data_1JFF # _model_server_result.job_id LkB-cepuOXG-DZZCPsLEew _model_server_result.datetime_utc '2024-11-24 21:36:35' _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 1jff # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":600}' # _entry.id 1JFF # _exptl.entry_id 1JFF _exptl.method 'ELECTRON CRYSTALLOGRAPHY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 1JFF _cell.length_a 81.2 _cell.length_b 93.5 _cell.length_c 90 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JFF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id E _struct_conn.ptnr1_label_atom_id O1G _struct_conn.ptnr1_label_comp_id GTP _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id GTP _struct_conn.ptnr1_auth_seq_id 500 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id MG _struct_conn.ptnr2_label_comp_id MG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id MG _struct_conn.ptnr2_auth_seq_id 501 _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 2.449 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 1JFF _atom_sites.fract_transf_matrix[1][1] 0.012315 _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] 0.010695 _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] 0.011111 _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 3 ZN A 1 900 900 ZN ZN . D 4 MG A 1 501 501 MG MG . E 5 GTP A 1 500 500 GTP GTP . F 6 GDP B 1 600 500 GDP GDP . G 7 TA1 B 1 601 1 TA1 TA1 . # 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 P PB GDP . . . F 6 -16.805 2.682 5.385 1 22.28 ? PB GDP 600 B 1 HETATM 2 O O1B GDP . . . F 6 -15.637 3.581 5.325 1 23.59 ? O1B GDP 600 B 1 HETATM 3 O O2B GDP . . . F 6 -16.992 1.996 6.589 1 23.44 ? O2B GDP 600 B 1 HETATM 4 O O3B GDP . . . F 6 -18.12 3.514 4.884 1 25.3 ? O3B GDP 600 B 1 HETATM 5 O O3A GDP . . . F 6 -16.537 1.55 4.323 1 19.52 ? O3A GDP 600 B 1 HETATM 6 P PA GDP . . . F 6 -16.459 -0.109 4.516 1 20.51 ? PA GDP 600 B 1 HETATM 7 O O1A GDP . . . F 6 -15.277 -0.445 5.358 1 23.36 ? O1A GDP 600 B 1 HETATM 8 O O2A GDP . . . F 6 -17.805 -0.534 5.079 1 18 ? O2A GDP 600 B 1 HETATM 9 O O5' GDP . . . F 6 -16.173 -0.564 3.057 1 16.66 ? O5' GDP 600 B 1 HETATM 10 C C5' GDP . . . F 6 -16.521 -1.906 2.6 1 7.65 ? C5' GDP 600 B 1 HETATM 11 C C4' GDP . . . F 6 -15.408 -2.685 2.086 1 2.51 ? C4' GDP 600 B 1 HETATM 12 O O4' GDP . . . F 6 -14.447 -2.92 3.19 1 2 ? O4' GDP 600 B 1 HETATM 13 C C3' GDP . . . F 6 -15.757 -4.158 1.664 1 3.46 ? C3' GDP 600 B 1 HETATM 14 O O3' GDP . . . F 6 -14.946 -4.436 0.465 1 2.32 ? O3' GDP 600 B 1 HETATM 15 C C2' GDP . . . F 6 -15.313 -5.128 2.785 1 2.23 ? C2' GDP 600 B 1 HETATM 16 O O2' GDP . . . F 6 -14.86 -6.446 2.432 1 2 ? O2' GDP 600 B 1 HETATM 17 C C1' GDP . . . F 6 -14.182 -4.363 3.469 1 2 ? C1' GDP 600 B 1 HETATM 18 N N9 GDP . . . F 6 -14.123 -4.533 4.921 1 5.88 ? N9 GDP 600 B 1 HETATM 19 C C8 GDP . . . F 6 -15.189 -3.907 5.775 1 9.42 ? C8 GDP 600 B 1 HETATM 20 N N7 GDP . . . F 6 -14.62 -4.371 6.974 1 10.36 ? N7 GDP 600 B 1 HETATM 21 C C5 GDP . . . F 6 -13.509 -5.1 6.96 1 10.45 ? C5 GDP 600 B 1 HETATM 22 C C6 GDP . . . F 6 -12.558 -5.796 7.736 1 13.51 ? C6 GDP 600 B 1 HETATM 23 O O6 GDP . . . F 6 -12.743 -5.763 9.067 1 11.34 ? O6 GDP 600 B 1 HETATM 24 N N1 GDP . . . F 6 -11.485 -6.448 7.236 1 10.31 ? N1 GDP 600 B 1 HETATM 25 C C2 GDP . . . F 6 -11.293 -6.458 5.761 1 5.81 ? C2 GDP 600 B 1 HETATM 26 N N2 GDP . . . F 6 -10.211 -7.16 5.501 1 6.23 ? N2 GDP 600 B 1 HETATM 27 N N3 GDP . . . F 6 -12.122 -5.868 5.005 1 4.23 ? N3 GDP 600 B 1 HETATM 28 C C4 GDP . . . F 6 -13.156 -5.202 5.552 1 7.64 ? C4 GDP 600 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #