data_1SA1 # _model_server_result.job_id 47pOig4qO3n0cPWU4-uaXQ _model_server_result.datetime_utc '2024-11-04 22:53:12' _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 1sa1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":602}' # _entry.id 1SA1 # _exptl.entry_id 1SA1 _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 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 1SA1 _cell.length_a 328.061 _cell.length_b 328.061 _cell.length_c 54.301 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SA1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,J,K,L,M _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 H 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 F MG MG . A MG 501 1_555 G O2B GTP . A GTP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc2 F MG MG . A MG 501 1_555 G O2G GTP . A GTP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc3 J MG MG . C MG 502 1_555 K O3G GTP . C GTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? metalc ? metalc4 J MG MG . C MG 502 1_555 K O2G GTP . C GTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? # _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 1SA1 _atom_sites.fract_transf_matrix[1][1] 0.003048 _atom_sites.fract_transf_matrix[1][2] 0.00176 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00352 _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] 0.018416 _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 F 4 MG A 1 501 501 MG MG . G 5 GTP A 1 600 600 GTP GTP . H 6 GDP B 1 602 602 GDP GDP . I 7 POD B 1 700 700 POD POD . J 4 MG C 1 502 502 MG MG . K 5 GTP C 1 601 601 GTP GTP . L 6 GDP D 1 603 603 GDP GDP . M 7 POD D 1 701 701 POD POD . # 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 . . . H 6 90.346 71.981 5.687 1 116.7 ? PB GDP 602 B 1 HETATM 2 O O1B GDP . . . H 6 90.81 73.223 6.382 1 116.53 ? O1B GDP 602 B 1 HETATM 3 O O2B GDP . . . H 6 91.456 70.927 5.814 1 116.57 ? O2B GDP 602 B 1 HETATM 4 O O3B GDP . . . H 6 89.016 71.347 6.22 1 116.43 ? O3B GDP 602 B 1 HETATM 5 O O3A GDP . . . H 6 90.158 72.397 4.148 1 116.61 ? O3A GDP 602 B 1 HETATM 6 P PA GDP . . . H 6 91.267 72.059 3.043 1 116.71 ? PA GDP 602 B 1 HETATM 7 O O1A GDP . . . H 6 92.546 71.703 3.723 1 116.42 ? O1A GDP 602 B 1 HETATM 8 O O2A GDP . . . H 6 90.656 70.991 2.093 1 116.48 ? O2A GDP 602 B 1 HETATM 9 O O5' GDP . . . H 6 91.478 73.442 2.241 1 116.65 ? O5' GDP 602 B 1 HETATM 10 C C5' GDP . . . H 6 90.646 73.692 1.136 1 116.56 ? C5' GDP 602 B 1 HETATM 11 C C4' GDP . . . H 6 91.334 74.608 0.134 1 116.44 ? C4' GDP 602 B 1 HETATM 12 O O4' GDP . . . H 6 92.728 74.557 0.272 1 116.16 ? O4' GDP 602 B 1 HETATM 13 C C3' GDP . . . H 6 90.968 74.167 -1.281 1 116.65 ? C3' GDP 602 B 1 HETATM 14 O O3' GDP . . . H 6 90.463 75.233 -2.062 1 116.87 ? O3' GDP 602 B 1 HETATM 15 C C2' GDP . . . H 6 92.232 73.724 -1.958 1 116.57 ? C2' GDP 602 B 1 HETATM 16 O O2' GDP . . . H 6 92.427 74.41 -3.199 1 116.64 ? O2' GDP 602 B 1 HETATM 17 C C1' GDP . . . H 6 93.295 73.987 -0.897 1 116.48 ? C1' GDP 602 B 1 HETATM 18 N N9 GDP . . . H 6 93.953 72.689 -0.629 1 116.59 ? N9 GDP 602 B 1 HETATM 19 C C8 GDP . . . H 6 93.414 71.482 -0.218 1 116.54 ? C8 GDP 602 B 1 HETATM 20 N N7 GDP . . . H 6 94.421 70.564 -0.13 1 116.49 ? N7 GDP 602 B 1 HETATM 21 C C5 GDP . . . H 6 95.587 71.172 -0.488 1 116.53 ? C5 GDP 602 B 1 HETATM 22 C C6 GDP . . . H 6 96.905 70.733 -0.593 1 116.43 ? C6 GDP 602 B 1 HETATM 23 O O6 GDP . . . H 6 97.085 69.534 -0.8 1 116.35 ? O6 GDP 602 B 1 HETATM 24 N N1 GDP . . . H 6 97.877 71.643 -0.998 1 116.4 ? N1 GDP 602 B 1 HETATM 25 C C2 GDP . . . H 6 97.567 72.962 -1.325 1 116.35 ? C2 GDP 602 B 1 HETATM 26 N N2 GDP . . . H 6 98.19 73.545 -2.337 1 116.36 ? N2 GDP 602 B 1 HETATM 27 N N3 GDP . . . H 6 96.272 73.372 -1.205 1 116.46 ? N3 GDP 602 B 1 HETATM 28 C C4 GDP . . . H 6 95.301 72.5 -0.811 1 116.63 ? C4 GDP 602 B 1 # _model_server_stats.io_time_ms 315 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 273 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #