data_3PYB # _model_server_result.job_id PS7zrWF98zcdAD3ueZrRZA _model_server_result.datetime_utc '2025-01-15 16:48:28' _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 3pyb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":901}' # _entry.id 3PYB # _exptl.entry_id 3PYB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 453.447 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-(methyl{2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]ethyl}amino)ethyl trihydrogen 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 3PYB _cell.length_a 63.738 _cell.length_b 188.554 _cell.length_c 229.071 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PYB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,H,N 1 1 B,I,J,K,O 2 1 C,L,M,P 3 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 2 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C19 H37 N O7 P2' _chem_comp.formula_weight 453.447 _chem_comp.id A3C _chem_comp.mon_nstd_flag . _chem_comp.name '2-(methyl{2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]ethyl}amino)ethyl trihydrogen diphosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '13-aza-13,14-dihydrocopalyl 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 O01 C01 A3C sing 38 n n C01 C02 A3C sing 39 n n C01 H01 A3C sing 40 n n C01 H01A A3C sing 41 n n P02 O01 A3C sing 42 n n C02 N03 A3C sing 43 n n C02 H02 A3C sing 44 n n C02 H02A A3C sing 45 n n O06 P02 A3C doub 46 n n O07 P02 A3C sing 47 n n P02 O03 A3C sing 48 n n C11 N03 A3C sing 49 n n N03 C13 A3C sing 50 n n P04 O03 A3C sing 51 n n O08 P04 A3C doub 52 n n O09 P04 A3C sing 53 n n P04 O05 A3C sing 54 n n O05 HO05 A3C sing 55 n n O07 HO07 A3C sing 56 n n O09 HO09 A3C sing 57 n n C11 C12 A3C sing 58 n n C11 H11 A3C sing 59 n n C11 H11A A3C sing 60 n n C12 C21 A3C sing 61 n n C12 H12 A3C sing 62 n n C12 H12A A3C sing 63 n n C13 H13 A3C sing 64 n n C13 H13A A3C sing 65 n n C13 H13B A3C sing 66 n n C30 C21 A3C sing 67 n n C21 C22 A3C sing 68 n n C21 H21 A3C sing 69 n n C22 C23 A3C sing 70 n n C22 C31 A3C doub 71 n n C24 C23 A3C sing 72 n n C23 H23 A3C sing 73 n n C23 H23A A3C sing 74 n n C25 C24 A3C sing 75 n n C24 H24 A3C sing 76 n n C24 H24A A3C sing 77 n n C26 C25 A3C sing 78 n n C30 C25 A3C sing 79 n n C25 H25 A3C sing 80 n n C27 C26 A3C sing 81 n n C33 C26 A3C sing 82 n n C26 C32 A3C sing 83 n n C28 C27 A3C sing 84 n n C27 H27 A3C sing 85 n n C27 H27A A3C sing 86 n n C28 C29 A3C sing 87 n n C28 H28 A3C sing 88 n n C28 H28A A3C sing 89 n n C29 C30 A3C sing 90 n n C29 H29 A3C sing 91 n n C29 H29A A3C sing 92 n n C30 C34 A3C sing 93 n n C31 H31 A3C sing 94 n n C31 H31A A3C sing 95 n n C32 H32 A3C sing 96 n n C32 H32A A3C sing 97 n n C32 H32B A3C sing 98 n n C33 H33 A3C sing 99 n n C33 H33A A3C sing 100 n n C33 H33B A3C sing 101 n n C34 H34 A3C sing 102 n n C34 H34A A3C sing 103 n n C34 H34B A3C sing 104 n n # _atom_sites.entry_id 3PYB _atom_sites.fract_transf_matrix[1][1] 0.015689 _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] 0.005304 _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] 0.004365 _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 A3C A 1 901 901 A3C A3C . E 3 1PE A 1 911 911 1PE 1PE . F 3 1PE A 1 921 921 1PE 1PE . G 3 1PE A 1 931 931 1PE 1PE . H 3 1PE A 1 811 921 1PE 1PE . I 3 1PE B 1 911 911 1PE 1PE . J 3 1PE B 1 931 931 1PE 1PE . K 3 1PE B 1 921 921 1PE 1PE . L 3 1PE C 1 911 911 1PE 1PE . M 3 1PE C 1 931 931 1PE 1PE . N 4 HOH A 1 1 1 HOH HOH . N 4 HOH A 2 5 5 HOH HOH . N 4 HOH A 3 10 10 HOH HOH . N 4 HOH A 4 11 11 HOH HOH . N 4 HOH A 5 13 13 HOH HOH . N 4 HOH A 6 17 17 HOH HOH . N 4 HOH A 7 19 19 HOH HOH . N 4 HOH A 8 22 22 HOH HOH . N 4 HOH A 9 23 23 HOH HOH . N 4 HOH A 10 24 24 HOH HOH . N 4 HOH A 11 25 25 HOH HOH . N 4 HOH A 12 26 26 HOH HOH . N 4 HOH A 13 31 31 HOH HOH . N 4 HOH A 14 32 32 HOH HOH . N 4 HOH A 15 36 36 HOH HOH . N 4 HOH A 16 37 37 HOH HOH . N 4 HOH A 17 39 39 HOH HOH . N 4 HOH A 18 40 40 HOH HOH . N 4 HOH A 19 43 43 HOH HOH . N 4 HOH A 20 46 46 HOH HOH . N 4 HOH A 21 50 50 HOH HOH . N 4 HOH A 22 51 51 HOH HOH . N 4 HOH A 23 55 55 HOH HOH . N 4 HOH A 24 57 57 HOH HOH . N 4 HOH A 25 59 59 HOH HOH . N 4 HOH A 26 62 62 HOH HOH . N 4 HOH A 27 63 63 HOH HOH . N 4 HOH A 28 64 64 HOH HOH . N 4 HOH A 29 66 66 HOH HOH . N 4 HOH A 30 68 68 HOH HOH . N 4 HOH A 31 69 69 HOH HOH . N 4 HOH A 32 70 70 HOH HOH . N 4 HOH A 33 78 78 HOH HOH . N 4 HOH A 34 79 79 HOH HOH . N 4 HOH A 35 81 81 HOH HOH . N 4 HOH A 36 82 82 HOH HOH . N 4 HOH A 37 83 83 HOH HOH . N 4 HOH A 38 812 84 HOH HOH . N 4 HOH A 39 813 87 HOH HOH . N 4 HOH A 40 814 88 HOH HOH . N 4 HOH A 41 815 89 HOH HOH . N 4 HOH A 42 816 90 HOH HOH . N 4 HOH A 43 817 91 HOH HOH . N 4 HOH A 44 818 93 HOH HOH . N 4 HOH A 45 819 99 HOH HOH . N 4 HOH A 46 820 100 HOH HOH . N 4 HOH A 47 821 112 HOH HOH . N 4 HOH A 48 822 114 HOH HOH . N 4 HOH A 49 823 115 HOH HOH . N 4 HOH A 50 824 117 HOH HOH . N 4 HOH A 51 825 118 HOH HOH . N 4 HOH A 52 826 119 HOH HOH . N 4 HOH A 53 827 120 HOH HOH . N 4 HOH A 54 828 136 HOH HOH . N 4 HOH A 55 829 143 HOH HOH . N 4 HOH A 56 830 144 HOH HOH . N 4 HOH A 57 831 145 HOH HOH . N 4 HOH A 58 832 146 HOH HOH . N 4 HOH A 59 833 150 HOH HOH . N 4 HOH A 60 834 151 HOH HOH . N 4 HOH A 61 835 153 HOH HOH . N 4 HOH A 62 836 154 HOH HOH . N 4 HOH A 63 837 159 HOH HOH . N 4 HOH A 64 838 160 HOH HOH . N 4 HOH A 65 839 161 HOH HOH . N 4 HOH A 66 840 162 HOH HOH . N 4 HOH A 67 841 163 HOH HOH . N 4 HOH A 68 842 164 HOH HOH . N 4 HOH A 69 843 165 HOH HOH . N 4 HOH A 70 844 166 HOH HOH . N 4 HOH A 71 845 167 HOH HOH . N 4 HOH A 72 846 172 HOH HOH . N 4 HOH A 73 847 174 HOH HOH . N 4 HOH A 74 848 175 HOH HOH . N 4 HOH A 75 849 178 HOH HOH . N 4 HOH A 76 850 183 HOH HOH . N 4 HOH A 77 851 190 HOH HOH . N 4 HOH A 78 852 191 HOH HOH . N 4 HOH A 79 853 192 HOH HOH . N 4 HOH A 80 854 193 HOH HOH . N 4 HOH A 81 855 198 HOH HOH . N 4 HOH A 82 856 199 HOH HOH . N 4 HOH A 83 857 200 HOH HOH . N 4 HOH A 84 858 201 HOH HOH . O 4 HOH B 1 3 3 HOH HOH . O 4 HOH B 2 4 4 HOH HOH . O 4 HOH B 3 7 7 HOH HOH . O 4 HOH B 4 8 8 HOH HOH . O 4 HOH B 5 14 14 HOH HOH . O 4 HOH B 6 15 15 HOH HOH . O 4 HOH B 7 27 27 HOH HOH . O 4 HOH B 8 29 29 HOH HOH . O 4 HOH B 9 30 30 HOH HOH . O 4 HOH B 10 34 34 HOH HOH . O 4 HOH B 11 35 35 HOH HOH . O 4 HOH B 12 38 38 HOH HOH . O 4 HOH B 13 41 41 HOH HOH . O 4 HOH B 14 42 42 HOH HOH . O 4 HOH B 15 44 44 HOH HOH . O 4 HOH B 16 54 54 HOH HOH . O 4 HOH B 17 56 56 HOH HOH . O 4 HOH B 18 58 58 HOH HOH . O 4 HOH B 19 61 61 HOH HOH . O 4 HOH B 20 67 67 HOH HOH . O 4 HOH B 21 71 71 HOH HOH . O 4 HOH B 22 74 74 HOH HOH . O 4 HOH B 23 75 75 HOH HOH . O 4 HOH B 24 76 76 HOH HOH . O 4 HOH B 25 80 80 HOH HOH . O 4 HOH B 26 811 85 HOH HOH . O 4 HOH B 27 812 86 HOH HOH . O 4 HOH B 28 813 94 HOH HOH . O 4 HOH B 29 814 96 HOH HOH . O 4 HOH B 30 815 98 HOH HOH . O 4 HOH B 31 816 103 HOH HOH . O 4 HOH B 32 817 105 HOH HOH . O 4 HOH B 33 818 107 HOH HOH . O 4 HOH B 34 819 109 HOH HOH . O 4 HOH B 35 820 110 HOH HOH . O 4 HOH B 36 821 123 HOH HOH . O 4 HOH B 37 822 124 HOH HOH . O 4 HOH B 38 823 126 HOH HOH . O 4 HOH B 39 824 127 HOH HOH . O 4 HOH B 40 825 128 HOH HOH . O 4 HOH B 41 826 129 HOH HOH . O 4 HOH B 42 827 130 HOH HOH . O 4 HOH B 43 828 134 HOH HOH . O 4 HOH B 44 829 135 HOH HOH . O 4 HOH B 45 830 137 HOH HOH . O 4 HOH B 46 831 138 HOH HOH . O 4 HOH B 47 832 139 HOH HOH . O 4 HOH B 48 833 140 HOH HOH . O 4 HOH B 49 834 141 HOH HOH . O 4 HOH B 50 835 142 HOH HOH . O 4 HOH B 51 836 147 HOH HOH . O 4 HOH B 52 837 148 HOH HOH . O 4 HOH B 53 838 152 HOH HOH . O 4 HOH B 54 839 155 HOH HOH . O 4 HOH B 55 840 157 HOH HOH . O 4 HOH B 56 841 168 HOH HOH . O 4 HOH B 57 842 169 HOH HOH . O 4 HOH B 58 843 170 HOH HOH . O 4 HOH B 59 844 177 HOH HOH . O 4 HOH B 60 845 179 HOH HOH . O 4 HOH B 61 846 182 HOH HOH . O 4 HOH B 62 847 184 HOH HOH . O 4 HOH B 63 848 186 HOH HOH . O 4 HOH B 64 849 187 HOH HOH . O 4 HOH B 65 850 188 HOH HOH . O 4 HOH B 66 851 189 HOH HOH . O 4 HOH B 67 852 194 HOH HOH . O 4 HOH B 68 853 196 HOH HOH . P 4 HOH C 1 2 2 HOH HOH . P 4 HOH C 2 6 6 HOH HOH . P 4 HOH C 3 9 9 HOH HOH . P 4 HOH C 4 12 12 HOH HOH . P 4 HOH C 5 16 16 HOH HOH . P 4 HOH C 6 18 18 HOH HOH . P 4 HOH C 7 20 20 HOH HOH . P 4 HOH C 8 21 21 HOH HOH . P 4 HOH C 9 28 28 HOH HOH . P 4 HOH C 10 33 33 HOH HOH . P 4 HOH C 11 45 45 HOH HOH . P 4 HOH C 12 47 47 HOH HOH . P 4 HOH C 13 48 48 HOH HOH . P 4 HOH C 14 49 49 HOH HOH . P 4 HOH C 15 52 52 HOH HOH . P 4 HOH C 16 53 53 HOH HOH . P 4 HOH C 17 60 60 HOH HOH . P 4 HOH C 18 65 65 HOH HOH . P 4 HOH C 19 72 72 HOH HOH . P 4 HOH C 20 73 73 HOH HOH . P 4 HOH C 21 77 77 HOH HOH . P 4 HOH C 22 811 92 HOH HOH . P 4 HOH C 23 812 95 HOH HOH . P 4 HOH C 24 813 97 HOH HOH . P 4 HOH C 25 814 101 HOH HOH . P 4 HOH C 26 815 102 HOH HOH . P 4 HOH C 27 816 104 HOH HOH . P 4 HOH C 28 817 106 HOH HOH . P 4 HOH C 29 818 108 HOH HOH . P 4 HOH C 30 819 111 HOH HOH . P 4 HOH C 31 820 113 HOH HOH . P 4 HOH C 32 821 116 HOH HOH . P 4 HOH C 33 822 121 HOH HOH . P 4 HOH C 34 823 122 HOH HOH . P 4 HOH C 35 824 125 HOH HOH . P 4 HOH C 36 825 131 HOH HOH . P 4 HOH C 37 826 132 HOH HOH . P 4 HOH C 38 827 133 HOH HOH . P 4 HOH C 39 828 149 HOH HOH . P 4 HOH C 40 829 156 HOH HOH . P 4 HOH C 41 830 158 HOH HOH . P 4 HOH C 42 831 171 HOH HOH . P 4 HOH C 43 832 173 HOH HOH . P 4 HOH C 44 833 176 HOH HOH . P 4 HOH C 45 834 180 HOH HOH . P 4 HOH C 46 835 181 HOH HOH . P 4 HOH C 47 836 185 HOH HOH . P 4 HOH C 48 837 195 HOH HOH . P 4 HOH C 49 838 197 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 C C01 A3C . . . D 2 -15.568 -26.367 -2.377 1 81.69 ? C01 A3C 901 A 1 HETATM 2 O O01 A3C . . . D 2 -16.771 -25.731 -2.728 1 110.68 ? O01 A3C 901 A 1 HETATM 3 C C02 A3C . . . D 2 -15.47 -26.526 -0.863 1 55.05 ? C02 A3C 901 A 1 HETATM 4 P P02 A3C . . . D 2 -17.169 -25.314 -4.239 1 96.44 ? P02 A3C 901 A 1 HETATM 5 N N03 A3C . . . D 2 -15.549 -25.24 -0.214 1 63.56 ? N03 A3C 901 A 1 HETATM 6 O O03 A3C . . . D 2 -17.259 -26.676 -5.11 1 97.44 ? O03 A3C 901 A 1 HETATM 7 P P04 A3C . . . D 2 -18.118 -27.882 -4.445 1 143.8 ? P04 A3C 901 A 1 HETATM 8 O O05 A3C . . . D 2 -18.554 -28.817 -5.511 1 112.7 ? O05 A3C 901 A 1 HETATM 9 O O06 A3C . . . D 2 -16.184 -24.34 -4.797 1 95.15 ? O06 A3C 901 A 1 HETATM 10 O O07 A3C . . . D 2 -18.514 -24.687 -4.221 1 93 ? O07 A3C 901 A 1 HETATM 11 O O08 A3C . . . D 2 -19.302 -27.419 -3.679 1 108.37 ? O08 A3C 901 A 1 HETATM 12 O O09 A3C . . . D 2 -17.263 -28.728 -3.554 1 112.61 ? O09 A3C 901 A 1 HETATM 13 C C11 A3C . . . D 2 -14.493 -24.464 -0.804 1 52.85 ? C11 A3C 901 A 1 HETATM 14 C C12 A3C . . . D 2 -13.203 -25.031 -0.22 1 49.33 ? C12 A3C 901 A 1 HETATM 15 C C13 A3C . . . D 2 -16.837 -24.587 -0.269 1 52.01 ? C13 A3C 901 A 1 HETATM 16 C C21 A3C . . . D 2 -11.875 -24.365 -0.616 1 54.96 ? C21 A3C 901 A 1 HETATM 17 C C22 A3C . . . D 2 -12.022 -23.224 -1.596 1 52.3 ? C22 A3C 901 A 1 HETATM 18 C C23 A3C . . . D 2 -10.677 -23.081 -2.22 1 43.56 ? C23 A3C 901 A 1 HETATM 19 C C24 A3C . . . D 2 -9.432 -23.118 -1.323 1 40.86 ? C24 A3C 901 A 1 HETATM 20 C C25 A3C . . . D 2 -9.503 -24.08 -0.127 1 48.37 ? C25 A3C 901 A 1 HETATM 21 C C26 A3C . . . D 2 -8.278 -23.93 0.78 1 46.74 ? C26 A3C 901 A 1 HETATM 22 C C27 A3C . . . D 2 -8.682 -24.518 2.13 1 42.99 ? C27 A3C 901 A 1 HETATM 23 C C28 A3C . . . D 2 -9.671 -25.665 1.978 1 39.69 ? C28 A3C 901 A 1 HETATM 24 C C29 A3C . . . D 2 -11.046 -25.145 1.58 1 44.84 ? C29 A3C 901 A 1 HETATM 25 C C30 A3C . . . D 2 -10.893 -24.055 0.518 1 55.83 ? C30 A3C 901 A 1 HETATM 26 C C31 A3C . . . D 2 -12.947 -22.337 -2.005 1 41.73 ? C31 A3C 901 A 1 HETATM 27 C C32 A3C . . . D 2 -7.881 -22.472 0.976 1 43.58 ? C32 A3C 901 A 1 HETATM 28 C C33 A3C . . . D 2 -7.07 -24.69 0.236 1 44.66 ? C33 A3C 901 A 1 HETATM 29 C C34 A3C . . . D 2 -11.42 -22.819 1.248 1 42.38 ? C34 A3C 901 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 29 #