data_6VP6 # _model_server_result.job_id 3fce20LH8-agl1sEcIMObQ _model_server_result.datetime_utc '2024-11-24 20:21:51' _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 6vp6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2601}' # _entry.id 6VP6 # _exptl.entry_id 6VP6 _exptl.method 'ELECTRON MICROSCOPY' # _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 6VP6 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VP6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 _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 ? _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 2 _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 covale ? covale1 A C ASN 16 A ASN 1342 1_555 A N TPO 17 A TPO 1343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C TPO 17 A TPO 1343 1_555 A N GLY 18 A GLY 1344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OG1 THR 22 A THR 1348 1_555 E MG MG . A MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc2 D O1B GDP . A GDP 2601 1_555 E MG MG . A MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? # _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 6VP6 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 2 GDP A 1 2601 1327 GDP GDP . E 3 MG A 1 2602 1327 MG GDP . # 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 2 235.693 163.019 153.452 1 74.01 ? PB GDP 2601 A 1 HETATM 2 O O1B GDP . . . D 2 234.752 161.852 153.556 1 76.67 ? O1B GDP 2601 A 1 HETATM 3 O O2B GDP . . . D 2 237.108 162.656 153.805 1 78.63 ? O2B GDP 2601 A 1 HETATM 4 O O3B GDP . . . D 2 235.247 164.1 154.344 1 76.28 ? O3B GDP 2601 A 1 HETATM 5 O O3A GDP . . . D 2 235.73 163.533 151.958 1 81.12 ? O3A GDP 2601 A 1 HETATM 6 P PA GDP . . . D 2 235.816 162.616 150.723 1 80.43 ? PA GDP 2601 A 1 HETATM 7 O O1A GDP . . . D 2 234.545 162.838 150.029 1 94.19 ? O1A GDP 2601 A 1 HETATM 8 O O2A GDP . . . D 2 236.39 161.247 150.935 1 83.8 ? O2A GDP 2601 A 1 HETATM 9 O O5' GDP . . . D 2 237.009 163.302 149.945 1 88.87 ? O5' GDP 2601 A 1 HETATM 10 C C5' GDP . . . D 2 237.458 162.889 148.659 1 94.56 ? C5' GDP 2601 A 1 HETATM 11 C C4' GDP . . . D 2 238.419 163.93 148.107 1 0.36 ? C4' GDP 2601 A 1 HETATM 12 O O4' GDP . . . D 2 239.769 163.74 148.53 1 4.11 ? O4' GDP 2601 A 1 HETATM 13 C C3' GDP . . . D 2 238.52 163.865 146.585 1 6.02 ? C3' GDP 2601 A 1 HETATM 14 O O3' GDP . . . D 2 238.521 165.188 146.103 1 9.81 ? O3' GDP 2601 A 1 HETATM 15 C C2' GDP . . . D 2 239.863 163.258 146.317 1 9.27 ? C2' GDP 2601 A 1 HETATM 16 O O2' GDP . . . D 2 240.453 163.564 145.07 1 13.81 ? O2' GDP 2601 A 1 HETATM 17 C C1' GDP . . . D 2 240.684 163.828 147.458 1 8.65 ? C1' GDP 2601 A 1 HETATM 18 N N9 GDP . . . D 2 241.729 162.868 147.801 1 0 ? N9 GDP 2601 A 1 HETATM 19 C C8 GDP . . . D 2 241.296 161.645 148.219 1 10.51 ? C8 GDP 2601 A 1 HETATM 20 N N7 GDP . . . D 2 242.218 160.705 147.977 1 14.06 ? N7 GDP 2601 A 1 HETATM 21 C C5 GDP . . . D 2 243.259 161.324 147.396 1 16.72 ? C5 GDP 2601 A 1 HETATM 22 C C6 GDP . . . D 2 244.586 160.925 146.899 1 18.76 ? C6 GDP 2601 A 1 HETATM 23 O O6 GDP . . . D 2 244.965 159.727 146.963 1 18.55 ? O6 GDP 2601 A 1 HETATM 24 N N1 GDP . . . D 2 245.365 161.893 146.374 1 17.47 ? N1 GDP 2601 A 1 HETATM 25 C C2 GDP . . . D 2 244.977 163.199 146.273 1 16.23 ? C2 GDP 2601 A 1 HETATM 26 N N2 GDP . . . D 2 245.829 164.131 145.737 1 22.11 ? N2 GDP 2601 A 1 HETATM 27 N N3 GDP . . . D 2 243.799 163.645 146.743 1 11.82 ? N3 GDP 2601 A 1 HETATM 28 C C4 GDP . . . D 2 242.924 162.76 147.282 1 11.95 ? C4 GDP 2601 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 370 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #