data_6PQ3 # _model_server_result.job_id wh4WMeyJ6SKcY2KojuQFXA _model_server_result.datetime_utc '2024-11-16 11:36:14' _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 6pq3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6PQ3 # _exptl.entry_id 6PQ3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 120 _cell.entry_id 6PQ3 _cell.length_a 82.9 _cell.length_b 82.9 _cell.length_c 41.13 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PQ3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,I _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc2 B O1B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc3 C MG MG . A MG 202 1_555 I O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc4 C MG MG . A MG 202 1_555 I O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc5 C MG MG . A MG 202 1_555 I O HOH . A HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc6 C MG MG . A MG 202 1_555 I O HOH . A HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? # _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 6PQ3 _atom_sites.fract_transf_matrix[1][1] 0.012063 _atom_sites.fract_transf_matrix[1][2] 0.006964 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013929 _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] 0.024313 _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 B 2 GDP A 1 201 1 GDP GDP . C 3 MG A 1 202 1 MG MG . D 4 SO4 A 1 203 1 SO4 SO4 . E 4 SO4 A 1 204 2 SO4 SO4 . F 4 SO4 A 1 205 3 SO4 SO4 . G 4 SO4 A 1 206 4 SO4 SO4 . H 4 SO4 A 1 207 5 SO4 SO4 . I 5 HOH A 1 301 26 HOH HOH . I 5 HOH A 2 302 39 HOH HOH . I 5 HOH A 3 303 12 HOH HOH . I 5 HOH A 4 304 31 HOH HOH . I 5 HOH A 5 305 3 HOH HOH . I 5 HOH A 6 306 9 HOH HOH . I 5 HOH A 7 307 7 HOH HOH . I 5 HOH A 8 308 13 HOH HOH . I 5 HOH A 9 309 30 HOH HOH . I 5 HOH A 10 310 4 HOH HOH . I 5 HOH A 11 311 10 HOH HOH . I 5 HOH A 12 312 19 HOH HOH . I 5 HOH A 13 313 34 HOH HOH . I 5 HOH A 14 314 5 HOH HOH . I 5 HOH A 15 315 1 HOH HOH . I 5 HOH A 16 316 8 HOH HOH . I 5 HOH A 17 317 6 HOH HOH . I 5 HOH A 18 318 2 HOH HOH . I 5 HOH A 19 319 18 HOH HOH . I 5 HOH A 20 320 27 HOH HOH . I 5 HOH A 21 321 11 HOH HOH . I 5 HOH A 22 322 20 HOH HOH . I 5 HOH A 23 323 24 HOH HOH . I 5 HOH A 24 324 33 HOH HOH . I 5 HOH A 25 325 25 HOH HOH . I 5 HOH A 26 326 15 HOH HOH . I 5 HOH A 27 327 14 HOH HOH . I 5 HOH A 28 328 17 HOH HOH . I 5 HOH A 29 329 22 HOH HOH . I 5 HOH A 30 330 36 HOH HOH . I 5 HOH A 31 331 23 HOH HOH . I 5 HOH A 32 332 16 HOH HOH . I 5 HOH A 33 333 29 HOH HOH . I 5 HOH A 34 334 21 HOH HOH . I 5 HOH A 35 335 38 HOH HOH . I 5 HOH A 36 336 37 HOH HOH . I 5 HOH A 37 337 28 HOH HOH . I 5 HOH A 38 338 35 HOH HOH . I 5 HOH A 39 339 32 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 . . . B 2 25.6 -27.363 0.134 1 25.84 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 24.185 -27.451 -0.388 1 26.05 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 25.718 -26.335 1.23 1 24.12 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 26.547 -27.029 -0.995 1 25.51 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 26.03 -28.776 0.787 1 24.8 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 25.347 -30.194 0.436 1 28 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 23.944 -30.271 0.988 1 30.85 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 25.4 -30.477 -1.046 1 27.35 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 26.331 -31.182 1.234 1 25.36 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 27.673 -31.355 0.775 1 27.18 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 28.175 -32.715 1.236 1 30.39 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 28.142 -32.764 2.662 1 27.99 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 27.259 -33.821 0.74 1 29.99 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 28.062 -34.92 0.297 1 31.99 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 26.449 -34.226 1.956 1 31.3 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 26.097 -35.613 1.938 1 32.01 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 27.382 -33.891 3.105 1 29.33 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 26.646 -33.519 4.332 1 24.55 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 25.728 -32.537 4.454 1 25.29 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 25.277 -32.458 5.733 1 26.49 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 25.927 -33.404 6.446 1 25.34 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 25.933 -33.865 7.85 1 25.99 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 25.191 -33.315 8.69 1 27.72 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 26.76 -34.873 8.186 1 26.11 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 27.576 -35.465 7.289 1 33.45 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 28.383 -36.478 7.7 1 31.91 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 27.622 -35.096 5.983 1 28.76 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 26.836 -34.089 5.521 1 26.65 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #