data_5HXP # _model_server_result.job_id d8-VY-P6afM_5mpVKGNU3Q _model_server_result.datetime_utc '2024-11-15 21:56:48' _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 5hxp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":404}' # _entry.id 5HXP # _exptl.entry_id 5HXP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 248.108 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ISOPENTYL PYROPHOSPHATE' _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 90 _cell.angle_gamma 90 _cell.entry_id 5HXP _cell.length_a 58.311 _cell.length_b 64.545 _cell.length_c 127.156 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HXP _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 G N N ? 2 H 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 B OD1 ASP 16 C ASP 86 1_555 D MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc2 D MG MG . C MG 401 1_555 G O13 IPR . C IPR 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc3 D MG MG . C MG 401 1_555 G O9 IPR . C IPR 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc4 D MG MG . C MG 401 1_555 H O8 IPR . C IPR 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc5 D MG MG . C MG 401 1_555 J O HOH . C HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc6 D MG MG . C MG 401 1_555 J O HOH . C HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? # _chem_comp.formula 'C5 H14 O7 P2' _chem_comp.formula_weight 248.108 _chem_comp.id IPR _chem_comp.mon_nstd_flag . _chem_comp.name 'ISOPENTYL PYROPHOSPHATE' _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 P11 O14 IPR sing 173 n n P11 O12 IPR sing 174 n n P11 O13 IPR doub 175 n n P11 O10 IPR sing 176 n n O14 H14 IPR sing 177 n n O12 H12 IPR sing 178 n n O10 P7 IPR sing 179 n n P7 O8 IPR sing 180 n n P7 O9 IPR doub 181 n n P7 O6 IPR sing 182 n n O8 HO8 IPR sing 183 n n O6 C5 IPR sing 184 n n C5 C4 IPR sing 185 n n C5 HC51 IPR sing 186 n n C5 HC52 IPR sing 187 n n C4 C2 IPR sing 188 n n C4 HC41 IPR sing 189 n n C4 HC42 IPR sing 190 n n C2 C1 IPR sing 191 n n C2 C3 IPR sing 192 n n C2 HC2 IPR sing 193 n n C1 HC11 IPR sing 194 n n C1 HC12 IPR sing 195 n n C1 HC13 IPR sing 196 n n C3 HC31 IPR sing 197 n n C3 HC32 IPR sing 198 n n C3 HC33 IPR sing 199 n n # _atom_sites.entry_id 5HXP _atom_sites.fract_transf_matrix[1][1] 0.017149 _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] 0.015493 _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] 0.007864 _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 C 2 IPR A 1 401 3 IPR IPR . D 3 MG C 1 401 1 MG MG . E 4 O4B C 1 402 1 O4B CRN . F 4 O4B C 1 403 2 O4B CRN . G 2 IPR C 1 404 1 IPR IPR . H 2 IPR C 1 405 2 IPR IPR . I 5 HOH A 1 501 194 HOH HOH . I 5 HOH A 2 502 141 HOH HOH . I 5 HOH A 3 503 91 HOH HOH . I 5 HOH A 4 504 38 HOH HOH . I 5 HOH A 5 505 156 HOH HOH . I 5 HOH A 6 506 116 HOH HOH . I 5 HOH A 7 507 31 HOH HOH . I 5 HOH A 8 508 181 HOH HOH . I 5 HOH A 9 509 9 HOH HOH . I 5 HOH A 10 510 76 HOH HOH . I 5 HOH A 11 511 24 HOH HOH . I 5 HOH A 12 512 192 HOH HOH . I 5 HOH A 13 513 152 HOH HOH . I 5 HOH A 14 514 8 HOH HOH . I 5 HOH A 15 515 125 HOH HOH . I 5 HOH A 16 516 77 HOH HOH . I 5 HOH A 17 517 105 HOH HOH . I 5 HOH A 18 518 146 HOH HOH . I 5 HOH A 19 519 123 HOH HOH . I 5 HOH A 20 520 178 HOH HOH . I 5 HOH A 21 521 93 HOH HOH . I 5 HOH A 22 522 19 HOH HOH . I 5 HOH A 23 523 179 HOH HOH . I 5 HOH A 24 524 182 HOH HOH . I 5 HOH A 25 525 199 HOH HOH . I 5 HOH A 26 526 110 HOH HOH . I 5 HOH A 27 527 129 HOH HOH . I 5 HOH A 28 528 2 HOH HOH . I 5 HOH A 29 529 112 HOH HOH . I 5 HOH A 30 530 67 HOH HOH . I 5 HOH A 31 531 46 HOH HOH . I 5 HOH A 32 532 45 HOH HOH . I 5 HOH A 33 533 17 HOH HOH . I 5 HOH A 34 534 74 HOH HOH . I 5 HOH A 35 535 109 HOH HOH . I 5 HOH A 36 536 106 HOH HOH . I 5 HOH A 37 537 140 HOH HOH . I 5 HOH A 38 538 71 HOH HOH . I 5 HOH A 39 539 185 HOH HOH . I 5 HOH A 40 540 40 HOH HOH . I 5 HOH A 41 541 23 HOH HOH . I 5 HOH A 42 542 92 HOH HOH . I 5 HOH A 43 543 7 HOH HOH . I 5 HOH A 44 544 14 HOH HOH . I 5 HOH A 45 545 127 HOH HOH . I 5 HOH A 46 546 49 HOH HOH . I 5 HOH A 47 547 48 HOH HOH . I 5 HOH A 48 548 111 HOH HOH . I 5 HOH A 49 549 22 HOH HOH . I 5 HOH A 50 550 177 HOH HOH . I 5 HOH A 51 551 175 HOH HOH . I 5 HOH A 52 552 145 HOH HOH . I 5 HOH A 53 553 15 HOH HOH . I 5 HOH A 54 554 18 HOH HOH . I 5 HOH A 55 555 154 HOH HOH . I 5 HOH A 56 556 20 HOH HOH . I 5 HOH A 57 557 100 HOH HOH . I 5 HOH A 58 558 197 HOH HOH . I 5 HOH A 59 559 82 HOH HOH . I 5 HOH A 60 560 162 HOH HOH . I 5 HOH A 61 561 193 HOH HOH . I 5 HOH A 62 562 5 HOH HOH . I 5 HOH A 63 563 84 HOH HOH . I 5 HOH A 64 564 21 HOH HOH . I 5 HOH A 65 565 44 HOH HOH . I 5 HOH A 66 566 153 HOH HOH . I 5 HOH A 67 567 75 HOH HOH . I 5 HOH A 68 568 13 HOH HOH . I 5 HOH A 69 569 158 HOH HOH . I 5 HOH A 70 570 32 HOH HOH . I 5 HOH A 71 571 120 HOH HOH . I 5 HOH A 72 572 113 HOH HOH . I 5 HOH A 73 573 131 HOH HOH . I 5 HOH A 74 574 16 HOH HOH . I 5 HOH A 75 575 176 HOH HOH . I 5 HOH A 76 576 88 HOH HOH . I 5 HOH A 77 577 195 HOH HOH . I 5 HOH A 78 578 73 HOH HOH . I 5 HOH A 79 579 90 HOH HOH . I 5 HOH A 80 580 119 HOH HOH . I 5 HOH A 81 581 10 HOH HOH . I 5 HOH A 82 582 124 HOH HOH . I 5 HOH A 83 583 130 HOH HOH . I 5 HOH A 84 584 12 HOH HOH . I 5 HOH A 85 585 139 HOH HOH . I 5 HOH A 86 586 183 HOH HOH . I 5 HOH A 87 587 196 HOH HOH . I 5 HOH A 88 588 155 HOH HOH . I 5 HOH A 89 589 205 HOH HOH . I 5 HOH A 90 590 147 HOH HOH . I 5 HOH A 91 591 122 HOH HOH . I 5 HOH A 92 592 78 HOH HOH . I 5 HOH A 93 593 128 HOH HOH . I 5 HOH A 94 594 126 HOH HOH . I 5 HOH A 95 595 107 HOH HOH . J 5 HOH C 1 501 204 HOH HOH . J 5 HOH C 2 502 165 HOH HOH . J 5 HOH C 3 503 117 HOH HOH . J 5 HOH C 4 504 138 HOH HOH . J 5 HOH C 5 505 83 HOH HOH . J 5 HOH C 6 506 108 HOH HOH . J 5 HOH C 7 507 81 HOH HOH . J 5 HOH C 8 508 103 HOH HOH . J 5 HOH C 9 509 198 HOH HOH . J 5 HOH C 10 510 6 HOH HOH . J 5 HOH C 11 511 41 HOH HOH . J 5 HOH C 12 512 53 HOH HOH . J 5 HOH C 13 513 61 HOH HOH . J 5 HOH C 14 514 86 HOH HOH . J 5 HOH C 15 515 36 HOH HOH . J 5 HOH C 16 516 11 HOH HOH . J 5 HOH C 17 517 27 HOH HOH . J 5 HOH C 18 518 118 HOH HOH . J 5 HOH C 19 519 203 HOH HOH . J 5 HOH C 20 520 47 HOH HOH . J 5 HOH C 21 521 25 HOH HOH . J 5 HOH C 22 522 28 HOH HOH . J 5 HOH C 23 523 134 HOH HOH . J 5 HOH C 24 524 80 HOH HOH . J 5 HOH C 25 525 87 HOH HOH . J 5 HOH C 26 526 39 HOH HOH . J 5 HOH C 27 527 191 HOH HOH . J 5 HOH C 28 528 54 HOH HOH . J 5 HOH C 29 529 135 HOH HOH . J 5 HOH C 30 530 33 HOH HOH . J 5 HOH C 31 531 68 HOH HOH . J 5 HOH C 32 532 201 HOH HOH . J 5 HOH C 33 533 59 HOH HOH . J 5 HOH C 34 534 188 HOH HOH . J 5 HOH C 35 535 142 HOH HOH . J 5 HOH C 36 536 26 HOH HOH . J 5 HOH C 37 537 37 HOH HOH . J 5 HOH C 38 538 104 HOH HOH . J 5 HOH C 39 539 137 HOH HOH . J 5 HOH C 40 540 50 HOH HOH . J 5 HOH C 41 541 29 HOH HOH . J 5 HOH C 42 542 150 HOH HOH . J 5 HOH C 43 543 190 HOH HOH . J 5 HOH C 44 544 42 HOH HOH . J 5 HOH C 45 545 65 HOH HOH . J 5 HOH C 46 546 57 HOH HOH . J 5 HOH C 47 547 85 HOH HOH . J 5 HOH C 48 548 186 HOH HOH . J 5 HOH C 49 549 171 HOH HOH . J 5 HOH C 50 550 56 HOH HOH . J 5 HOH C 51 551 98 HOH HOH . J 5 HOH C 52 552 187 HOH HOH . J 5 HOH C 53 553 64 HOH HOH . J 5 HOH C 54 554 30 HOH HOH . J 5 HOH C 55 555 94 HOH HOH . J 5 HOH C 56 556 70 HOH HOH . J 5 HOH C 57 557 4 HOH HOH . J 5 HOH C 58 558 95 HOH HOH . J 5 HOH C 59 559 35 HOH HOH . J 5 HOH C 60 560 101 HOH HOH . J 5 HOH C 61 561 52 HOH HOH . J 5 HOH C 62 562 167 HOH HOH . J 5 HOH C 63 563 69 HOH HOH . J 5 HOH C 64 564 189 HOH HOH . J 5 HOH C 65 565 60 HOH HOH . J 5 HOH C 66 566 148 HOH HOH . J 5 HOH C 67 567 72 HOH HOH . J 5 HOH C 68 568 63 HOH HOH . J 5 HOH C 69 569 136 HOH HOH . J 5 HOH C 70 570 1 HOH HOH . J 5 HOH C 71 571 55 HOH HOH . J 5 HOH C 72 572 66 HOH HOH . J 5 HOH C 73 573 172 HOH HOH . J 5 HOH C 74 574 96 HOH HOH . J 5 HOH C 75 575 159 HOH HOH . J 5 HOH C 76 576 169 HOH HOH . J 5 HOH C 77 577 3 HOH HOH . J 5 HOH C 78 578 164 HOH HOH . J 5 HOH C 79 579 173 HOH HOH . J 5 HOH C 80 580 144 HOH HOH . J 5 HOH C 81 581 97 HOH HOH . J 5 HOH C 82 582 133 HOH HOH . J 5 HOH C 83 583 58 HOH HOH . J 5 HOH C 84 584 166 HOH HOH . J 5 HOH C 85 585 200 HOH HOH . J 5 HOH C 86 586 115 HOH HOH . J 5 HOH C 87 587 149 HOH HOH . J 5 HOH C 88 588 43 HOH HOH . J 5 HOH C 89 589 89 HOH HOH . J 5 HOH C 90 590 51 HOH HOH . J 5 HOH C 91 591 99 HOH HOH . J 5 HOH C 92 592 157 HOH HOH . J 5 HOH C 93 593 62 HOH HOH . J 5 HOH C 94 594 79 HOH HOH . J 5 HOH C 95 595 170 HOH HOH . J 5 HOH C 96 596 151 HOH HOH . J 5 HOH C 97 597 161 HOH HOH . J 5 HOH C 98 598 168 HOH HOH . J 5 HOH C 99 599 163 HOH HOH . J 5 HOH C 100 600 121 HOH HOH . J 5 HOH C 101 601 114 HOH HOH . J 5 HOH C 102 602 132 HOH HOH . J 5 HOH C 103 603 202 HOH HOH . J 5 HOH C 104 604 102 HOH HOH . J 5 HOH C 105 605 34 HOH HOH . J 5 HOH C 106 606 143 HOH HOH . J 5 HOH C 107 607 184 HOH HOH . J 5 HOH C 108 608 174 HOH HOH . J 5 HOH C 109 609 160 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 P P11 IPR . . . G 2 -37.275 9.251 14.367 1 26.8 ? P11 IPR 404 C 1 HETATM 2 O O14 IPR . . . G 2 -38.729 9.192 14.752 1 24.01 ? O14 IPR 404 C 1 HETATM 3 O O12 IPR . . . G 2 -36.896 10.625 14.013 1 23.26 ? O12 IPR 404 C 1 HETATM 4 O O13 IPR . . . G 2 -37.098 8.365 13.19 1 25.81 ? O13 IPR 404 C 1 HETATM 5 O O10 IPR . . . G 2 -36.416 8.675 15.629 1 27.58 ? O10 IPR 404 C 1 HETATM 6 P P7 IPR . . . G 2 -34.785 8.71 15.535 1 28.7 ? P7 IPR 404 C 1 HETATM 7 O O8 IPR . . . G 2 -34.219 9.82 16.342 1 29.8 ? O8 IPR 404 C 1 HETATM 8 O O9 IPR . . . G 2 -34.294 8.881 14.138 1 29.5 ? O9 IPR 404 C 1 HETATM 9 O O6 IPR . . . G 2 -34.256 7.412 16.21 1 30.39 ? O6 IPR 404 C 1 HETATM 10 C C5 IPR . . . G 2 -33.198 6.67 15.638 1 32.93 ? C5 IPR 404 C 1 HETATM 11 C C4 IPR . . . G 2 -31.933 7.517 15.645 1 33.34 ? C4 IPR 404 C 1 HETATM 12 C C2 IPR . . . G 2 -31.281 7.364 17.041 1 32.66 ? C2 IPR 404 C 1 HETATM 13 C C1 IPR . . . G 2 -31.272 6.036 17.819 1 33.55 ? C1 IPR 404 C 1 HETATM 14 C C3 IPR . . . G 2 -30.572 8.558 17.653 1 32.41 ? C3 IPR 404 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #