data_2RGN # _model_server_result.job_id Sn_3YyNdAG0YacYEGzFtfA _model_server_result.datetime_utc '2025-06-21 20:19:22' _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 2rgn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":360}' # _entry.id 2RGN # _exptl.entry_id 2RGN _exptl.method 'X-RAY DIFFRACTION' # _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 80.87 _cell.angle_beta 85.16 _cell.angle_gamma 87.09 _cell.entry_id 2RGN _cell.length_a 67.187 _cell.length_b 68.056 _cell.length_c 138.018 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RGN _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H,I,M 1 1 D,E,F,J,K,L,N 2 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 ? 6 I N N ? 6 L 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 metalc ? metalc1 A OG SER 47 A SER 53 1_555 H MG MG . A MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc2 A OG1 THR 180 A THR 186 1_555 H MG MG . A MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc3 I O3B GDP . A GDP 360 1_555 G AL ALF . A ALF 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc4 I O2B GDP . A GDP 360 1_555 H MG MG . A MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc5 G AL ALF . A ALF 361 1_555 M O HOH . A HOH 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? metalc ? metalc6 H MG MG . A MG 362 1_555 M O HOH . A HOH 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc7 H MG MG . A MG 362 1_555 M O HOH . A HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc8 D OG SER 47 D SER 53 1_555 K MG MG . D MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc9 D OG1 THR 180 D THR 186 1_555 K MG MG . D MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc10 L O3B GDP . D GDP 360 1_555 J AL ALF . D ALF 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc11 L O2B GDP . D GDP 360 1_555 K MG MG . D MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc12 J AL ALF . D ALF 361 1_555 N O HOH . D HOH 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? metalc ? metalc13 K MG MG . D MG 362 1_555 N O HOH . D HOH 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc14 K MG MG . D MG 362 1_555 N O HOH . D HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 2RGN _atom_sites.fract_transf_matrix[1][1] 0.014884 _atom_sites.fract_transf_matrix[1][2] -0.000758 _atom_sites.fract_transf_matrix[1][3] -0.001156 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014713 _atom_sites.fract_transf_matrix[2][3] -0.00231 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.00736 _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 G 4 ALF A 1 361 361 ALF ALF . H 5 MG A 1 362 362 MG MG . I 6 GDP A 1 360 360 GDP GDP . J 4 ALF D 1 361 361 ALF ALF . K 5 MG D 1 362 362 MG MG . L 6 GDP D 1 360 360 GDP GDP . M 7 HOH A 1 363 363 HOH HOH . M 7 HOH A 2 364 364 HOH HOH . M 7 HOH A 3 365 365 HOH HOH . N 7 HOH D 1 363 363 HOH HOH . N 7 HOH D 2 364 364 HOH HOH . N 7 HOH D 3 365 365 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 P PB GDP . . . I 6 25.164 -4.144 1.699 1 137.97 ? PB GDP 360 A 1 HETATM 2 O O1B GDP . . . I 6 26.04 -3.963 0.498 1 139.3 ? O1B GDP 360 A 1 HETATM 3 O O2B GDP . . . I 6 24.566 -5.514 1.604 1 142.34 ? O2B GDP 360 A 1 HETATM 4 O O3B GDP . . . I 6 25.989 -4.037 2.948 1 145.89 ? O3B GDP 360 A 1 HETATM 5 O O3A GDP . . . I 6 24.028 -3.008 1.664 1 138.33 ? O3A GDP 360 A 1 HETATM 6 P PA GDP . . . I 6 22.43 -3.249 1.678 1 135.25 ? PA GDP 360 A 1 HETATM 7 O O1A GDP . . . I 6 21.897 -4.094 0.557 1 134.45 ? O1A GDP 360 A 1 HETATM 8 O O2A GDP . . . I 6 22.028 -3.783 3.02 1 136.11 ? O2A GDP 360 A 1 HETATM 9 O O5' GDP . . . I 6 21.83 -1.782 1.456 1 136.42 ? O5' GDP 360 A 1 HETATM 10 C C5' GDP . . . I 6 22.397 -0.649 2.127 1 137.25 ? C5' GDP 360 A 1 HETATM 11 C C4' GDP . . . I 6 21.335 0.385 2.486 1 136.83 ? C4' GDP 360 A 1 HETATM 12 O O4' GDP . . . I 6 21.252 1.34 1.428 1 135.62 ? O4' GDP 360 A 1 HETATM 13 C C3' GDP . . . I 6 19.94 -0.214 2.674 1 136.11 ? C3' GDP 360 A 1 HETATM 14 O O3' GDP . . . I 6 19.319 0.32 3.839 1 137.08 ? O3' GDP 360 A 1 HETATM 15 C C2' GDP . . . I 6 19.143 0.191 1.46 1 134.87 ? C2' GDP 360 A 1 HETATM 16 O O2' GDP . . . I 6 17.827 0.614 1.818 1 133.5 ? O2' GDP 360 A 1 HETATM 17 C C1' GDP . . . I 6 19.931 1.35 0.877 1 134.56 ? C1' GDP 360 A 1 HETATM 18 N N9 GDP . . . I 6 20.05 1.253 -0.588 1 134.44 ? N9 GDP 360 A 1 HETATM 19 C C8 GDP . . . I 6 20.651 0.276 -1.288 1 134.55 ? C8 GDP 360 A 1 HETATM 20 N N7 GDP . . . I 6 20.577 0.539 -2.619 1 134.56 ? N7 GDP 360 A 1 HETATM 21 C C5 GDP . . . I 6 19.928 1.701 -2.771 1 134.07 ? C5 GDP 360 A 1 HETATM 22 C C6 GDP . . . I 6 19.507 2.553 -3.897 1 134.11 ? C6 GDP 360 A 1 HETATM 23 O O6 GDP . . . I 6 19.762 2.224 -5.072 1 134.63 ? O6 GDP 360 A 1 HETATM 24 N N1 GDP . . . I 6 18.848 3.685 -3.62 1 134.34 ? N1 GDP 360 A 1 HETATM 25 C C2 GDP . . . I 6 18.555 4.068 -2.361 1 134.64 ? C2 GDP 360 A 1 HETATM 26 N N2 GDP . . . I 6 17.886 5.223 -2.147 1 134.68 ? N2 GDP 360 A 1 HETATM 27 N N3 GDP . . . I 6 18.905 3.332 -1.277 1 134.87 ? N3 GDP 360 A 1 HETATM 28 C C4 GDP . . . I 6 19.582 2.168 -1.426 1 134.42 ? C4 GDP 360 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #