data_8FW5 # _model_server_result.job_id 7x5bP1uM0UdUprExJ77fbQ _model_server_result.datetime_utc '2024-11-22 20:47:59' _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 8fw5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":501}' # _entry.id 8FW5 # _exptl.entry_id 8FW5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 10 _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 8FW5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FW5 _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 nonameric _pdbx_struct_assembly.oligomeric_count 9 _pdbx_struct_assembly.details author_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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 10 J N N ? 10 M 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 D OG SER 16 D SER 16 1_555 L MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc2 D OG1 THR 37 D THR 37 1_555 L MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc3 J O1B GDP . D GDP 501 1_555 L MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? metalc ? metalc4 J O3B GDP . D GDP 501 1_555 L MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? # _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 8FW5 _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 J 10 GDP D 1 501 501 GDP GDP . K 11 AF3 D 1 502 502 AF3 AF3 . L 12 MG D 1 503 503 MG MG . M 10 GDP E 1 501 501 GDP 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 . . . M 10 130.248 166.002 185.509 1 136.69 ? PB GDP 501 E 1 HETATM 2 O O1B GDP . . . M 10 130.534 167.478 185.372 1 136.69 ? O1B GDP 501 E 1 HETATM 3 O O2B GDP . . . M 10 128.806 165.803 185.909 1 136.69 ? O2B GDP 501 E 1 HETATM 4 O O3B GDP . . . M 10 131.15 165.414 186.567 1 136.69 ? O3B GDP 501 E 1 HETATM 5 O O3A GDP . . . M 10 130.522 165.272 184.1 1 136.69 ? O3A GDP 501 E 1 HETATM 6 P PA GDP . . . M 10 132.02 165.175 183.522 1 136.69 ? PA GDP 501 E 1 HETATM 7 O O1A GDP . . . M 10 132.693 166.524 183.559 1 136.69 ? O1A GDP 501 E 1 HETATM 8 O O2A GDP . . . M 10 132.821 164.172 184.312 1 136.69 ? O2A GDP 501 E 1 HETATM 9 O O5' GDP . . . M 10 131.83 164.662 182.008 1 136.69 ? O5' GDP 501 E 1 HETATM 10 C C5' GDP . . . M 10 132.941 164.689 181.116 1 136.69 ? C5' GDP 501 E 1 HETATM 11 C C4' GDP . . . M 10 132.66 163.854 179.876 1 136.69 ? C4' GDP 501 E 1 HETATM 12 O O4' GDP . . . M 10 133.829 163.842 179.055 1 136.69 ? O4' GDP 501 E 1 HETATM 13 C C3' GDP . . . M 10 132.343 162.412 180.232 1 136.69 ? C3' GDP 501 E 1 HETATM 14 O O3' GDP . . . M 10 130.965 162.133 179.971 1 136.69 ? O3' GDP 501 E 1 HETATM 15 C C2' GDP . . . M 10 133.229 161.56 179.344 1 136.69 ? C2' GDP 501 E 1 HETATM 16 O O2' GDP . . . M 10 132.43 160.81 178.424 1 136.69 ? O2' GDP 501 E 1 HETATM 17 C C1' GDP . . . M 10 134.125 162.525 178.587 1 136.69 ? C1' GDP 501 E 1 HETATM 18 N N9 GDP . . . M 10 135.548 162.21 178.868 1 136.69 ? N9 GDP 501 E 1 HETATM 19 C C8 GDP . . . M 10 136.217 162.561 179.982 1 136.69 ? C8 GDP 501 E 1 HETATM 20 N N7 GDP . . . M 10 137.502 162.129 179.939 1 136.69 ? N7 GDP 501 E 1 HETATM 21 C C5 GDP . . . M 10 137.672 161.485 178.772 1 136.69 ? C5 GDP 501 E 1 HETATM 22 C C6 GDP . . . M 10 138.788 160.786 178.093 1 136.69 ? C6 GDP 501 E 1 HETATM 23 O O6 GDP . . . M 10 139.913 160.698 178.63 1 136.69 ? O6 GDP 501 E 1 HETATM 24 N N1 GDP . . . M 10 138.554 160.251 176.889 1 136.69 ? N1 GDP 501 E 1 HETATM 25 C C2 GDP . . . M 10 137.351 160.331 176.288 1 136.69 ? C2 GDP 501 E 1 HETATM 26 N N2 GDP . . . M 10 137.198 159.763 175.068 1 136.69 ? N2 GDP 501 E 1 HETATM 27 N N3 GDP . . . M 10 136.285 160.956 176.851 1 136.69 ? N3 GDP 501 E 1 HETATM 28 C C4 GDP . . . M 10 136.383 161.541 178.069 1 136.69 ? C4 GDP 501 E 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #