8.349 -12.002 -38.487 1 34.1 ? N7A FE9 401 A 1 HETATM 41 C C8A FE9 . . . C 2 -8.019 -13.267 -38.169 1 33.01 ? C8A FE9 401 A 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 513 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 41 #