data_2DPX # _model_server_result.job_id N8WQOJxxU83AORBBI7s5yw _model_server_result.datetime_utc '2025-04-14 02:43:47' _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 2dpx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 2DPX # _exptl.entry_id 2DPX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 90 _cell.angle_beta 97.98 _cell.angle_gamma 90 _cell.entry_id 2DPX _cell.length_a 52.163 _cell.length_b 58.608 _cell.length_c 53.44 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DPX _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 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 ? 3 D N N ? 3 F 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 G O HOH . A HOH 51 1_555 C MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc2 G O HOH . A HOH 52 1_555 C MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc3 G O HOH . A HOH 53 1_555 C MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc4 G O HOH . A HOH 54 1_555 C MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc5 A OG SER 21 A SER 105 1_555 C MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc6 C MG MG . A MG 400 1_555 D O3B GDP . A GDP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc7 H O HOH . B HOH 56 1_555 E MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc8 H O HOH . B HOH 57 1_555 E MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc9 H O HOH . B HOH 58 1_555 E MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc10 H O HOH . B HOH 59 1_555 E MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc11 B OG SER 21 B SER 105 1_555 E MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc12 E MG MG . B MG 400 1_555 F O3B GDP . B GDP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? # _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 2DPX _atom_sites.fract_transf_matrix[1][1] 0.019171 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002689 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017063 _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] 0.018896 _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 MG A 1 400 400 MG MG . D 3 GDP A 1 500 500 GDP GDP . E 2 MG B 1 400 400 MG MG . F 3 GDP B 1 500 500 GDP GDP . G 4 HOH A 1 3 3 HOH HOH . G 4 HOH A 2 4 4 HOH HOH . G 4 HOH A 3 5 5 HOH HOH . G 4 HOH A 4 6 6 HOH HOH . G 4 HOH A 5 7 7 HOH HOH . G 4 HOH A 6 9 9 HOH HOH . G 4 HOH A 7 10 10 HOH HOH . G 4 HOH A 8 12 12 HOH HOH . G 4 HOH A 9 13 13 HOH HOH . G 4 HOH A 10 14 14 HOH HOH . G 4 HOH A 11 16 16 HOH HOH . G 4 HOH A 12 17 17 HOH HOH . G 4 HOH A 13 19 19 HOH HOH . G 4 HOH A 14 20 20 HOH HOH . G 4 HOH A 15 24 24 HOH HOH . G 4 HOH A 16 25 25 HOH HOH . G 4 HOH A 17 29 29 HOH HOH . G 4 HOH A 18 30 30 HOH HOH . G 4 HOH A 19 31 31 HOH HOH . G 4 HOH A 20 32 32 HOH HOH . G 4 HOH A 21 33 33 HOH HOH . G 4 HOH A 22 34 34 HOH HOH . G 4 HOH A 23 35 35 HOH HOH . G 4 HOH A 24 36 36 HOH HOH . G 4 HOH A 25 39 39 HOH HOH . G 4 HOH A 26 41 41 HOH HOH . G 4 HOH A 27 42 42 HOH HOH . G 4 HOH A 28 44 44 HOH HOH . G 4 HOH A 29 46 46 HOH HOH . G 4 HOH A 30 50 50 HOH HOH . G 4 HOH A 31 51 51 HOH HOH . G 4 HOH A 32 52 52 HOH HOH . G 4 HOH A 33 53 53 HOH HOH . G 4 HOH A 34 54 54 HOH HOH . G 4 HOH A 35 55 55 HOH HOH . G 4 HOH A 36 64 64 HOH HOH . G 4 HOH A 37 72 72 HOH HOH . G 4 HOH A 38 73 73 HOH HOH . G 4 HOH A 39 75 75 HOH HOH . G 4 HOH A 40 76 76 HOH HOH . G 4 HOH A 41 77 77 HOH HOH . G 4 HOH A 42 78 78 HOH HOH . G 4 HOH A 43 82 82 HOH HOH . G 4 HOH A 44 83 83 HOH HOH . H 4 HOH B 1 1 1 HOH HOH . H 4 HOH B 2 2 2 HOH HOH . H 4 HOH B 3 8 8 HOH HOH . H 4 HOH B 4 11 11 HOH HOH . H 4 HOH B 5 15 15 HOH HOH . H 4 HOH B 6 18 18 HOH HOH . H 4 HOH B 7 21 21 HOH HOH . H 4 HOH B 8 22 22 HOH HOH . H 4 HOH B 9 23 23 HOH HOH . H 4 HOH B 10 26 26 HOH HOH . H 4 HOH B 11 27 27 HOH HOH . H 4 HOH B 12 28 28 HOH HOH . H 4 HOH B 13 37 37 HOH HOH . H 4 HOH B 14 38 38 HOH HOH . H 4 HOH B 15 40 40 HOH HOH . H 4 HOH B 16 43 43 HOH HOH . H 4 HOH B 17 45 45 HOH HOH . H 4 HOH B 18 47 47 HOH HOH . H 4 HOH B 19 48 48 HOH HOH . H 4 HOH B 20 49 49 HOH HOH . H 4 HOH B 21 56 56 HOH HOH . H 4 HOH B 22 57 57 HOH HOH . H 4 HOH B 23 58 58 HOH HOH . H 4 HOH B 24 59 59 HOH HOH . H 4 HOH B 25 60 60 HOH HOH . H 4 HOH B 26 61 61 HOH HOH . H 4 HOH B 27 62 62 HOH HOH . H 4 HOH B 28 63 63 HOH HOH . H 4 HOH B 29 65 65 HOH HOH . H 4 HOH B 30 66 66 HOH HOH . H 4 HOH B 31 67 67 HOH HOH . H 4 HOH B 32 68 68 HOH HOH . H 4 HOH B 33 69 69 HOH HOH . H 4 HOH B 34 70 70 HOH HOH . H 4 HOH B 35 71 71 HOH HOH . H 4 HOH B 36 74 74 HOH HOH . H 4 HOH B 37 79 79 HOH HOH . H 4 HOH B 38 80 80 HOH HOH . H 4 HOH B 39 81 81 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 . . . D 3 15.478 7.093 24.147 1 24.83 ? PB GDP 500 A 1 HETATM 2 O O1B GDP . . . D 3 14.236 7.846 24.116 1 22.82 ? O1B GDP 500 A 1 HETATM 3 O O2B GDP . . . D 3 15.83 6.598 22.744 1 22.2 ? O2B GDP 500 A 1 HETATM 4 O O3B GDP . . . D 3 16.587 7.851 24.713 1 21.47 ? O3B GDP 500 A 1 HETATM 5 O O3A GDP . . . D 3 15.237 5.748 25.01 1 27.78 ? O3A GDP 500 A 1 HETATM 6 P PA GDP . . . D 3 15.427 5.602 26.6 1 28.53 ? PA GDP 500 A 1 HETATM 7 O O1A GDP . . . D 3 16.85 5.355 26.947 1 23.55 ? O1A GDP 500 A 1 HETATM 8 O O2A GDP . . . D 3 14.863 6.828 27.326 1 26.71 ? O2A GDP 500 A 1 HETATM 9 O O5' GDP . . . D 3 14.619 4.308 26.991 1 25.25 ? O5' GDP 500 A 1 HETATM 10 C C5' GDP . . . D 3 13.284 4.166 26.545 1 21.37 ? C5' GDP 500 A 1 HETATM 11 C C4' GDP . . . D 3 12.603 3.005 27.277 1 27.59 ? C4' GDP 500 A 1 HETATM 12 O O4' GDP . . . D 3 13.095 1.744 26.791 1 24.37 ? O4' GDP 500 A 1 HETATM 13 C C3' GDP . . . D 3 12.858 2.989 28.785 1 28.02 ? C3' GDP 500 A 1 HETATM 14 O O3' GDP . . . D 3 11.608 2.544 29.346 1 34.96 ? O3' GDP 500 A 1 HETATM 15 C C2' GDP . . . D 3 14.043 2.06 28.96 1 26.63 ? C2' GDP 500 A 1 HETATM 16 O O2' GDP . . . D 3 14.038 1.463 30.258 1 24.97 ? O2' GDP 500 A 1 HETATM 17 C C1' GDP . . . D 3 13.74 1.032 27.894 1 25.21 ? C1' GDP 500 A 1 HETATM 18 N N9 GDP . . . D 3 14.921 0.377 27.326 1 24.03 ? N9 GDP 500 A 1 HETATM 19 C C8 GDP . . . D 3 15.965 0.972 26.657 1 23 ? C8 GDP 500 A 1 HETATM 20 N N7 GDP . . . D 3 16.847 0.012 26.24 1 24.88 ? N7 GDP 500 A 1 HETATM 21 C C5 GDP . . . D 3 16.344 -1.182 26.655 1 25.98 ? C5 GDP 500 A 1 HETATM 22 C C6 GDP . . . D 3 16.753 -2.585 26.54 1 28.3 ? C6 GDP 500 A 1 HETATM 23 O O6 GDP . . . D 3 17.797 -2.864 25.934 1 25.72 ? O6 GDP 500 A 1 HETATM 24 N N1 GDP . . . D 3 15.956 -3.557 27.118 1 26.35 ? N1 GDP 500 A 1 HETATM 25 C C2 GDP . . . D 3 14.792 -3.221 27.794 1 27.08 ? C2 GDP 500 A 1 HETATM 26 N N2 GDP . . . D 3 14.03 -4.157 28.363 1 22.34 ? N2 GDP 500 A 1 HETATM 27 N N3 GDP . . . D 3 14.38 -1.929 27.903 1 23.93 ? N3 GDP 500 A 1 HETATM 28 C C4 GDP . . . D 3 15.108 -0.915 27.362 1 23.14 ? C4 GDP 500 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #