data_1N21 # _model_server_result.job_id pq5yrqFArmPoUxaDF2r-OA _model_server_result.datetime_utc '2024-12-19 00:25:54' _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 1n21 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":900}' # _entry.id 1N21 # _exptl.entry_id 1N21 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.189 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[METHYL-(4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-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 1N21 _cell.length_a 198.38 _cell.length_b 198.38 _cell.length_c 122.84 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1N21 _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 99.19 171.80212 61.42 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _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 metalc ? metalc1 A OD1 ASP 302 A ASP 351 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc2 A OD2 ASP 302 A ASP 351 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc3 A OD1 ASP 302 A ASP 351 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.11 ? metalc ? metalc4 A OD2 ASP 306 A ASP 355 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc5 A OD2 ASP 306 A ASP 355 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc6 A OD1 ASP 447 A ASP 496 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc7 A OG1 THR 451 A THR 500 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc8 A OE2 GLU 455 A GLU 504 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc9 B MG MG . A MG 701 1_555 E O5 3AG . A 3AG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc10 B MG MG . A MG 701 1_555 F O HOH . A HOH 921 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc11 B MG MG . A MG 701 1_555 F O HOH . A HOH 922 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc12 C MG MG . A MG 702 1_555 E O4 3AG . A 3AG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.789 ? metalc ? metalc13 C MG MG . A MG 702 1_555 E O6 3AG . A 3AG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc14 C MG MG . A MG 702 1_555 F O HOH . A HOH 919 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc15 D MG MG . A MG 703 1_555 E O1 3AG . A 3AG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc16 D MG MG . A MG 703 1_555 E O3 3AG . A 3AG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.026 ? metalc ? metalc17 D MG MG . A MG 703 1_555 E O5 3AG . A 3AG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc18 D MG MG . A MG 703 1_555 F O HOH . A HOH 920 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc19 D MG MG . A MG 703 1_555 F O HOH . A HOH 921 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc20 D MG MG . A MG 703 1_555 F O HOH . A HOH 923 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? # _chem_comp.formula 'C9 H18 N O7 P2 -3' _chem_comp.formula_weight 314.189 _chem_comp.id 3AG _chem_comp.mon_nstd_flag . _chem_comp.name 2-[METHYL-(4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '3-AZA-2,3-DIHYDROGERANYL DIPHOSPHATE' # 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 C1 C2 3AG sing 1 n n C1 HC11 3AG sing 2 n n C1 HC12 3AG sing 3 n n C1 HC13 3AG sing 4 n n C2 C3 3AG sing 5 n n C2 C4 3AG doub 6 n n C3 HC31 3AG sing 7 n n C3 HC32 3AG sing 8 n n C3 HC33 3AG sing 9 n n C4 C5 3AG sing 10 n n C4 HC4 3AG sing 11 n n O1 P1 3AG doub 12 n n C5 C6 3AG sing 13 n n C5 HC51 3AG sing 14 n n C5 HC52 3AG sing 15 n n C6 N1 3AG sing 16 n n C6 HC61 3AG sing 17 n n C6 HC62 3AG sing 18 n n N1 C7 3AG sing 19 n n N1 C9 3AG sing 20 n n C7 C8 3AG sing 21 n n C7 HC71 3AG sing 22 n n C7 HC72 3AG sing 23 n n C8 O2 3AG sing 24 n n C8 HC81 3AG sing 25 n n C8 HC82 3AG sing 26 n n C9 HC91 3AG sing 27 n n C9 HC92 3AG sing 28 n n C9 HC93 3AG sing 29 n n O2 P1 3AG sing 30 n n P1 O3 3AG sing 31 n n P1 O4 3AG sing 32 n n O3 P2 3AG sing 33 n n P2 O5 3AG doub 34 n n P2 O6 3AG sing 35 n n P2 O7 3AG sing 36 n n # _atom_sites.entry_id 1N21 _atom_sites.fract_transf_matrix[1][1] 0.005041 _atom_sites.fract_transf_matrix[1][2] 0.00291 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005821 _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] 0.008141 _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 MG A 1 701 701 MG MG . C 2 MG A 1 702 702 MG MG . D 2 MG A 1 703 703 MG MG . E 3 3AG A 1 900 900 3AG 3AG . F 4 HOH A 1 901 1 HOH WAT . F 4 HOH A 2 902 2 HOH WAT . F 4 HOH A 3 903 3 HOH WAT . F 4 HOH A 4 904 4 HOH WAT . F 4 HOH A 5 905 5 HOH WAT . F 4 HOH A 6 906 6 HOH WAT . F 4 HOH A 7 907 7 HOH WAT . F 4 HOH A 8 908 8 HOH WAT . F 4 HOH A 9 909 9 HOH WAT . F 4 HOH A 10 910 10 HOH WAT . F 4 HOH A 11 911 11 HOH WAT . F 4 HOH A 12 912 12 HOH WAT . F 4 HOH A 13 913 13 HOH WAT . F 4 HOH A 14 914 14 HOH WAT . F 4 HOH A 15 915 15 HOH WAT . F 4 HOH A 16 916 16 HOH WAT . F 4 HOH A 17 917 17 HOH WAT . F 4 HOH A 18 918 18 HOH WAT . F 4 HOH A 19 919 19 HOH WAT . F 4 HOH A 20 920 20 HOH WAT . F 4 HOH A 21 921 21 HOH WAT . F 4 HOH A 22 922 22 HOH WAT . F 4 HOH A 23 923 23 HOH WAT . F 4 HOH A 24 924 24 HOH WAT . F 4 HOH A 25 925 110 HOH WAT . F 4 HOH A 26 926 111 HOH WAT . # 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 C C1 3AG . . . E 3 68.291 76.641 51.445 1 22.53 ? C1 3AG 900 A 1 HETATM 2 C C2 3AG . . . E 3 68.635 76.043 52.786 1 27.69 ? C2 3AG 900 A 1 HETATM 3 C C3 3AG . . . E 3 67.546 75.193 53.375 1 26.53 ? C3 3AG 900 A 1 HETATM 4 C C4 3AG . . . E 3 69.799 76.224 53.442 1 25.35 ? C4 3AG 900 A 1 HETATM 5 O O1 3AG . . . E 3 70.945 84.247 56.024 1 16.34 ? O1 3AG 900 A 1 HETATM 6 C C5 3AG . . . E 3 70.974 77.044 52.982 1 26.54 ? C5 3AG 900 A 1 HETATM 7 C C6 3AG . . . E 3 71.129 78.332 53.802 1 31.02 ? C6 3AG 900 A 1 HETATM 8 N N1 3AG . . . E 3 69.896 79.044 54.161 1 33.98 ? N1 3AG 900 A 1 HETATM 9 C C7 3AG . . . E 3 69.995 79.594 55.533 1 33.96 ? C7 3AG 900 A 1 HETATM 10 C C8 3AG . . . E 3 71.299 80.336 55.947 1 27.5 ? C8 3AG 900 A 1 HETATM 11 C C9 3AG . . . E 3 69.594 80.103 53.189 1 33.26 ? C9 3AG 900 A 1 HETATM 12 O O2 3AG . . . E 3 71.245 81.7 55.549 1 31.2 ? O2 3AG 900 A 1 HETATM 13 P P1 3AG . . . E 3 70.423 82.771 56.409 1 20.76 ? P1 3AG 900 A 1 HETATM 14 O O3 3AG . . . E 3 68.88 82.592 55.984 1 28.25 ? O3 3AG 900 A 1 HETATM 15 O O4 3AG . . . E 3 70.628 82.467 57.967 1 28.72 ? O4 3AG 900 A 1 HETATM 16 P P2 3AG . . . E 3 67.744 83.372 56.801 1 24.65 ? P2 3AG 900 A 1 HETATM 17 O O5 3AG . . . E 3 67.431 84.763 56.077 1 19.61 ? O5 3AG 900 A 1 HETATM 18 O O6 3AG . . . E 3 68.22 83.635 58.308 1 25.22 ? O6 3AG 900 A 1 HETATM 19 O O7 3AG . . . E 3 66.453 82.442 56.787 1 27.35 ? O7 3AG 900 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 433 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #