data_4P4T # _model_server_result.job_id dTpXt1hWvVRto76HfmR4nQ _model_server_result.datetime_utc '2024-12-26 18:04:45' _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 4p4t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 4P4T # _exptl.entry_id 4P4T _exptl.method 'X-RAY DIFFRACTION' # _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 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 4P4T _cell.length_a 47.02 _cell.length_b 77.59 _cell.length_c 212.33 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4P4T _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 21 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-y+1/2,z -1 0 0 0 -1 0 0 0 1 0 38.795 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 4P4T _atom_sites.fract_transf_matrix[1][1] 0.021268 _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] 0.012888 _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] 0.00471 _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 B 2 GDP A 1 701 180 GDP GDP . C 3 SO4 A 1 702 1 SO4 SO4 . D 3 SO4 A 1 703 2 SO4 SO4 . E 3 SO4 A 1 704 3 SO4 SO4 . F 4 HOH A 1 801 36 HOH HOH . F 4 HOH A 2 802 1036 HOH HOH . F 4 HOH A 3 803 43 HOH HOH . F 4 HOH A 4 804 1007 HOH HOH . F 4 HOH A 5 805 1037 HOH HOH . F 4 HOH A 6 806 30 HOH HOH . F 4 HOH A 7 807 1039 HOH HOH . F 4 HOH A 8 808 1030 HOH HOH . F 4 HOH A 9 809 15 HOH HOH . F 4 HOH A 10 810 18 HOH HOH . F 4 HOH A 11 811 61 HOH HOH . F 4 HOH A 12 812 38 HOH HOH . F 4 HOH A 13 813 1027 HOH HOH . F 4 HOH A 14 814 21 HOH HOH . F 4 HOH A 15 815 35 HOH HOH . F 4 HOH A 16 816 28 HOH HOH . F 4 HOH A 17 817 1023 HOH HOH . F 4 HOH A 18 818 53 HOH HOH . F 4 HOH A 19 819 1 HOH HOH . F 4 HOH A 20 820 1005 HOH HOH . F 4 HOH A 21 821 1048 HOH HOH . F 4 HOH A 22 822 2 HOH HOH . F 4 HOH A 23 823 3 HOH HOH . F 4 HOH A 24 824 5 HOH HOH . F 4 HOH A 25 825 7 HOH HOH . F 4 HOH A 26 826 8 HOH HOH . F 4 HOH A 27 827 9 HOH HOH . F 4 HOH A 28 828 10 HOH HOH . F 4 HOH A 29 829 11 HOH HOH . F 4 HOH A 30 830 12 HOH HOH . F 4 HOH A 31 831 13 HOH HOH . F 4 HOH A 32 832 14 HOH HOH . F 4 HOH A 33 833 17 HOH HOH . F 4 HOH A 34 834 19 HOH HOH . F 4 HOH A 35 835 20 HOH HOH . F 4 HOH A 36 836 24 HOH HOH . F 4 HOH A 37 837 26 HOH HOH . F 4 HOH A 38 838 27 HOH HOH . F 4 HOH A 39 839 31 HOH HOH . F 4 HOH A 40 840 32 HOH HOH . F 4 HOH A 41 841 33 HOH HOH . F 4 HOH A 42 842 34 HOH HOH . F 4 HOH A 43 843 37 HOH HOH . F 4 HOH A 44 844 39 HOH HOH . F 4 HOH A 45 845 41 HOH HOH . F 4 HOH A 46 846 42 HOH HOH . F 4 HOH A 47 847 44 HOH HOH . F 4 HOH A 48 848 45 HOH HOH . F 4 HOH A 49 849 46 HOH HOH . F 4 HOH A 50 850 47 HOH HOH . F 4 HOH A 51 851 49 HOH HOH . F 4 HOH A 52 852 50 HOH HOH . F 4 HOH A 53 853 51 HOH HOH . F 4 HOH A 54 854 52 HOH HOH . F 4 HOH A 55 855 54 HOH HOH . F 4 HOH A 56 856 55 HOH HOH . F 4 HOH A 57 857 57 HOH HOH . F 4 HOH A 58 858 58 HOH HOH . F 4 HOH A 59 859 59 HOH HOH . F 4 HOH A 60 860 62 HOH HOH . F 4 HOH A 61 861 63 HOH HOH . F 4 HOH A 62 862 64 HOH HOH . F 4 HOH A 63 863 65 HOH HOH . F 4 HOH A 64 864 66 HOH HOH . F 4 HOH A 65 865 67 HOH HOH . F 4 HOH A 66 866 68 HOH HOH . F 4 HOH A 67 867 1002 HOH HOH . F 4 HOH A 68 868 1006 HOH HOH . F 4 HOH A 69 869 1008 HOH HOH . F 4 HOH A 70 870 1009 HOH HOH . F 4 HOH A 71 871 1010 HOH HOH . F 4 HOH A 72 872 1011 HOH HOH . F 4 HOH A 73 873 1012 HOH HOH . F 4 HOH A 74 874 1017 HOH HOH . F 4 HOH A 75 875 1020 HOH HOH . F 4 HOH A 76 876 1021 HOH HOH . F 4 HOH A 77 877 1024 HOH HOH . F 4 HOH A 78 878 1025 HOH HOH . F 4 HOH A 79 879 1028 HOH HOH . F 4 HOH A 80 880 1035 HOH HOH . F 4 HOH A 81 881 1040 HOH HOH . F 4 HOH A 82 882 1041 HOH HOH . F 4 HOH A 83 883 1045 HOH HOH . F 4 HOH A 84 884 1047 HOH HOH . F 4 HOH A 85 885 1049 HOH HOH . F 4 HOH A 86 886 1051 HOH HOH . F 4 HOH A 87 887 1052 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 . A . B 2 9.235 11.48 85.598 1 36.66 ? PB GDP 701 A 1 HETATM 2 O O1B GDP . A . B 2 7.829 11.3 85.065 1 40.09 ? O1B GDP 701 A 1 HETATM 3 O O2B GDP . A . B 2 10.047 10.211 85.573 1 36.54 ? O2B GDP 701 A 1 HETATM 4 O O3B GDP . A . B 2 9.937 12.718 85.115 1 40.14 ? O3B GDP 701 A 1 HETATM 5 O O3A GDP . A . B 2 8.913 11.84 87.129 1 39.47 ? O3A GDP 701 A 1 HETATM 6 P PA GDP . A . B 2 9.645 11.267 88.453 1 37.25 ? PA GDP 701 A 1 HETATM 7 O O1A GDP . A . B 2 11.06 11.785 88.419 1 40.71 ? O1A GDP 701 A 1 HETATM 8 O O2A GDP . A . B 2 9.399 9.798 88.687 1 35.3 ? O2A GDP 701 A 1 HETATM 9 O O5' GDP . A . B 2 8.739 12.098 89.496 1 36.49 ? O5' GDP 701 A 1 HETATM 10 C C5' GDP . A . B 2 8.643 13.526 89.482 1 36.14 ? C5' GDP 701 A 1 HETATM 11 C C4' GDP . A . B 2 8.684 14.006 90.932 1 38.29 ? C4' GDP 701 A 1 HETATM 12 O O4' GDP . A . B 2 7.452 13.702 91.6 1 37.72 ? O4' GDP 701 A 1 HETATM 13 C C3' GDP . A . B 2 9.799 13.344 91.739 1 37.62 ? C3' GDP 701 A 1 HETATM 14 O O3' GDP . A . B 2 10.459 14.398 92.427 1 37.67 ? O3' GDP 701 A 1 HETATM 15 C C2' GDP . A . B 2 9.115 12.42 92.733 1 38.93 ? C2' GDP 701 A 1 HETATM 16 O O2' GDP . A . B 2 9.727 12.441 94.04 1 39.83 ? O2' GDP 701 A 1 HETATM 17 C C1' GDP . A . B 2 7.708 12.996 92.81 1 38.73 ? C1' GDP 701 A 1 HETATM 18 N N9 GDP . A . B 2 6.665 11.97 93.019 1 39.86 ? N9 GDP 701 A 1 HETATM 19 C C8 GDP . A . B 2 6.402 10.89 92.247 1 40.63 ? C8 GDP 701 A 1 HETATM 20 N N7 GDP . A . B 2 5.358 10.174 92.75 1 39.29 ? N7 GDP 701 A 1 HETATM 21 C C5 GDP . A . B 2 4.941 10.812 93.869 1 40.02 ? C5 GDP 701 A 1 HETATM 22 C C6 GDP . A . B 2 3.885 10.606 94.896 1 39.22 ? C6 GDP 701 A 1 HETATM 23 O O6 GDP . A . B 2 3.105 9.627 94.824 1 38.12 ? O6 GDP 701 A 1 HETATM 24 N N1 GDP . A . B 2 3.79 11.502 95.897 1 39.52 ? N1 GDP 701 A 1 HETATM 25 C C2 GDP . A . B 2 4.614 12.566 96.002 1 39.49 ? C2 GDP 701 A 1 HETATM 26 N N2 GDP . A . B 2 4.45 13.413 97.043 1 40.51 ? N2 GDP 701 A 1 HETATM 27 N N3 GDP . A . B 2 5.599 12.825 95.098 1 39.25 ? N3 GDP 701 A 1 HETATM 28 C C4 GDP . A . B 2 5.802 11.997 94.037 1 39.56 ? C4 GDP 701 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 28 #