data_3LVQ # _model_server_result.job_id nYxBlXtVfvhtxZzvillnsg _model_server_result.datetime_utc '2024-11-26 01:16:56' _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 3lvq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":682}' # _entry.id 3LVQ # _exptl.entry_id 3LVQ _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 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 120 _cell.entry_id 3LVQ _cell.length_a 146.29 _cell.length_b 146.29 _cell.length_c 49.52 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LVQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 29 E CYS 444 1_555 A SG CYS 49 E CYS 464 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? metalc ? metalc1 A OG1 THR 336 E THR 27 1_555 C MG MG . E MG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc2 A OG1 THR 353 E THR 44 1_555 C MG MG . E MG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc3 G O HOH . E HOH 220 1_555 C MG MG . E MG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc4 G O HOH . E HOH 230 1_555 C MG MG . E MG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc5 A SG CYS 26 E CYS 441 1_555 B ZN ZN . E ZN 680 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc6 A SG CYS 46 E CYS 461 1_555 B ZN ZN . E ZN 680 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc7 A SG CYS 49 E CYS 464 1_555 B ZN ZN . E ZN 680 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc8 C MG MG . E MG 681 1_555 D O2B GDP . E GDP 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc9 C MG MG . E MG 681 1_555 D O3B GDP . E GDP 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? # _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 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 3LVQ _atom_sites.fract_transf_matrix[1][1] 0.006836 _atom_sites.fract_transf_matrix[1][2] 0.003947 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007893 _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] 0.020194 _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 ZN E 1 680 600 ZN ZN . C 3 MG E 1 681 168 MG MG . D 4 GDP E 1 682 167 GDP GDP . E 5 AF3 E 1 683 169 AF3 AF3 . F 3 MG E 1 684 170 MG MG . G 6 HOH E 1 211 211 HOH HOH . G 6 HOH E 2 212 212 HOH HOH . G 6 HOH E 3 220 220 HOH HOH . G 6 HOH E 4 230 230 HOH HOH . G 6 HOH E 5 231 231 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 . . . D 4 -28.41 53.948 -1.422 1 58.04 ? PB GDP 682 E 1 HETATM 2 O O1B GDP . . . D 4 -28.204 53.428 -2.84 1 62.28 ? O1B GDP 682 E 1 HETATM 3 O O2B GDP . . . D 4 -27.865 55.298 -1.334 1 48.73 ? O2B GDP 682 E 1 HETATM 4 O O3B GDP . . . D 4 -29.894 54.085 -1.274 1 57.43 ? O3B GDP 682 E 1 HETATM 5 O O3A GDP . . . D 4 -27.763 53.037 -0.283 1 54.7 ? O3A GDP 682 E 1 HETATM 6 P PA GDP . . . D 4 -27.706 53.708 1.19 1 55.19 ? PA GDP 682 E 1 HETATM 7 O O1A GDP . . . D 4 -26.748 54.898 1.147 1 53.74 ? O1A GDP 682 E 1 HETATM 8 O O2A GDP . . . D 4 -29.096 54.148 1.609 1 61.67 ? O2A GDP 682 E 1 HETATM 9 O O5' GDP . . . D 4 -27.293 52.378 2.122 1 51.27 ? O5' GDP 682 E 1 HETATM 10 C C5' GDP . . . D 4 -28.138 51.137 1.967 1 54.87 ? C5' GDP 682 E 1 HETATM 11 C C4' GDP . . . D 4 -27.899 50.29 3.183 1 60 ? C4' GDP 682 E 1 HETATM 12 O O4' GDP . . . D 4 -26.572 49.7 2.924 1 60.28 ? O4' GDP 682 E 1 HETATM 13 C C3' GDP . . . D 4 -27.686 51.302 4.339 1 64.03 ? C3' GDP 682 E 1 HETATM 14 O O3' GDP . . . D 4 -28.486 50.926 5.481 1 61.78 ? O3' GDP 682 E 1 HETATM 15 C C2' GDP . . . D 4 -26.21 51.261 4.709 1 63.86 ? C2' GDP 682 E 1 HETATM 16 O O2' GDP . . . D 4 -26.053 51.21 6.143 1 64.69 ? O2' GDP 682 E 1 HETATM 17 C C1' GDP . . . D 4 -25.721 49.964 4.049 1 62.87 ? C1' GDP 682 E 1 HETATM 18 N N9 GDP . . . D 4 -24.321 50.076 3.572 1 67.95 ? N9 GDP 682 E 1 HETATM 19 C C8 GDP . . . D 4 -23.828 51.032 2.758 1 68.61 ? C8 GDP 682 E 1 HETATM 20 N N7 GDP . . . D 4 -22.509 50.814 2.531 1 70.87 ? N7 GDP 682 E 1 HETATM 21 C C5 GDP . . . D 4 -22.159 49.708 3.208 1 70.6 ? C5 GDP 682 E 1 HETATM 22 C C6 GDP . . . D 4 -20.916 48.929 3.398 1 69.64 ? C6 GDP 682 E 1 HETATM 23 O O6 GDP . . . D 4 -19.858 49.291 2.84 1 70.23 ? O6 GDP 682 E 1 HETATM 24 N N1 GDP . . . D 4 -20.964 47.824 4.171 1 64.69 ? N1 GDP 682 E 1 HETATM 25 C C2 GDP . . . D 4 -22.103 47.409 4.782 1 65.02 ? C2 GDP 682 E 1 HETATM 26 N N2 GDP . . . D 4 -22.042 46.283 5.546 1 62.42 ? N2 GDP 682 E 1 HETATM 27 N N3 GDP . . . D 4 -23.288 48.086 4.651 1 70.29 ? N3 GDP 682 E 1 HETATM 28 C C4 GDP . . . D 4 -23.36 49.214 3.895 1 69.7 ? C4 GDP 682 E 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #