data_6UPA # _model_server_result.job_id 43FOQG0GF-zSf2eZIn422g _model_server_result.datetime_utc '2024-10-20 09:20:46' _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 6upa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1401}' # _entry.id 6UPA # _exptl.entry_id 6UPA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 6UPA _cell.length_a 82.73 _cell.length_b 82.73 _cell.length_c 170.35 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6UPA _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 5 _struct_asym.id E _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 disulf ? disulf1 B SG CYS 78 A CYS 111 1_555 B SG CYS 81 A CYS 114 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A OG SER 31 B SER 56 1_555 D MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc2 C O3G GTP . B GTP 401 1_555 D MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc3 C O1B GTP . B GTP 401 1_555 D MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc4 D MG MG . B MG 402 1_555 F O HOH . B HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc5 D MG MG . B MG 402 1_555 F O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc6 D MG MG . B MG 402 1_555 F O HOH . B HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? # _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 6UPA _atom_sites.fract_transf_matrix[1][1] 0.012088 _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] 0.012088 _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] 0.00587 _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 GTP B 1 401 500 GTP GTP . D 4 MG B 1 402 1 MG MG . E 5 GDP A 1 1401 1401 GDP GDP . F 6 HOH B 1 501 24 HOH HOH . F 6 HOH B 2 502 21 HOH HOH . F 6 HOH B 3 503 23 HOH HOH . F 6 HOH B 4 504 29 HOH HOH . F 6 HOH B 5 505 4 HOH HOH . F 6 HOH B 6 506 1 HOH HOH . F 6 HOH B 7 507 17 HOH HOH . F 6 HOH B 8 508 15 HOH HOH . F 6 HOH B 9 509 5 HOH HOH . F 6 HOH B 10 510 18 HOH HOH . F 6 HOH B 11 511 16 HOH HOH . F 6 HOH B 12 512 11 HOH HOH . F 6 HOH B 13 513 6 HOH HOH . F 6 HOH B 14 514 12 HOH HOH . F 6 HOH B 15 515 2 HOH HOH . F 6 HOH B 16 516 8 HOH HOH . F 6 HOH B 17 517 7 HOH HOH . G 6 HOH A 1 1501 25 HOH HOH . G 6 HOH A 2 1502 20 HOH HOH . G 6 HOH A 3 1503 27 HOH HOH . G 6 HOH A 4 1504 30 HOH HOH . G 6 HOH A 5 1505 9 HOH HOH . G 6 HOH A 6 1506 3 HOH HOH . G 6 HOH A 7 1507 26 HOH HOH . G 6 HOH A 8 1508 14 HOH HOH . G 6 HOH A 9 1509 32 HOH HOH . G 6 HOH A 10 1510 13 HOH HOH . G 6 HOH A 11 1511 10 HOH HOH . G 6 HOH A 12 1512 19 HOH HOH . G 6 HOH A 13 1513 22 HOH HOH . G 6 HOH A 14 1514 28 HOH HOH . G 6 HOH A 15 1515 31 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 . . . E 5 -11.704 43.746 -21.322 1 53.15 ? PB GDP 1401 A 1 HETATM 2 O O1B GDP . . . E 5 -11.306 42.759 -22.394 1 59.71 ? O1B GDP 1401 A 1 HETATM 3 O O2B GDP . . . E 5 -12.632 44.785 -21.896 1 57.45 ? O2B GDP 1401 A 1 HETATM 4 O O3B GDP . . . E 5 -10.451 44.41 -20.81 1 54.17 ? O3B GDP 1401 A 1 HETATM 5 O O3A GDP . . . E 5 -12.425 42.95 -20.123 1 55.15 ? O3A GDP 1401 A 1 HETATM 6 P PA GDP . . . E 5 -14.022 42.963 -19.897 1 55.35 ? PA GDP 1401 A 1 HETATM 7 O O1A GDP . . . E 5 -14.781 42.675 -21.171 1 54.19 ? O1A GDP 1401 A 1 HETATM 8 O O2A GDP . . . E 5 -14.494 44.255 -19.276 1 42.93 ? O2A GDP 1401 A 1 HETATM 9 O O5' GDP . . . E 5 -14.2 41.757 -18.856 1 56.96 ? O5' GDP 1401 A 1 HETATM 10 C C5' GDP . . . E 5 -14.46 40.436 -19.317 1 54.67 ? C5' GDP 1401 A 1 HETATM 11 C C4' GDP . . . E 5 -14.982 39.648 -18.131 1 50.57 ? C4' GDP 1401 A 1 HETATM 12 O O4' GDP . . . E 5 -14.287 40.065 -16.952 1 49.32 ? O4' GDP 1401 A 1 HETATM 13 C C3' GDP . . . E 5 -16.453 39.948 -17.914 1 45.05 ? C3' GDP 1401 A 1 HETATM 14 O O3' GDP . . . E 5 -17.165 38.711 -17.855 1 50.54 ? O3' GDP 1401 A 1 HETATM 15 C C2' GDP . . . E 5 -16.525 40.651 -16.576 1 48.43 ? C2' GDP 1401 A 1 HETATM 16 O O2' GDP . . . E 5 -17.662 40.231 -15.82 1 49.65 ? O2' GDP 1401 A 1 HETATM 17 C C1' GDP . . . E 5 -15.23 40.251 -15.892 1 51.36 ? C1' GDP 1401 A 1 HETATM 18 N N9 GDP . . . E 5 -14.811 41.315 -14.95 1 50.51 ? N9 GDP 1401 A 1 HETATM 19 C C8 GDP . . . E 5 -14.965 42.64 -15.123 1 51.12 ? C8 GDP 1401 A 1 HETATM 20 N N7 GDP . . . E 5 -14.47 43.327 -14.065 1 53.18 ? N7 GDP 1401 A 1 HETATM 21 C C5 GDP . . . E 5 -13.976 42.427 -13.193 1 48.98 ? C5 GDP 1401 A 1 HETATM 22 C C6 GDP . . . E 5 -13.308 42.471 -11.871 1 47.62 ? C6 GDP 1401 A 1 HETATM 23 O O6 GDP . . . E 5 -13.081 43.56 -11.305 1 46.45 ? O6 GDP 1401 A 1 HETATM 24 N N1 GDP . . . E 5 -12.956 41.31 -11.304 1 48.64 ? N1 GDP 1401 A 1 HETATM 25 C C2 GDP . . . E 5 -13.192 40.122 -11.893 1 49.3 ? C2 GDP 1401 A 1 HETATM 26 N N2 GDP . . . E 5 -12.803 38.994 -11.255 1 44.56 ? N2 GDP 1401 A 1 HETATM 27 N N3 GDP . . . E 5 -13.799 40.006 -13.102 1 51.71 ? N3 GDP 1401 A 1 HETATM 28 C C4 GDP . . . E 5 -14.204 41.103 -13.783 1 49.7 ? C4 GDP 1401 A 1 # _model_server_stats.io_time_ms 152 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #