data_4JJG # _model_server_result.job_id j6FyMVsQvPz6UncImwAzKQ _model_server_result.datetime_utc '2024-11-07 00:40:51' _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":"E","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 . . . E 2 2.834 -22.647 25.499 1 39.21 ? O2 FE9 401 B 1 HETATM 2 FE FE FE9 . . . E 2 4.842 -22.284 23.472 0.9 33.78 ? FE FE9 401 B 1 HETATM 3 C C1F FE9 . . . E 2 5.73 -23.676 24.307 0.9 35.38 ? C1F FE9 401 B 1 HETATM 4 O O1F FE9 . . . E 2 6.315 -24.593 24.843 0.9 36.24 ? O1F FE9 401 B 1 HETATM 5 C C2F FE9 . . . E 2 4.998 -23.042 21.792 0.9 34.4 ? C2F FE9 401 B 1 HETATM 6 O O2F FE9 . . . E 2 5.112 -23.538 20.693 0.9 35.01 ? O2F FE9 401 B 1 HETATM 7 C C8 FE9 . . . E 2 6.367 -21.027 23.715 1 33.4 ? C8 FE9 401 B 1 HETATM 8 O O18 FE9 . . . E 2 7.15 -21.184 22.509 1 31.71 ? O18 FE9 401 B 1 HETATM 9 C C7 FE9 . . . E 2 6.647 -20.086 24.847 1 33.28 ? C7 FE9 401 B 1 HETATM 10 C C6 FE9 . . . E 2 5.495 -20.441 25.744 1 34.55 ? C6 FE9 401 B 1 HETATM 11 N N1 FE9 . . . E 2 4.656 -21.396 25.309 1 35 ? N1 FE9 401 B 1 HETATM 12 C C5 FE9 . . . E 2 5.293 -19.801 26.972 1 35.17 ? C5 FE9 401 B 1 HETATM 13 C C5M FE9 . . . E 2 6.264 -18.739 27.455 1 34.55 ? C5M FE9 401 B 1 HETATM 14 C C4 FE9 . . . E 2 4.192 -20.171 27.741 1 36.16 ? C4 FE9 401 B 1 HETATM 15 C C3 FE9 . . . E 2 3.321 -21.135 27.264 1 36.91 ? C3 FE9 401 B 1 HETATM 16 C C3M FE9 . . . E 2 2.11 -21.575 28.057 1 37.77 ? C3M FE9 401 B 1 HETATM 17 C C2 FE9 . . . E 2 3.611 -21.688 26.029 1 36.58 ? C2 FE9 401 B 1 HETATM 18 O O3P FE9 . . . E 2 3.936 -19.576 28.945 1 37 ? O3P FE9 401 B 1 HETATM 19 P P1 FE9 . . . E 2 4.283 -20.251 30.34 1 38.22 ? P1 FE9 401 B 1 HETATM 20 O O1P FE9 . . . E 2 3.185 -19.937 31.34 1 39.9 ? O1P FE9 401 B 1 HETATM 21 O O2P FE9 . . . E 2 4.723 -21.666 30.056 1 38.93 ? O2P FE9 401 B 1 HETATM 22 O O5' FE9 . . . E 2 5.617 -19.449 30.722 1 38.66 ? O5' FE9 401 B 1 HETATM 23 C C5' FE9 . . . E 2 5.49 -18.085 31.128 1 39.05 ? C5' FE9 401 B 1 HETATM 24 C C4' FE9 . . . E 2 6.552 -17.893 32.185 1 40.29 ? C4' FE9 401 B 1 HETATM 25 O O4' FE9 . . . E 2 6.881 -16.509 32.307 1 40.88 ? O4' FE9 401 B 1 HETATM 26 C C1' FE9 . . . E 2 7.202 -16.322 33.677 1 42.58 ? C1' FE9 401 B 1 HETATM 27 C C2' FE9 . . . E 2 6.199 -17.176 34.447 1 43.67 ? C2' FE9 401 B 1 HETATM 28 O O2' FE9 . . . E 2 6.637 -17.468 35.786 1 45 ? O2' FE9 401 B 1 HETATM 29 C C3' FE9 . . . E 2 6.119 -18.42 33.554 1 42.27 ? C3' FE9 401 B 1 HETATM 30 O O3' FE9 . . . E 2 7.039 -19.451 33.983 1 43.08 ? O3' FE9 401 B 1 HETATM 31 N N9A FE9 . . . E 2 7.223 -14.914 34.094 1 44.06 ? N9A FE9 401 B 1 HETATM 32 C C4A FE9 . . . E 2 8.377 -14.279 34.335 1 45.23 ? C4A FE9 401 B 1 HETATM 33 N N3A FE9 . . . E 2 9.668 -14.684 34.258 1 44.79 ? N3A FE9 401 B 1 HETATM 34 C C2A FE9 . . . E 2 10.662 -13.844 34.565 1 46.65 ? C2A FE9 401 B 1 HETATM 35 N N2A FE9 . . . E 2 11.927 -14.306 34.472 1 47.23 ? N2A FE9 401 B 1 HETATM 36 N N1A FE9 . . . E 2 10.409 -12.566 34.954 1 48.6 ? N1A FE9 401 B 1 HETATM 37 C C6A FE9 . . . E 2 9.137 -12.111 35.039 1 48.84 ? C6A FE9 401 B 1 HETATM 38 O O6A FE9 . . . E 2 8.906 -10.822 35.443 1 51.12 ? O6A FE9 401 B 1 HETATM 39 C C5A FE9 . . . E 2 8.076 -12.982 34.73 1 47.1 ? C5A FE9 401 B 1 HETATM 40 N N7A FE9 . . . E 2 6.712 -12.883 34.707 1 46.96 ? N7A FE9 401 B 1 HETATM 41 C C8A FE9 . . . E 2 6.19 -14.071 34.312 1 45.05 ? C8A FE9 401 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 41 #