data_8TYM # _model_server_result.job_id nxxU4NzRv6OZ-vwoqgyXFQ _model_server_result.datetime_utc '2024-10-19 14:18:16' _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 8tym # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":901}' # _entry.id 8TYM # _exptl.entry_id 8TYM _exptl.method 'ELECTRON MICROSCOPY' # _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 4 _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 8TYM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TYM _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K 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 49 c SER 45 1_555 F MG MG . c MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc2 A OG1 THR 69 c THR 65 1_555 F MG MG . c MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc3 B OG SER 49 f SER 45 1_555 H MG MG . f MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc4 B OG1 THR 69 f THR 65 1_555 H MG MG . f MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc5 G O3B GDP . f GDP 901 1_555 H MG MG . f MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc6 C OG SER 49 B SER 45 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc7 C OG1 THR 69 B THR 65 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc8 I O2B GDP . B GDP 901 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? metalc ? metalc9 D OG SER 49 C SER 45 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc10 D OG1 THR 69 C THR 65 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc11 K O3B GDP . C GDP 901 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? # _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 8TYM _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 E 2 GDP c 1 901 901 GDP GDP . F 3 MG c 1 902 902 MG MG . G 2 GDP f 1 901 901 GDP GDP . H 3 MG f 1 902 902 MG MG . I 2 GDP B 1 901 901 GDP GDP . J 3 MG B 1 902 902 MG MG . K 2 GDP C 1 901 901 GDP GDP . L 3 MG C 1 902 902 MG MG . # 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 2 163.228 314.746 371.779 1 3.96 ? PB GDP 901 B 1 HETATM 2 O O1B GDP . . . I 2 163.499 314.936 370.317 1 3.95 ? O1B GDP 901 B 1 HETATM 3 O O2B GDP . . . I 2 162.74 313.382 372.159 1 3.81 ? O2B GDP 901 B 1 HETATM 4 O O3B GDP . . . I 2 164.333 315.269 372.649 1 4.05 ? O3B GDP 901 B 1 HETATM 5 O O3A GDP . . . I 2 162.015 315.722 372.096 1 4.71 ? O3A GDP 901 B 1 HETATM 6 P PA GDP . . . I 2 160.563 315.169 371.771 1 5.53 ? PA GDP 901 B 1 HETATM 7 O O1A GDP . . . I 2 160.735 314.166 370.69 1 5.97 ? O1A GDP 901 B 1 HETATM 8 O O2A GDP . . . I 2 159.929 314.723 373.036 1 5.88 ? O2A GDP 901 B 1 HETATM 9 O O5' GDP . . . I 2 159.744 316.378 371.147 1 5.52 ? O5' GDP 901 B 1 HETATM 10 C C5' GDP . . . I 2 159.681 317.585 371.879 1 5.56 ? C5' GDP 901 B 1 HETATM 11 C C4' GDP . . . I 2 158.432 318.341 371.491 1 5.44 ? C4' GDP 901 B 1 HETATM 12 O O4' GDP . . . I 2 158.698 319.373 370.558 1 5.47 ? O4' GDP 901 B 1 HETATM 13 C C3' GDP . . . I 2 157.456 317.492 370.741 1 5.5 ? C3' GDP 901 B 1 HETATM 14 O O3' GDP . . . I 2 156.75 316.662 371.643 1 5.58 ? O3' GDP 901 B 1 HETATM 15 C C2' GDP . . . I 2 156.541 318.52 370.171 1 5.39 ? C2' GDP 901 B 1 HETATM 16 O O2' GDP . . . I 2 155.598 318.989 371.132 1 5.4 ? O2' GDP 901 B 1 HETATM 17 C C1' GDP . . . I 2 157.526 319.587 369.763 1 5.05 ? C1' GDP 901 B 1 HETATM 18 N N9 GDP . . . I 2 157.826 319.457 368.327 1 4.21 ? N9 GDP 901 B 1 HETATM 19 C C8 GDP . . . I 2 158.779 318.677 367.801 1 3.97 ? C8 GDP 901 B 1 HETATM 20 N N7 GDP . . . I 2 158.789 318.789 366.457 1 3.97 ? N7 GDP 901 B 1 HETATM 21 C C5 GDP . . . I 2 157.828 319.651 366.118 1 4.22 ? C5 GDP 901 B 1 HETATM 22 C C6 GDP . . . I 2 157.312 320.212 364.87 1 4.1 ? C6 GDP 901 B 1 HETATM 23 O O6 GDP . . . I 2 157.807 319.88 363.788 1 4.06 ? O6 GDP 901 B 1 HETATM 24 N N1 GDP . . . I 2 156.311 321.076 364.912 1 3.89 ? N1 GDP 901 B 1 HETATM 25 C C2 GDP . . . I 2 155.774 321.437 366.073 1 3.74 ? C2 GDP 901 B 1 HETATM 26 N N2 GDP . . . I 2 154.76 322.321 366.026 1 3.84 ? N2 GDP 901 B 1 HETATM 27 N N3 GDP . . . I 2 156.192 320.967 367.27 1 4 ? N3 GDP 901 B 1 HETATM 28 C C4 GDP . . . I 2 157.197 320.088 367.35 1 4.09 ? C4 GDP 901 B 1 HETATM 29 H H5' GDP . . . I 2 159.658 317.385 372.95 1 6.67 ? H5' GDP 901 B 1 HETATM 30 H "H5''" GDP . . . I 2 160.564 318.184 371.664 1 6.67 ? "H5''" GDP 901 B 1 HETATM 31 H H4' GDP . . . I 2 157.953 318.736 372.388 1 6.53 ? H4' GDP 901 B 1 HETATM 32 H H3' GDP . . . I 2 157.931 316.931 369.938 1 6.6 ? H3' GDP 901 B 1 HETATM 33 H HO3' GDP . . . I 2 157.35 315.984 371.99 1 6.7 ? HO3' GDP 901 B 1 HETATM 34 H H2' GDP . . . I 2 156.053 318.126 369.284 1 6.47 ? H2' GDP 901 B 1 HETATM 35 H HO2' GDP . . . I 2 155.728 318.51 371.968 1 6.48 ? HO2' GDP 901 B 1 HETATM 36 H H1' GDP . . . I 2 157.098 320.567 369.97 1 6.06 ? H1' GDP 901 B 1 HETATM 37 H H8 GDP . . . I 2 159.446 318.047 368.372 1 4.76 ? H8 GDP 901 B 1 HETATM 38 H HN1 GDP . . . I 2 155.949 321.467 364.048 1 4.67 ? HN1 GDP 901 B 1 HETATM 39 H HN21 GDP . . . I 2 154.439 322.679 365.131 1 4.61 ? HN21 GDP 901 B 1 HETATM 40 H HN22 GDP . . . I 2 154.318 322.629 366.885 1 4.61 ? HN22 GDP 901 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #