data_5B00 # _model_server_result.job_id rlzu1DMPp9E5cBpvc6jhbg _model_server_result.datetime_utc '2024-11-14 21:06:53' _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 5b00 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 5B00 # _exptl.entry_id 5B00 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.209 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GERANYL DIPHOSPHATE' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.3 _cell.angle_gamma 90 _cell.entry_id 5B00 _cell.length_a 206.85 _cell.length_b 58.547 _cell.length_c 92.678 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B00 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1,2 B,C,E,F,H,I 2 1 # 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' 2_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 206.85 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C10 H20 O7 P2' _chem_comp.formula_weight 314.209 _chem_comp.id GPP _chem_comp.mon_nstd_flag . _chem_comp.name 'GERANYL DIPHOSPHATE' _chem_comp.type non-polymer _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 C1 O1 GPP sing 129 n n C1 C2 GPP sing 130 n n C1 H11 GPP sing 131 n n C1 H12 GPP sing 132 n n O1 PA GPP sing 133 n n C2 C3 GPP doub 134 e n C2 H2 GPP sing 135 n n C3 C4 GPP sing 136 n n C3 C5 GPP sing 137 n n C4 H41 GPP sing 138 n n C4 H42 GPP sing 139 n n C4 H43 GPP sing 140 n n C5 C6 GPP sing 141 n n C5 H51 GPP sing 142 n n C5 H52 GPP sing 143 n n C6 C7 GPP sing 144 n n C6 H61 GPP sing 145 n n C6 H62 GPP sing 146 n n C7 C8 GPP doub 147 n n C7 H7 GPP sing 148 n n C8 C9 GPP sing 149 n n C8 C10 GPP sing 150 n n C9 H91 GPP sing 151 n n C9 H92 GPP sing 152 n n C9 H93 GPP sing 153 n n C10 H101 GPP sing 154 n n C10 H102 GPP sing 155 n n C10 H103 GPP sing 156 n n PA O1A GPP doub 157 n n PA O2A GPP sing 158 n n PA O3A GPP sing 159 n n O2A HOA2 GPP sing 160 n n O3A PB GPP sing 161 n n PB O1B GPP doub 162 n n PB O2B GPP sing 163 n n PB O3B GPP sing 164 n n O2B HOB2 GPP sing 165 n n O3B HOB3 GPP sing 166 n n # _atom_sites.entry_id 5B00 _atom_sites.fract_transf_matrix[1][1] 0.004834 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00011 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01708 _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] 0.010793 _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 GPP A 1 500 500 GPP GPP . E 2 GPP B 1 500 500 GPP GPP . F 2 GPP C 1 500 500 GPP GPP . G 3 HOH A 1 601 190 HOH HOH . G 3 HOH A 2 602 180 HOH HOH . G 3 HOH A 3 603 177 HOH HOH . G 3 HOH A 4 604 126 HOH HOH . G 3 HOH A 5 605 124 HOH HOH . G 3 HOH A 6 606 125 HOH HOH . G 3 HOH A 7 607 14 HOH HOH . G 3 HOH A 8 608 178 HOH HOH . G 3 HOH A 9 609 135 HOH HOH . G 3 HOH A 10 610 63 HOH HOH . G 3 HOH A 11 611 1 HOH HOH . G 3 HOH A 12 612 2 HOH HOH . G 3 HOH A 13 613 127 HOH HOH . G 3 HOH A 14 614 170 HOH HOH . G 3 HOH A 15 615 152 HOH HOH . G 3 HOH A 16 616 9 HOH HOH . G 3 HOH A 17 617 128 HOH HOH . G 3 HOH A 18 618 151 HOH HOH . G 3 HOH A 19 619 8 HOH HOH . G 3 HOH A 20 620 6 HOH HOH . G 3 HOH A 21 621 153 HOH HOH . G 3 HOH A 22 622 179 HOH HOH . G 3 HOH A 23 623 111 HOH HOH . G 3 HOH A 24 624 120 HOH HOH . G 3 HOH A 25 625 81 HOH HOH . G 3 HOH A 26 626 62 HOH HOH . G 3 HOH A 27 627 7 HOH HOH . G 3 HOH A 28 628 110 HOH HOH . G 3 HOH A 29 629 100 HOH HOH . G 3 HOH A 30 630 122 HOH HOH . G 3 HOH A 31 631 136 HOH HOH . G 3 HOH A 32 632 106 HOH HOH . G 3 HOH A 33 633 155 HOH HOH . G 3 HOH A 34 634 24 HOH HOH . G 3 HOH A 35 635 119 HOH HOH . G 3 HOH A 36 636 61 HOH HOH . G 3 HOH A 37 637 16 HOH HOH . G 3 HOH A 38 638 82 HOH HOH . G 3 HOH A 39 639 4 HOH HOH . G 3 HOH A 40 640 129 HOH HOH . G 3 HOH A 41 641 20 HOH HOH . G 3 HOH A 42 642 80 HOH HOH . G 3 HOH A 43 643 182 HOH HOH . G 3 HOH A 44 644 146 HOH HOH . G 3 HOH A 45 645 3 HOH HOH . G 3 HOH A 46 646 117 HOH HOH . G 3 HOH A 47 647 5 HOH HOH . G 3 HOH A 48 648 105 HOH HOH . G 3 HOH A 49 649 15 HOH HOH . G 3 HOH A 50 650 36 HOH HOH . G 3 HOH A 51 651 17 HOH HOH . G 3 HOH A 52 652 187 HOH HOH . G 3 HOH A 53 653 115 HOH HOH . G 3 HOH A 54 654 25 HOH HOH . G 3 HOH A 55 655 118 HOH HOH . G 3 HOH A 56 656 186 HOH HOH . G 3 HOH A 57 657 145 HOH HOH . G 3 HOH A 58 658 137 HOH HOH . G 3 HOH A 59 659 112 HOH HOH . G 3 HOH A 60 660 65 HOH HOH . G 3 HOH A 61 661 189 HOH HOH . G 3 HOH A 62 662 11 HOH HOH . G 3 HOH A 63 663 107 HOH HOH . G 3 HOH A 64 664 156 HOH HOH . G 3 HOH A 65 665 150 HOH HOH . G 3 HOH A 66 666 10 HOH HOH . G 3 HOH A 67 667 104 HOH HOH . G 3 HOH A 68 668 21 HOH HOH . G 3 HOH A 69 669 171 HOH HOH . G 3 HOH A 70 670 108 HOH HOH . G 3 HOH A 71 671 173 HOH HOH . G 3 HOH A 72 672 123 HOH HOH . G 3 HOH A 73 673 109 HOH HOH . G 3 HOH A 74 674 175 HOH HOH . G 3 HOH A 75 675 172 HOH HOH . G 3 HOH A 76 676 113 HOH HOH . G 3 HOH A 77 677 23 HOH HOH . G 3 HOH A 78 678 114 HOH HOH . G 3 HOH A 79 679 181 HOH HOH . H 3 HOH B 1 601 53 HOH HOH . H 3 HOH B 2 602 49 HOH HOH . H 3 HOH B 3 603 132 HOH HOH . H 3 HOH B 4 604 131 HOH HOH . H 3 HOH B 5 605 50 HOH HOH . H 3 HOH B 6 606 75 HOH HOH . H 3 HOH B 7 607 134 HOH HOH . H 3 HOH B 8 608 142 HOH HOH . H 3 HOH B 9 609 184 HOH HOH . H 3 HOH B 10 610 32 HOH HOH . H 3 HOH B 11 611 73 HOH HOH . H 3 HOH B 12 612 13 HOH HOH . H 3 HOH B 13 613 74 HOH HOH . H 3 HOH B 14 614 85 HOH HOH . H 3 HOH B 15 615 30 HOH HOH . H 3 HOH B 16 616 141 HOH HOH . H 3 HOH B 17 617 33 HOH HOH . H 3 HOH B 18 618 51 HOH HOH . H 3 HOH B 19 619 160 HOH HOH . H 3 HOH B 20 620 77 HOH HOH . H 3 HOH B 21 621 83 HOH HOH . H 3 HOH B 22 622 64 HOH HOH . H 3 HOH B 23 623 84 HOH HOH . H 3 HOH B 24 624 140 HOH HOH . H 3 HOH B 25 625 70 HOH HOH . H 3 HOH B 26 626 169 HOH HOH . H 3 HOH B 27 627 44 HOH HOH . H 3 HOH B 28 628 67 HOH HOH . H 3 HOH B 29 629 69 HOH HOH . H 3 HOH B 30 630 86 HOH HOH . H 3 HOH B 31 631 31 HOH HOH . H 3 HOH B 32 632 54 HOH HOH . H 3 HOH B 33 633 138 HOH HOH . H 3 HOH B 34 634 66 HOH HOH . H 3 HOH B 35 635 133 HOH HOH . H 3 HOH B 36 636 139 HOH HOH . H 3 HOH B 37 637 143 HOH HOH . H 3 HOH B 38 638 38 HOH HOH . H 3 HOH B 39 639 34 HOH HOH . H 3 HOH B 40 640 121 HOH HOH . H 3 HOH B 41 641 76 HOH HOH . H 3 HOH B 42 642 46 HOH HOH . H 3 HOH B 43 643 68 HOH HOH . H 3 HOH B 44 644 158 HOH HOH . H 3 HOH B 45 645 37 HOH HOH . H 3 HOH B 46 646 157 HOH HOH . H 3 HOH B 47 647 147 HOH HOH . H 3 HOH B 48 648 40 HOH HOH . H 3 HOH B 49 649 78 HOH HOH . H 3 HOH B 50 650 79 HOH HOH . H 3 HOH B 51 651 93 HOH HOH . H 3 HOH B 52 652 87 HOH HOH . H 3 HOH B 53 653 149 HOH HOH . H 3 HOH B 54 654 154 HOH HOH . I 3 HOH C 1 601 29 HOH HOH . I 3 HOH C 2 602 185 HOH HOH . I 3 HOH C 3 603 57 HOH HOH . I 3 HOH C 4 604 159 HOH HOH . I 3 HOH C 5 605 130 HOH HOH . I 3 HOH C 6 606 58 HOH HOH . I 3 HOH C 7 607 98 HOH HOH . I 3 HOH C 8 608 99 HOH HOH . I 3 HOH C 9 609 55 HOH HOH . I 3 HOH C 10 610 48 HOH HOH . I 3 HOH C 11 611 52 HOH HOH . I 3 HOH C 12 612 18 HOH HOH . I 3 HOH C 13 613 188 HOH HOH . I 3 HOH C 14 614 97 HOH HOH . I 3 HOH C 15 615 39 HOH HOH . I 3 HOH C 16 616 72 HOH HOH . I 3 HOH C 17 617 96 HOH HOH . I 3 HOH C 18 618 71 HOH HOH . I 3 HOH C 19 619 116 HOH HOH . I 3 HOH C 20 620 56 HOH HOH . I 3 HOH C 21 621 22 HOH HOH . I 3 HOH C 22 622 164 HOH HOH . I 3 HOH C 23 623 165 HOH HOH . I 3 HOH C 24 624 12 HOH HOH . I 3 HOH C 25 625 161 HOH HOH . I 3 HOH C 26 626 26 HOH HOH . I 3 HOH C 27 627 95 HOH HOH . I 3 HOH C 28 628 102 HOH HOH . I 3 HOH C 29 629 59 HOH HOH . I 3 HOH C 30 630 101 HOH HOH . I 3 HOH C 31 631 47 HOH HOH . I 3 HOH C 32 632 166 HOH HOH . I 3 HOH C 33 633 167 HOH HOH . I 3 HOH C 34 634 27 HOH HOH . I 3 HOH C 35 635 19 HOH HOH . I 3 HOH C 36 636 91 HOH HOH . I 3 HOH C 37 637 90 HOH HOH . I 3 HOH C 38 638 168 HOH HOH . I 3 HOH C 39 639 60 HOH HOH . I 3 HOH C 40 640 148 HOH HOH . I 3 HOH C 41 641 163 HOH HOH . I 3 HOH C 42 642 89 HOH HOH . I 3 HOH C 43 643 28 HOH HOH . I 3 HOH C 44 644 162 HOH HOH . I 3 HOH C 45 645 35 HOH HOH . I 3 HOH C 46 646 88 HOH HOH . I 3 HOH C 47 647 45 HOH HOH . I 3 HOH C 48 648 92 HOH HOH . I 3 HOH C 49 649 144 HOH HOH . I 3 HOH C 50 650 191 HOH HOH . I 3 HOH C 51 651 176 HOH HOH . I 3 HOH C 52 652 183 HOH HOH . I 3 HOH C 53 653 41 HOH HOH . I 3 HOH C 54 654 42 HOH HOH . I 3 HOH C 55 655 94 HOH HOH . I 3 HOH C 56 656 174 HOH HOH . I 3 HOH C 57 657 103 HOH HOH . I 3 HOH C 58 658 43 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 C1 GPP . . . D 2 93.145 8.113 9.361 1 151.58 ? C1 GPP 500 A 1 HETATM 2 O O1 GPP . . . D 2 92.812 6.727 9.42 1 156.54 ? O1 GPP 500 A 1 HETATM 3 C C2 GPP . . . D 2 94.261 8.358 8.359 1 147 ? C2 GPP 500 A 1 HETATM 4 C C3 GPP . . . D 2 95.321 9.075 8.629 1 143.66 ? C3 GPP 500 A 1 HETATM 5 C C4 GPP . . . D 2 95.519 9.725 9.981 1 143.39 ? C4 GPP 500 A 1 HETATM 6 C C5 GPP . . . D 2 96.36 9.254 7.561 1 141.58 ? C5 GPP 500 A 1 HETATM 7 C C6 GPP . . . D 2 97.572 8.345 7.805 1 138.83 ? C6 GPP 500 A 1 HETATM 8 C C7 GPP . . . D 2 98.598 9.045 8.682 1 136.06 ? C7 GPP 500 A 1 HETATM 9 C C8 GPP . . . D 2 99.762 9.473 8.308 1 134.16 ? C8 GPP 500 A 1 HETATM 10 C C9 GPP . . . D 2 100.292 9.336 6.9 1 133.05 ? C9 GPP 500 A 1 HETATM 11 C C10 GPP . . . D 2 100.579 10.123 9.355 1 133.12 ? C10 GPP 500 A 1 HETATM 12 P PA GPP . . . D 2 92.065 6.15 10.636 1 159.3 ? PA GPP 500 A 1 HETATM 13 O O1A GPP . . . D 2 90.802 6.982 10.938 1 158.45 ? O1A GPP 500 A 1 HETATM 14 O O2A GPP . . . D 2 92.968 6.206 11.847 1 159.11 ? O2A GPP 500 A 1 HETATM 15 O O3A GPP . . . D 2 91.659 4.548 10.349 1 160.87 ? O3A GPP 500 A 1 HETATM 16 P PB GPP . . . D 2 92.283 3.394 9.297 1 162.49 ? PB GPP 500 A 1 HETATM 17 O O1B GPP . . . D 2 92.539 4.046 7.942 1 162.36 ? O1B GPP 500 A 1 HETATM 18 O O2B GPP . . . D 2 91.254 2.263 9.116 1 161.72 ? O2B GPP 500 A 1 HETATM 19 O O3B GPP . . . D 2 93.604 2.774 9.834 1 162.12 ? O3B GPP 500 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #