data_7U2P # _model_server_result.job_id zPV1dylEnYgOcRVB4w1S6A _model_server_result.datetime_utc '2024-12-04 16:49:22' _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 7u2p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 7U2P # _exptl.entry_id 7U2P _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 90 _cell.angle_gamma 90 _cell.entry_id 7U2P _cell.length_a 114.641 _cell.length_b 122.798 _cell.length_c 127.474 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7U2P _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,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 6 _struct_asym.id F _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 OD2 ASP 288 A ASP 287 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc2 A OE1 GLU 515 A GLU 514 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc3 C O1A UPG . A UPG 601 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.84 ? metalc ? metalc4 C O1B UPG . A UPG 601 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.902 ? metalc ? metalc5 D MN MN . A MN 602 1_555 H O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc6 D MN MN . A MN 602 1_555 H O HOH . A HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc7 B OG1 THR 24 B THR 19 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc8 F O3B GDP . B GDP 201 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.893 ? metalc ? metalc9 G MG MG . B MG 202 1_555 I O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc10 G MG MG . B MG 202 1_555 I O HOH . B HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc11 G MG MG . B MG 202 1_555 I O HOH . B HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc12 G MG MG . B MG 202 1_555 I O HOH . B HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? # _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 7U2P _atom_sites.fract_transf_matrix[1][1] 0.008723 _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] 0.008143 _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] 0.007845 _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 UPG A 1 601 601 UPG UPG . D 4 MN A 1 602 551 MN MN . E 5 SO4 A 1 603 1 SO4 SO4 . F 6 GDP B 1 201 201 GDP GDP . G 7 MG B 1 202 1 MG MG . H 8 HOH A 1 701 40 HOH HOH . H 8 HOH A 2 702 24 HOH HOH . H 8 HOH A 3 703 14 HOH HOH . H 8 HOH A 4 704 49 HOH HOH . H 8 HOH A 5 705 31 HOH HOH . H 8 HOH A 6 706 11 HOH HOH . H 8 HOH A 7 707 1 HOH HOH . H 8 HOH A 8 708 9 HOH HOH . H 8 HOH A 9 709 12 HOH HOH . H 8 HOH A 10 710 46 HOH HOH . H 8 HOH A 11 711 21 HOH HOH . H 8 HOH A 12 712 34 HOH HOH . H 8 HOH A 13 713 27 HOH HOH . H 8 HOH A 14 714 20 HOH HOH . H 8 HOH A 15 715 3 HOH HOH . H 8 HOH A 16 716 45 HOH HOH . H 8 HOH A 17 717 4 HOH HOH . H 8 HOH A 18 718 29 HOH HOH . H 8 HOH A 19 719 13 HOH HOH . H 8 HOH A 20 720 32 HOH HOH . H 8 HOH A 21 721 16 HOH HOH . H 8 HOH A 22 722 17 HOH HOH . H 8 HOH A 23 723 15 HOH HOH . H 8 HOH A 24 724 10 HOH HOH . H 8 HOH A 25 725 25 HOH HOH . H 8 HOH A 26 726 33 HOH HOH . H 8 HOH A 27 727 38 HOH HOH . H 8 HOH A 28 728 28 HOH HOH . H 8 HOH A 29 729 42 HOH HOH . H 8 HOH A 30 730 26 HOH HOH . H 8 HOH A 31 731 19 HOH HOH . H 8 HOH A 32 732 18 HOH HOH . H 8 HOH A 33 733 23 HOH HOH . H 8 HOH A 34 734 43 HOH HOH . H 8 HOH A 35 735 37 HOH HOH . H 8 HOH A 36 736 2 HOH HOH . H 8 HOH A 37 737 7 HOH HOH . H 8 HOH A 38 738 39 HOH HOH . H 8 HOH A 39 739 35 HOH HOH . H 8 HOH A 40 740 48 HOH HOH . H 8 HOH A 41 741 5 HOH HOH . H 8 HOH A 42 742 44 HOH HOH . I 8 HOH B 1 301 53 HOH HOH . I 8 HOH B 2 302 41 HOH HOH . I 8 HOH B 3 303 8 HOH HOH . I 8 HOH B 4 304 30 HOH HOH . I 8 HOH B 5 305 47 HOH HOH . I 8 HOH B 6 306 36 HOH HOH . I 8 HOH B 7 307 50 HOH HOH . I 8 HOH B 8 308 22 HOH HOH . I 8 HOH B 9 309 52 HOH HOH . I 8 HOH B 10 310 51 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 . . . F 6 -36.142 -27.265 -6.608 1 75.42 ? PB GDP 201 B 1 HETATM 2 O O1B GDP . . . F 6 -36.392 -28.145 -7.803 1 68.38 ? O1B GDP 201 B 1 HETATM 3 O O2B GDP . . . F 6 -35.45 -25.974 -6.953 1 75.89 ? O2B GDP 201 B 1 HETATM 4 O O3B GDP . . . F 6 -35.521 -27.976 -5.422 1 58.63 ? O3B GDP 201 B 1 HETATM 5 O O3A GDP . . . F 6 -37.642 -26.78 -6.198 1 74.89 ? O3A GDP 201 B 1 HETATM 6 P PA GDP . . . F 6 -38.136 -26.609 -4.66 1 72.7 ? PA GDP 201 B 1 HETATM 7 O O1A GDP . . . F 6 -38.742 -27.898 -4.172 1 73.91 ? O1A GDP 201 B 1 HETATM 8 O O2A GDP . . . F 6 -37.004 -25.977 -3.895 1 73.66 ? O2A GDP 201 B 1 HETATM 9 O O5' GDP . . . F 6 -39.329 -25.567 -4.79 1 68.49 ? O5' GDP 201 B 1 HETATM 10 C C5' GDP . . . F 6 -39.124 -24.345 -5.484 1 70.63 ? C5' GDP 201 B 1 HETATM 11 C C4' GDP . . . F 6 -40.123 -23.327 -4.933 1 75.41 ? C4' GDP 201 B 1 HETATM 12 O O4' GDP . . . F 6 -41.398 -23.552 -5.534 1 72.14 ? O4' GDP 201 B 1 HETATM 13 C C3' GDP . . . F 6 -40.314 -23.436 -3.416 1 76.26 ? C3' GDP 201 B 1 HETATM 14 O O3' GDP . . . F 6 -39.908 -22.244 -2.743 1 85.41 ? O3' GDP 201 B 1 HETATM 15 C C2' GDP . . . F 6 -41.792 -23.662 -3.18 1 73.26 ? C2' GDP 201 B 1 HETATM 16 O O2' GDP . . . F 6 -42.367 -22.709 -2.277 1 79.5 ? O2' GDP 201 B 1 HETATM 17 C C1' GDP . . . F 6 -42.431 -23.562 -4.556 1 70.94 ? C1' GDP 201 B 1 HETATM 18 N N9 GDP . . . F 6 -43.255 -24.767 -4.744 1 70.42 ? N9 GDP 201 B 1 HETATM 19 C C8 GDP . . . F 6 -42.817 -26.04 -4.642 1 71.42 ? C8 GDP 201 B 1 HETATM 20 N N7 GDP . . . F 6 -43.824 -26.93 -4.859 1 69.01 ? N7 GDP 201 B 1 HETATM 21 C C5 GDP . . . F 6 -44.936 -26.209 -5.103 1 67.71 ? C5 GDP 201 B 1 HETATM 22 C C6 GDP . . . F 6 -46.353 -26.51 -5.408 1 66.63 ? C6 GDP 201 B 1 HETATM 23 O O6 GDP . . . F 6 -46.752 -27.692 -5.493 1 70.87 ? O6 GDP 201 B 1 HETATM 24 N N1 GDP . . . F 6 -47.198 -25.485 -5.585 1 65.23 ? N1 GDP 201 B 1 HETATM 25 C C2 GDP . . . F 6 -46.796 -24.201 -5.51 1 67.25 ? C2 GDP 201 B 1 HETATM 26 N N2 GDP . . . F 6 -47.695 -23.212 -5.714 1 64.14 ? N2 GDP 201 B 1 HETATM 27 N N3 GDP . . . F 6 -45.512 -23.848 -5.241 1 71.05 ? N3 GDP 201 B 1 HETATM 28 C C4 GDP . . . F 6 -44.558 -24.788 -5.025 1 69.92 ? C4 GDP 201 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #