data_5Y7C
#
_model_server_result.job_id            TzcoM6l6wW3XYmVBHlOdMQ 
_model_server_result.datetime_utc      '2024-11-19 06:27:25' 
_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          5y7c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    5Y7C 
#
_exptl.entry_id    5Y7C 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              262.158 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DIMETHYLALLYL S-THIOLODIPHOSPHATE' 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         105.23 
_cell.angle_beta          106.6 
_cell.angle_gamma         98.51 
_cell.entry_id            5Y7C 
_cell.length_a            46.465 
_cell.length_b            54.724 
_cell.length_c            77.991 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5Y7C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C,D,G 1 1 
B,E,F,H 2 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 E N N 
#
_chem_comp.formula           'C5 H12 O6 P2 S' 
_chem_comp.formula_weight    262.158 
_chem_comp.id                DST 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DIMETHYLALLYL S-THIOLODIPHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'DMASPP;DMAPP;DMADP;Dimethylallyl pyrophosphate;dimethylallyl diphosphate;isoprenyl pyrophosphate' 
#
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
O4 P1 DST sing 133 n n 
O4 HO4 DST sing 134 n n 
P1 O6 DST sing 135 n n 
P1 O5 DST doub 136 n n 
P1 O2 DST sing 137 n n 
O6 HO6 DST sing 138 n n 
O2 P3 DST sing 139 n n 
P3 O8 DST sing 140 n n 
P3 O7 DST doub 141 n n 
P3 S9 DST sing 142 n n 
O8 HO8 DST sing 143 n n 
S9 C10 DST sing 144 n n 
C10 C11 DST sing 145 n n 
C10 H101 DST sing 146 n n 
C10 H102 DST sing 147 n n 
C11 C12 DST doub 148 n n 
C11 H111 DST sing 149 n n 
C12 C13 DST sing 150 n n 
C12 C14 DST sing 151 n n 
C13 H131 DST sing 152 n n 
C13 H132 DST sing 153 n n 
C13 H133 DST sing 154 n n 
C14 H141 DST sing 155 n n 
C14 H142 DST sing 156 n n 
C14 H143 DST sing 157 n n 
#
_atom_sites.entry_id                     5Y7C 
_atom_sites.fract_transf_matrix[1][1]    0.021522 
_atom_sites.fract_transf_matrix[1][2]    0.003219 
_atom_sites.fract_transf_matrix[1][3]    0.007869 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018477 
_atom_sites.fract_transf_matrix[2][3]    0.00628 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.014131 
_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 DST A 1 401 1 DST DST . 
D 3 8O0 A 1 402 2 8O0 LIG . 
E 2 DST B 1 401 3 DST DST . 
F 3 8O0 B 1 402 4 8O0 LIG . 
G 4 HOH A 1 501 179 HOH HOH . 
G 4 HOH A 2 502 187 HOH HOH . 
G 4 HOH A 3 503 42 HOH HOH . 
G 4 HOH A 4 504 144 HOH HOH . 
G 4 HOH A 5 505 171 HOH HOH . 
G 4 HOH A 6 506 92 HOH HOH . 
G 4 HOH A 7 507 275 HOH HOH . 
G 4 HOH A 8 508 25 HOH HOH . 
G 4 HOH A 9 509 119 HOH HOH . 
G 4 HOH A 10 510 229 HOH HOH . 
G 4 HOH A 11 511 20 HOH HOH . 
G 4 HOH A 12 512 96 HOH HOH . 
G 4 HOH A 13 513 180 HOH HOH . 
G 4 HOH A 14 514 78 HOH HOH . 
G 4 HOH A 15 515 123 HOH HOH . 
G 4 HOH A 16 516 13 HOH HOH . 
G 4 HOH A 17 517 8 HOH HOH . 
G 4 HOH A 18 518 183 HOH HOH . 
G 4 HOH A 19 519 26 HOH HOH . 
G 4 HOH A 20 520 191 HOH HOH . 
G 4 HOH A 21 521 176 HOH HOH . 
G 4 HOH A 22 522 277 HOH HOH . 
G 4 HOH A 23 523 6 HOH HOH . 
G 4 HOH A 24 524 10 HOH HOH . 
G 4 HOH A 25 525 244 HOH HOH . 
G 4 HOH A 26 526 113 HOH HOH . 
G 4 HOH A 27 527 35 HOH HOH . 
G 4 HOH A 28 528 161 HOH HOH . 
G 4 HOH A 29 529 28 HOH HOH . 
G 4 HOH A 30 530 76 HOH HOH . 
G 4 HOH A 31 531 87 HOH HOH . 
G 4 HOH A 32 532 214 HOH HOH . 
G 4 HOH A 33 533 237 HOH HOH . 
G 4 HOH A 34 534 29 HOH HOH . 
G 4 HOH A 35 535 102 HOH HOH . 
G 4 HOH A 36 536 7 HOH HOH . 
G 4 HOH A 37 537 31 HOH HOH . 
G 4 HOH A 38 538 16 HOH HOH . 
G 4 HOH A 39 539 3 HOH HOH . 
G 4 HOH A 40 540 140 HOH HOH . 
G 4 HOH A 41 541 4 HOH HOH . 
G 4 HOH A 42 542 79 HOH HOH . 
G 4 HOH A 43 543 71 HOH HOH . 
G 4 HOH A 44 544 150 HOH HOH . 
G 4 HOH A 45 545 65 HOH HOH . 
G 4 HOH A 46 546 154 HOH HOH . 
G 4 HOH A 47 547 90 HOH HOH . 
G 4 HOH A 48 548 245 HOH HOH . 
G 4 HOH A 49 549 98 HOH HOH . 
G 4 HOH A 50 550 30 HOH HOH . 
G 4 HOH A 51 551 120 HOH HOH . 
G 4 HOH A 52 552 128 HOH HOH . 
G 4 HOH A 53 553 38 HOH HOH . 
G 4 HOH A 54 554 218 HOH HOH . 
G 4 HOH A 55 555 198 HOH HOH . 
G 4 HOH A 56 556 60 HOH HOH . 
G 4 HOH A 57 557 192 HOH HOH . 
G 4 HOH A 58 558 62 HOH HOH . 
G 4 HOH A 59 559 51 HOH HOH . 
G 4 HOH A 60 560 67 HOH HOH . 
G 4 HOH A 61 561 105 HOH HOH . 
G 4 HOH A 62 562 281 HOH HOH . 
G 4 HOH A 63 563 264 HOH HOH . 
G 4 HOH A 64 564 177 HOH HOH . 
G 4 HOH A 65 565 259 HOH HOH . 
G 4 HOH A 66 566 59 HOH HOH . 
G 4 HOH A 67 567 205 HOH HOH . 
G 4 HOH A 68 568 208 HOH HOH . 
G 4 HOH A 69 569 43 HOH HOH . 
G 4 HOH A 70 570 142 HOH HOH . 
G 4 HOH A 71 571 84 HOH HOH . 
G 4 HOH A 72 572 202 HOH HOH . 
G 4 HOH A 73 573 57 HOH HOH . 
G 4 HOH A 74 574 56 HOH HOH . 
G 4 HOH A 75 575 239 HOH HOH . 
G 4 HOH A 76 576 292 HOH HOH . 
G 4 HOH A 77 577 34 HOH HOH . 
G 4 HOH A 78 578 112 HOH HOH . 
G 4 HOH A 79 579 86 HOH HOH . 
G 4 HOH A 80 580 132 HOH HOH . 
G 4 HOH A 81 581 126 HOH HOH . 
G 4 HOH A 82 582 173 HOH HOH . 
G 4 HOH A 83 583 100 HOH HOH . 
G 4 HOH A 84 584 241 HOH HOH . 
G 4 HOH A 85 585 149 HOH HOH . 
G 4 HOH A 86 586 248 HOH HOH . 
G 4 HOH A 87 587 134 HOH HOH . 
G 4 HOH A 88 588 206 HOH HOH . 
G 4 HOH A 89 589 168 HOH HOH . 
G 4 HOH A 90 590 163 HOH HOH . 
G 4 HOH A 91 591 223 HOH HOH . 
G 4 HOH A 92 592 44 HOH HOH . 
G 4 HOH A 93 593 136 HOH HOH . 
G 4 HOH A 94 594 122 HOH HOH . 
G 4 HOH A 95 595 246 HOH HOH . 
G 4 HOH A 96 596 37 HOH HOH . 
G 4 HOH A 97 597 211 HOH HOH . 
G 4 HOH A 98 598 225 HOH HOH . 
G 4 HOH A 99 599 55 HOH HOH . 
G 4 HOH A 100 600 125 HOH HOH . 
G 4 HOH A 101 601 224 HOH HOH . 
G 4 HOH A 102 602 165 HOH HOH . 
G 4 HOH A 103 603 48 HOH HOH . 
G 4 HOH A 104 604 109 HOH HOH . 
G 4 HOH A 105 605 41 HOH HOH . 
G 4 HOH A 106 606 265 HOH HOH . 
G 4 HOH A 107 607 178 HOH HOH . 
G 4 HOH A 108 608 282 HOH HOH . 
G 4 HOH A 109 609 221 HOH HOH . 
G 4 HOH A 110 610 70 HOH HOH . 
G 4 HOH A 111 611 107 HOH HOH . 
G 4 HOH A 112 612 280 HOH HOH . 
G 4 HOH A 113 613 153 HOH HOH . 
G 4 HOH A 114 614 285 HOH HOH . 
G 4 HOH A 115 615 243 HOH HOH . 
G 4 HOH A 116 616 174 HOH HOH . 
G 4 HOH A 117 617 106 HOH HOH . 
G 4 HOH A 118 618 249 HOH HOH . 
G 4 HOH A 119 619 114 HOH HOH . 
G 4 HOH A 120 620 258 HOH HOH . 
G 4 HOH A 121 621 266 HOH HOH . 
G 4 HOH A 122 622 288 HOH HOH . 
G 4 HOH A 123 623 242 HOH HOH . 
G 4 HOH A 124 624 254 HOH HOH . 
H 4 HOH B 1 501 209 HOH HOH . 
H 4 HOH B 2 502 247 HOH HOH . 
H 4 HOH B 3 503 133 HOH HOH . 
H 4 HOH B 4 504 219 HOH HOH . 
H 4 HOH B 5 505 32 HOH HOH . 
H 4 HOH B 6 506 111 HOH HOH . 
H 4 HOH B 7 507 240 HOH HOH . 
H 4 HOH B 8 508 73 HOH HOH . 
H 4 HOH B 9 509 94 HOH HOH . 
H 4 HOH B 10 510 166 HOH HOH . 
H 4 HOH B 11 511 162 HOH HOH . 
H 4 HOH B 12 512 235 HOH HOH . 
H 4 HOH B 13 513 24 HOH HOH . 
H 4 HOH B 14 514 18 HOH HOH . 
H 4 HOH B 15 515 5 HOH HOH . 
H 4 HOH B 16 516 83 HOH HOH . 
H 4 HOH B 17 517 108 HOH HOH . 
H 4 HOH B 18 518 17 HOH HOH . 
H 4 HOH B 19 519 11 HOH HOH . 
H 4 HOH B 20 520 80 HOH HOH . 
H 4 HOH B 21 521 74 HOH HOH . 
H 4 HOH B 22 522 146 HOH HOH . 
H 4 HOH B 23 523 127 HOH HOH . 
H 4 HOH B 24 524 9 HOH HOH . 
H 4 HOH B 25 525 1 HOH HOH . 
H 4 HOH B 26 526 22 HOH HOH . 
H 4 HOH B 27 527 77 HOH HOH . 
H 4 HOH B 28 528 89 HOH HOH . 
H 4 HOH B 29 529 19 HOH HOH . 
H 4 HOH B 30 530 138 HOH HOH . 
H 4 HOH B 31 531 27 HOH HOH . 
H 4 HOH B 32 532 14 HOH HOH . 
H 4 HOH B 33 533 93 HOH HOH . 
H 4 HOH B 34 534 274 HOH HOH . 
H 4 HOH B 35 535 82 HOH HOH . 
H 4 HOH B 36 536 152 HOH HOH . 
H 4 HOH B 37 537 15 HOH HOH . 
H 4 HOH B 38 538 289 HOH HOH . 
H 4 HOH B 39 539 12 HOH HOH . 
H 4 HOH B 40 540 227 HOH HOH . 
H 4 HOH B 41 541 228 HOH HOH . 
H 4 HOH B 42 542 23 HOH HOH . 
H 4 HOH B 43 543 72 HOH HOH . 
H 4 HOH B 44 544 36 HOH HOH . 
H 4 HOH B 45 545 21 HOH HOH . 
H 4 HOH B 46 546 68 HOH HOH . 
H 4 HOH B 47 547 88 HOH HOH . 
H 4 HOH B 48 548 251 HOH HOH . 
H 4 HOH B 49 549 203 HOH HOH . 
H 4 HOH B 50 550 2 HOH HOH . 
H 4 HOH B 51 551 226 HOH HOH . 
H 4 HOH B 52 552 49 HOH HOH . 
H 4 HOH B 53 553 33 HOH HOH . 
H 4 HOH B 54 554 181 HOH HOH . 
H 4 HOH B 55 555 216 HOH HOH . 
H 4 HOH B 56 556 199 HOH HOH . 
H 4 HOH B 57 557 47 HOH HOH . 
H 4 HOH B 58 558 200 HOH HOH . 
H 4 HOH B 59 559 81 HOH HOH . 
H 4 HOH B 60 560 273 HOH HOH . 
H 4 HOH B 61 561 151 HOH HOH . 
H 4 HOH B 62 562 147 HOH HOH . 
H 4 HOH B 63 563 260 HOH HOH . 
H 4 HOH B 64 564 137 HOH HOH . 
H 4 HOH B 65 565 45 HOH HOH . 
H 4 HOH B 66 566 54 HOH HOH . 
H 4 HOH B 67 567 188 HOH HOH . 
H 4 HOH B 68 568 46 HOH HOH . 
H 4 HOH B 69 569 197 HOH HOH . 
H 4 HOH B 70 570 148 HOH HOH . 
H 4 HOH B 71 571 286 HOH HOH . 
H 4 HOH B 72 572 50 HOH HOH . 
H 4 HOH B 73 573 130 HOH HOH . 
H 4 HOH B 74 574 193 HOH HOH . 
H 4 HOH B 75 575 97 HOH HOH . 
H 4 HOH B 76 576 91 HOH HOH . 
H 4 HOH B 77 577 101 HOH HOH . 
H 4 HOH B 78 578 252 HOH HOH . 
H 4 HOH B 79 579 141 HOH HOH . 
H 4 HOH B 80 580 257 HOH HOH . 
H 4 HOH B 81 581 63 HOH HOH . 
H 4 HOH B 82 582 156 HOH HOH . 
H 4 HOH B 83 583 220 HOH HOH . 
H 4 HOH B 84 584 116 HOH HOH . 
H 4 HOH B 85 585 207 HOH HOH . 
H 4 HOH B 86 586 217 HOH HOH . 
H 4 HOH B 87 587 58 HOH HOH . 
H 4 HOH B 88 588 139 HOH HOH . 
H 4 HOH B 89 589 75 HOH HOH . 
H 4 HOH B 90 590 52 HOH HOH . 
H 4 HOH B 91 591 115 HOH HOH . 
H 4 HOH B 92 592 232 HOH HOH . 
H 4 HOH B 93 593 85 HOH HOH . 
H 4 HOH B 94 594 234 HOH HOH . 
H 4 HOH B 95 595 236 HOH HOH . 
H 4 HOH B 96 596 255 HOH HOH . 
H 4 HOH B 97 597 129 HOH HOH . 
H 4 HOH B 98 598 131 HOH HOH . 
H 4 HOH B 99 599 230 HOH HOH . 
H 4 HOH B 100 600 145 HOH HOH . 
H 4 HOH B 101 601 256 HOH HOH . 
H 4 HOH B 102 602 95 HOH HOH . 
H 4 HOH B 103 603 233 HOH HOH . 
H 4 HOH B 104 604 182 HOH HOH . 
H 4 HOH B 105 605 261 HOH HOH . 
H 4 HOH B 106 606 272 HOH HOH . 
H 4 HOH B 107 607 164 HOH HOH . 
H 4 HOH B 108 608 99 HOH HOH . 
H 4 HOH B 109 609 157 HOH HOH . 
H 4 HOH B 110 610 135 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 O O4 DST . . . C 2 8.49 17.215 40.602 1 32.71 -1 O4 DST 401 A 1 
HETATM 2 P P1 DST . . . C 2 7.358 18.188 40.825 1 35.49 ? P1 DST 401 A 1 
HETATM 3 O O6 DST . . . C 2 7.134 18.323 42.315 1 32.27 -1 O6 DST 401 A 1 
HETATM 4 O O5 DST . . . C 2 7.691 19.554 40.27 1 29.96 ? O5 DST 401 A 1 
HETATM 5 O O2 DST . . . C 2 5.965 17.693 40.097 1 30.01 ? O2 DST 401 A 1 
HETATM 6 P P3 DST . . . C 2 5.639 16.198 39.493 1 30.52 ? P3 DST 401 A 1 
HETATM 7 O O8 DST . . . C 2 5.737 15.155 40.563 1 32.23 -1 O8 DST 401 A 1 
HETATM 8 O O7 DST . . . C 2 6.588 15.852 38.369 1 36.55 ? O7 DST 401 A 1 
HETATM 9 S S9 DST . . . C 2 3.668 16.085 38.776 1 51.48 ? S9 DST 401 A 1 
HETATM 10 C C10 DST . . . C 2 3.55 14.961 37.337 1 38.64 ? C10 DST 401 A 1 
HETATM 11 C C11 DST . . . C 2 3.618 13.481 37.713 1 41.26 ? C11 DST 401 A 1 
HETATM 12 C C12 DST . . . C 2 4.518 12.765 36.698 1 47.76 ? C12 DST 401 A 1 
HETATM 13 C C13 DST . . . C 2 3.77 12.527 35.384 1 46.61 ? C13 DST 401 A 1 
HETATM 14 C C14 DST . . . C 2 5.013 11.43 37.252 1 40.55 ? C14 DST 401 A 1 
#
_model_server_stats.io_time_ms              38 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           243 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#