data_7Z02 # _model_server_result.job_id zjiGXIQHftrPVxq1brua7w _model_server_result.datetime_utc '2024-11-05 04:37:51' _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 7z02 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 7Z02 # _exptl.entry_id 7Z02 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.39 _cell.angle_gamma 90 _cell.entry_id 7Z02 _cell.length_a 73.683 _cell.length_b 91.615 _cell.length_c 83.11 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Z02 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 6 _struct_asym.id G _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 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc2 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc3 D O1G GTP . A GTP 501 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc4 D O2B GTP . A GTP 501 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? # _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 7Z02 _atom_sites.fract_transf_matrix[1][1] 0.013572 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001761 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010915 _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] 0.012133 _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 D 4 GTP A 1 501 501 GTP GTP . E 5 MG A 1 502 502 MG MG . F 5 MG A 1 503 1 MG MG . G 6 GDP B 1 501 501 GDP GDP . H 7 I8N B 1 502 601 I8N 558 . I 8 HOH A 1 601 6 HOH HOH . I 8 HOH A 2 602 7 HOH HOH . I 8 HOH A 3 603 5 HOH HOH . J 8 HOH B 1 601 9 HOH HOH . J 8 HOH B 2 602 8 HOH HOH . J 8 HOH B 3 603 2 HOH HOH . J 8 HOH B 4 604 3 HOH HOH . J 8 HOH B 5 605 1 HOH HOH . J 8 HOH B 6 606 4 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 . . . G 6 27.703 -24.136 -10.486 1 48.45 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . G 6 28.012 -23.764 -11.921 1 53.55 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . G 6 27.184 -25.552 -10.443 1 49.64 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . G 6 26.686 -23.187 -9.898 1 50.35 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . G 6 29.054 -24.052 -9.62 1 47.67 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . G 6 29.332 -25.061 -8.399 1 49.93 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . G 6 30.043 -26.312 -8.858 1 52.06 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . G 6 28.04 -25.416 -7.704 1 48.26 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . G 6 30.29 -24.179 -7.45 1 52.84 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . G 6 31.62 -24.6 -7.149 1 48.57 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . G 6 31.884 -24.43 -5.659 1 48.88 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . G 6 30.871 -25.147 -4.951 1 48.37 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . G 6 33.225 -25.014 -5.246 1 47.33 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . G 6 33.892 -24.154 -4.315 1 51.77 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . G 6 32.889 -26.351 -4.61 1 47.66 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . G 6 33.742 -26.655 -3.507 1 46.38 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . G 6 31.441 -26.203 -4.173 1 52.34 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . G 6 30.689 -27.457 -4.404 1 50.19 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . G 6 30.338 -27.959 -5.605 1 50.36 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . G 6 29.648 -29.12 -5.452 1 51.67 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . G 6 29.547 -29.367 -4.134 1 48.07 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . G 6 28.945 -30.419 -3.286 1 50.86 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . G 6 28.341 -31.393 -3.786 1 52.47 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . G 6 29.063 -30.299 -1.96 1 50.29 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . G 6 29.706 -29.264 -1.383 1 50.7 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . G 6 29.784 -29.216 -0.031 1 49.17 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . G 6 30.282 -28.264 -2.096 1 48.6 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . G 6 30.233 -28.265 -3.448 1 53.15 ? C4 GDP 501 B 1 HETATM 29 H H4' GDP . . . G 6 31.879 -23.356 -5.429 1 65.43 ? H4' GDP 501 B 1 HETATM 30 H H3' GDP . . . G 6 33.913 -25.123 -6.097 1 74.87 ? H3' GDP 501 B 1 HETATM 31 H HO3' GDP . . . G 6 34.767 -24.512 -4.114 1 66.66 ? HO3' GDP 501 B 1 HETATM 32 H H2' GDP . . . G 6 33.038 -27.187 -5.308 1 64.11 ? H2' GDP 501 B 1 HETATM 33 H HO2' GDP . . . G 6 34.629 -26.86 -3.832 1 58.82 ? HO2' GDP 501 B 1 HETATM 34 H H1' GDP . . . G 6 31.404 -25.98 -3.097 1 58.27 ? H1' GDP 501 B 1 HETATM 35 H H8 GDP . . . G 6 30.573 -27.501 -6.558 1 76.71 ? H8 GDP 501 B 1 HETATM 36 H HN1 GDP . . . G 6 28.643 -31.03 -1.351 1 75.57 ? HN1 GDP 501 B 1 HETATM 37 H HN21 GDP . . . G 6 29.366 -29.946 0.526 1 71.18 ? HN21 GDP 501 B 1 HETATM 38 H HN22 GDP . . . G 6 30.26 -28.449 0.419 1 66.85 ? HN22 GDP 501 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #