data_8EFF # _model_server_result.job_id v9ETHM2C9gy7AQjYuiAuWA _model_server_result.datetime_utc '2024-11-05 12:48:05' _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 8eff # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":1001}' # _entry.id 8EFF # _exptl.entry_id 8EFF _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 4 _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 8EFF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EFF _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,N,O,P,Q,R,S,T _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 ? 2 E N N ? 2 I N N ? 2 M N N ? 2 Q 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 disulf ? disulf1 A SG CYS 662 A CYS 856 1_555 A SG CYS 680 A CYS 874 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 662 B CYS 856 1_555 B SG CYS 680 B CYS 874 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 C SG CYS 662 C CYS 856 1_555 C SG CYS 680 C CYS 874 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 D SG CYS 662 D CYS 856 1_555 D SG CYS 680 D CYS 874 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 E O3B GDP . A GDP 1001 1_555 G MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc2 E O2B GDP . A GDP 1001 1_555 H K K . A K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc3 B O GLN 103 B GLN 297 1_555 L K K . B K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc4 B O GLU 126 B GLU 320 1_555 L K K . B K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.077 ? metalc ? metalc5 B OG1 THR 129 B THR 323 1_555 K MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc6 I O2B GDP . B GDP 1001 1_555 K MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc7 I O3B GDP . B GDP 1001 1_555 K MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc8 I O1B GDP . B GDP 1001 1_555 L K K . B K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc9 I O1A GDP . B GDP 1001 1_555 L K K . B K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc10 M O3B GDP . C GDP 1001 1_555 O MG MG . C MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc11 M O2B GDP . C GDP 1001 1_555 P K K . C K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc12 D O GLN 103 D GLN 297 1_555 T K K . D K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc13 D O GLU 126 D GLU 320 1_555 T K K . D K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.078 ? metalc ? metalc14 D OG1 THR 129 D THR 323 1_555 S MG MG . D MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc15 Q O2B GDP . D GDP 1001 1_555 S MG MG . D MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc16 Q O3B GDP . D GDP 1001 1_555 S MG MG . D MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc17 Q O1B GDP . D GDP 1001 1_555 T K K . D K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc18 Q O1A GDP . D GDP 1001 1_555 T K K . D K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 8EFF _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 E 2 GDP A 1 1001 961 GDP GDP . F 3 ALF A 1 1002 962 ALF ALF . G 4 MG A 1 1003 963 MG MG . H 5 K A 1 1004 964 K K . I 2 GDP B 1 1001 961 GDP GDP . J 3 ALF B 1 1002 962 ALF ALF . K 4 MG B 1 1003 963 MG MG . L 5 K B 1 1004 964 K K . M 2 GDP C 1 1001 961 GDP GDP . N 3 ALF C 1 1002 962 ALF ALF . O 4 MG C 1 1003 963 MG MG . P 5 K C 1 1004 964 K K . Q 2 GDP D 1 1001 961 GDP GDP . R 3 ALF D 1 1002 962 ALF ALF . S 4 MG D 1 1003 963 MG MG . T 5 K D 1 1004 964 K K . # 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 2 423.37 176.583 369.64 1 7.82 ? PB GDP 1001 C 1 HETATM 2 O O1B GDP . . . M 2 424.397 176.887 368.575 1 7.08 ? O1B GDP 1001 C 1 HETATM 3 O O2B GDP . . . M 2 423.669 177.404 370.873 1 6.26 ? O2B GDP 1001 C 1 HETATM 4 O O3B GDP . . . M 2 421.984 176.912 369.137 1 9.73 ? O3B GDP 1001 C 1 HETATM 5 O O3A GDP . . . M 2 423.414 175.023 370.022 1 9.1 ? O3A GDP 1001 C 1 HETATM 6 P PA GDP . . . M 2 423.619 173.911 368.877 1 8.31 ? PA GDP 1001 C 1 HETATM 7 O O1A GDP . . . M 2 423.823 174.558 367.529 1 6.82 ? O1A GDP 1001 C 1 HETATM 8 O O2A GDP . . . M 2 422.478 172.921 368.86 1 8.75 ? O2A GDP 1001 C 1 HETATM 9 O O5' GDP . . . M 2 424.962 173.21 369.39 1 7.79 ? O5' GDP 1001 C 1 HETATM 10 C C5' GDP . . . M 2 426.191 173.882 369.127 1 8.27 ? C5' GDP 1001 C 1 HETATM 11 C C4' GDP . . . M 2 427.185 173.453 370.183 1 9.29 ? C4' GDP 1001 C 1 HETATM 12 O O4' GDP . . . M 2 426.478 172.968 371.329 1 9.49 ? O4' GDP 1001 C 1 HETATM 13 C C3' GDP . . . M 2 428.055 172.338 369.633 1 9.95 ? C3' GDP 1001 C 1 HETATM 14 O O3' GDP . . . M 2 429.436 172.646 369.871 1 11 ? O3' GDP 1001 C 1 HETATM 15 C C2' GDP . . . M 2 427.583 171.111 370.397 1 9.71 ? C2' GDP 1001 C 1 HETATM 16 O O2' GDP . . . M 2 428.651 170.216 370.717 1 10.53 ? O2' GDP 1001 C 1 HETATM 17 C C1' GDP . . . M 2 426.946 171.663 371.668 1 8.59 ? C1' GDP 1001 C 1 HETATM 18 N N9 GDP . . . M 2 425.84 170.785 372.133 1 7.86 ? N9 GDP 1001 C 1 HETATM 19 C C8 GDP . . . M 2 424.682 170.552 371.481 1 5.52 ? C8 GDP 1001 C 1 HETATM 20 N N7 GDP . . . M 2 423.901 169.7 372.191 1 4.36 ? N7 GDP 1001 C 1 HETATM 21 C C5 GDP . . . M 2 424.555 169.381 373.321 1 6.2 ? C5 GDP 1001 C 1 HETATM 22 C C6 GDP . . . M 2 424.294 168.532 374.504 1 7.42 ? C6 GDP 1001 C 1 HETATM 23 O O6 GDP . . . M 2 423.223 167.894 374.601 1 8.6 ? O6 GDP 1001 C 1 HETATM 24 N N1 GDP . . . M 2 425.233 168.469 375.46 1 7.2 ? N1 GDP 1001 C 1 HETATM 25 C C2 GDP . . . M 2 426.387 169.152 375.36 1 7.2 ? C2 GDP 1001 C 1 HETATM 26 N N2 GDP . . . M 2 427.299 169.052 376.354 1 8.04 ? N2 GDP 1001 C 1 HETATM 27 N N3 GDP . . . M 2 426.695 169.951 374.303 1 6.58 ? N3 GDP 1001 C 1 HETATM 28 C C4 GDP . . . M 2 425.834 170.101 373.273 1 6.76 ? C4 GDP 1001 C 1 HETATM 29 H H4' GDP . . . M 2 427.739 174.21 370.432 1 9.29 ? H4' GDP 1001 C 1 HETATM 30 H H3' GDP . . . M 2 427.982 172.206 368.675 1 9.95 ? H3' GDP 1001 C 1 HETATM 31 H HO3' GDP . . . M 2 429.796 172.014 370.291 1 11 ? HO3' GDP 1001 C 1 HETATM 32 H H2' GDP . . . M 2 426.966 170.587 369.862 1 9.71 ? H2' GDP 1001 C 1 HETATM 33 H HO2' GDP . . . M 2 429.037 169.976 370.011 1 10.53 ? HO2' GDP 1001 C 1 HETATM 34 H H1' GDP . . . M 2 427.579 171.7 372.402 1 8.59 ? H1' GDP 1001 C 1 HETATM 35 H H8 GDP . . . M 2 424.442 170.939 370.625 1 5.52 ? H8 GDP 1001 C 1 HETATM 36 H HN1 GDP . . . M 2 425.094 167.98 376.154 1 7.2 ? HN1 GDP 1001 C 1 HETATM 37 H HN21 GDP . . . M 2 427.137 168.557 377.038 1 8.04 ? HN21 GDP 1001 C 1 HETATM 38 H HN22 GDP . . . M 2 428.041 169.484 376.302 1 8.04 ? HN22 GDP 1001 C 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #