data_3HND # _model_server_result.job_id acvx0JwvMU2cBMicz5twlQ _model_server_result.datetime_utc '2024-11-07 18:36:22' _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 3hnd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":803}' # _entry.id 3HND # _exptl.entry_id 3HND _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 90 _cell.entry_id 3HND _cell.length_a 73.159 _cell.length_b 115.834 _cell.length_c 221.305 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HND _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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,G,H,I,J,K,L,M,N _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 ? 4 E N N ? 4 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 C MG MG . A MG 801 1_555 D O2A TTP . A TTP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc2 C MG MG . A MG 801 1_555 D O3B TTP . A TTP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc3 C MG MG . A MG 801 1_555 D O3G TTP . A TTP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc4 I MG MG . B MG 801 1_555 J O2A TTP . B TTP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc5 I MG MG . B MG 801 1_555 J O3B TTP . B TTP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc6 I MG MG . B MG 801 1_555 J O3G TTP . B TTP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? # _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 3HND _atom_sites.fract_transf_matrix[1][1] 0.013669 _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] 0.008633 _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] 0.004519 _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 2 MG A 1 801 801 MG MG . D 3 TTP A 1 802 802 TTP TTP . E 4 GDP A 1 803 803 GDP GDP . F 5 SO4 A 1 805 805 SO4 SO4 . G 5 SO4 A 1 806 806 SO4 SO4 . H 5 SO4 A 1 807 807 SO4 SO4 . I 2 MG B 1 801 801 MG MG . J 3 TTP B 1 802 802 TTP TTP . K 4 GDP B 1 803 803 GDP GDP . L 5 SO4 B 1 804 804 SO4 SO4 . M 6 HOH A 1 901 901 HOH HOH . M 6 HOH A 2 902 902 HOH HOH . M 6 HOH A 3 906 906 HOH HOH . M 6 HOH A 4 910 910 HOH HOH . M 6 HOH A 5 912 912 HOH HOH . M 6 HOH A 6 913 913 HOH HOH . M 6 HOH A 7 915 915 HOH HOH . M 6 HOH A 8 916 916 HOH HOH . M 6 HOH A 9 917 917 HOH HOH . M 6 HOH A 10 918 918 HOH HOH . M 6 HOH A 11 920 920 HOH HOH . M 6 HOH A 12 921 921 HOH HOH . M 6 HOH A 13 938 938 HOH HOH . M 6 HOH A 14 939 939 HOH HOH . M 6 HOH A 15 940 940 HOH HOH . M 6 HOH A 16 941 941 HOH HOH . M 6 HOH A 17 942 942 HOH HOH . M 6 HOH A 18 943 943 HOH HOH . N 6 HOH B 1 909 909 HOH HOH . N 6 HOH B 2 922 922 HOH HOH . N 6 HOH B 3 926 926 HOH HOH . N 6 HOH B 4 928 928 HOH HOH . N 6 HOH B 5 930 930 HOH HOH . N 6 HOH B 6 931 931 HOH HOH . N 6 HOH B 7 932 932 HOH HOH . N 6 HOH B 8 933 933 HOH HOH . N 6 HOH B 9 934 934 HOH HOH . N 6 HOH B 10 935 935 HOH HOH . N 6 HOH B 11 947 947 HOH HOH . N 6 HOH B 12 948 948 HOH HOH . N 6 HOH B 13 949 949 HOH HOH . N 6 HOH B 14 950 950 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 . . . K 4 -23.825 20.918 27.966 1 115.85 ? PB GDP 803 B 1 HETATM 2 O O1B GDP . . . K 4 -25.111 21.705 27.777 1 114.8 ? O1B GDP 803 B 1 HETATM 3 O O2B GDP . . . K 4 -22.667 21.875 28.167 1 115.1 ? O2B GDP 803 B 1 HETATM 4 O O3B GDP . . . K 4 -23.971 19.994 29.151 1 114.4 ? O3B GDP 803 B 1 HETATM 5 O O3A GDP . . . K 4 -23.451 19.979 26.69 1 118.35 ? O3A GDP 803 B 1 HETATM 6 P PA GDP . . . K 4 -24.381 19.653 25.391 1 119.21 ? PA GDP 803 B 1 HETATM 7 O O1A GDP . . . K 4 -25.027 18.277 25.457 1 119.39 ? O1A GDP 803 B 1 HETATM 8 O O2A GDP . . . K 4 -25.484 20.675 25.304 1 119.09 ? O2A GDP 803 B 1 HETATM 9 O O5' GDP . . . K 4 -23.313 19.796 24.185 1 117.89 ? O5' GDP 803 B 1 HETATM 10 C C5' GDP . . . K 4 -23.183 18.822 23.15 1 117.07 ? C5' GDP 803 B 1 HETATM 11 C C4' GDP . . . K 4 -21.772 18.257 23.134 1 116.22 ? C4' GDP 803 B 1 HETATM 12 O O4' GDP . . . K 4 -21.451 17.668 24.4 1 116.46 ? O4' GDP 803 B 1 HETATM 13 C C3' GDP . . . K 4 -21.675 17.147 22.106 1 115.21 ? C3' GDP 803 B 1 HETATM 14 O O3' GDP . . . K 4 -21.147 17.648 20.885 1 114.38 ? O3' GDP 803 B 1 HETATM 15 C C2' GDP . . . K 4 -20.873 16.015 22.757 1 115.38 ? C2' GDP 803 B 1 HETATM 16 O O2' GDP . . . K 4 -19.495 15.908 22.34 1 113.61 ? O2' GDP 803 B 1 HETATM 17 C C1' GDP . . . K 4 -21.009 16.305 24.253 1 115.4 ? C1' GDP 803 B 1 HETATM 18 N N9 GDP . . . K 4 -22.053 15.418 24.832 1 115.1 ? N9 GDP 803 B 1 HETATM 19 C C8 GDP . . . K 4 -23.39 15.592 24.701 1 115.17 ? C8 GDP 803 B 1 HETATM 20 N N7 GDP . . . K 4 -24.101 14.624 25.335 1 115.18 ? N7 GDP 803 B 1 HETATM 21 C C5 GDP . . . K 4 -23.198 13.8 25.889 1 114.98 ? C5 GDP 803 B 1 HETATM 22 C C6 GDP . . . K 4 -23.27 12.57 26.701 1 115.18 ? C6 GDP 803 B 1 HETATM 23 O O6 GDP . . . K 4 -24.388 12.105 27.004 1 115.44 ? O6 GDP 803 B 1 HETATM 24 N N1 GDP . . . K 4 -22.119 11.994 27.097 1 115.02 ? N1 GDP 803 B 1 HETATM 25 C C2 GDP . . . K 4 -20.913 12.503 26.776 1 114.83 ? C2 GDP 803 B 1 HETATM 26 N N2 GDP . . . K 4 -19.809 11.86 27.221 1 114.75 ? N2 GDP 803 B 1 HETATM 27 N N3 GDP . . . K 4 -20.768 13.634 26.023 1 115.05 ? N3 GDP 803 B 1 HETATM 28 C C4 GDP . . . K 4 -21.853 14.316 25.562 1 114.89 ? C4 GDP 803 B 1 # _model_server_stats.io_time_ms 100 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #