data_1UBY
#
_model_server_result.job_id            lG2kt3eF9gLCgI8wxsPs-g 
_model_server_result.datetime_utc      '2024-11-25 08:19:22' 
_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          1uby 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    1UBY 
#
_exptl.entry_id    1UBY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              246.092 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DIMETHYLALLYL 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            1UBY 
_cell.length_a            88.3 
_cell.length_b            88.3 
_cell.length_c            274.7 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1UBY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        98 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 41 2 2' 
#
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,PQS dimeric 2 author_and_software_defined_assembly 1 
PQS dimeric 2 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,B,C,D,E 1 1,2 
A,B,C,D,E 2 1,3 
#
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_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 88.3 0 
3 'crystal symmetry operation' 5_555 -x+1/2,y,-z+3/4 -1 0 0 0 1 0 0 0 -1 44.15 0 206.025 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_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 OD2 ASP 117 A ASP 117 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? 
metalc ? metalc2 A OD1 ASP 117 A ASP 117 1_555 C MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc3 A OD2 ASP 121 A ASP 121 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc4 A OD2 ASP 121 A ASP 121 1_555 C MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? 
metalc ? metalc5 D O3A DMA . A DMA 401 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? 
metalc ? metalc6 D O1A DMA . A DMA 401 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? 
metalc ? metalc7 D O1A DMA . A DMA 401 1_555 C MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? 
#
_chem_comp.formula           'C5 H12 O7 P2' 
_chem_comp.formula_weight    246.092 
_chem_comp.id                DMA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DIMETHYLALLYL 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 DMA sing 83 n n 
C1 C2 DMA sing 84 n n 
C1 H11 DMA sing 85 n n 
C1 H12 DMA sing 86 n n 
O1 PA DMA sing 87 n n 
C2 C3 DMA doub 88 n n 
C2 H2 DMA sing 89 n n 
C3 C4 DMA sing 90 n n 
C3 C5 DMA sing 91 n n 
C4 H41 DMA sing 92 n n 
C4 H42 DMA sing 93 n n 
C4 H43 DMA sing 94 n n 
C5 H51 DMA sing 95 n n 
C5 H52 DMA sing 96 n n 
C5 H53 DMA sing 97 n n 
PA O1A DMA doub 98 n n 
PA O2A DMA sing 99 n n 
PA O3A DMA sing 100 n n 
O2A HOA2 DMA sing 101 n n 
O3A PB DMA sing 102 n n 
PB O1B DMA doub 103 n n 
PB O2B DMA sing 104 n n 
PB O3B DMA sing 105 n n 
O2B HOB2 DMA sing 106 n n 
O3B HOB3 DMA sing 107 n n 
#
_atom_sites.entry_id                     1UBY 
_atom_sites.fract_transf_matrix[1][1]    0.011325 
_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]    0.011325 
_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]    0.00364 
_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 1 402 402 MG MG . 
C 2 MG A 1 403 403 MG MG . 
D 3 DMA A 1 401 401 DMA DMA . 
E 4 HOH A 1 405 405 HOH HOH . 
E 4 HOH A 2 406 406 HOH HOH . 
E 4 HOH A 3 408 408 HOH HOH . 
E 4 HOH A 4 409 409 HOH HOH . 
E 4 HOH A 5 411 411 HOH HOH . 
E 4 HOH A 6 412 412 HOH HOH . 
E 4 HOH A 7 413 413 HOH HOH . 
E 4 HOH A 8 414 414 HOH HOH . 
E 4 HOH A 9 415 415 HOH HOH . 
E 4 HOH A 10 417 417 HOH HOH . 
E 4 HOH A 11 418 418 HOH HOH . 
E 4 HOH A 12 419 419 HOH HOH . 
E 4 HOH A 13 421 421 HOH HOH . 
E 4 HOH A 14 422 422 HOH HOH . 
E 4 HOH A 15 423 423 HOH HOH . 
E 4 HOH A 16 424 424 HOH HOH . 
E 4 HOH A 17 426 426 HOH HOH . 
E 4 HOH A 18 427 427 HOH HOH . 
E 4 HOH A 19 428 428 HOH HOH . 
E 4 HOH A 20 429 429 HOH HOH . 
E 4 HOH A 21 431 431 HOH HOH . 
E 4 HOH A 22 433 433 HOH HOH . 
E 4 HOH A 23 434 434 HOH HOH . 
E 4 HOH A 24 435 435 HOH HOH . 
E 4 HOH A 25 436 436 HOH HOH . 
E 4 HOH A 26 437 437 HOH HOH . 
E 4 HOH A 27 438 438 HOH HOH . 
E 4 HOH A 28 439 439 HOH HOH . 
E 4 HOH A 29 440 440 HOH HOH . 
E 4 HOH A 30 441 441 HOH HOH . 
E 4 HOH A 31 442 442 HOH HOH . 
E 4 HOH A 32 446 446 HOH HOH . 
E 4 HOH A 33 447 447 HOH HOH . 
E 4 HOH A 34 449 449 HOH HOH . 
E 4 HOH A 35 450 450 HOH HOH . 
E 4 HOH A 36 451 451 HOH HOH . 
E 4 HOH A 37 452 452 HOH HOH . 
E 4 HOH A 38 453 453 HOH HOH . 
E 4 HOH A 39 454 454 HOH HOH . 
E 4 HOH A 40 455 455 HOH HOH . 
E 4 HOH A 41 456 456 HOH HOH . 
E 4 HOH A 42 457 457 HOH HOH . 
E 4 HOH A 43 458 458 HOH HOH . 
E 4 HOH A 44 460 460 HOH HOH . 
E 4 HOH A 45 461 461 HOH HOH . 
E 4 HOH A 46 462 462 HOH HOH . 
E 4 HOH A 47 464 464 HOH HOH . 
E 4 HOH A 48 465 465 HOH HOH . 
E 4 HOH A 49 466 466 HOH HOH . 
E 4 HOH A 50 467 467 HOH HOH . 
E 4 HOH A 51 470 470 HOH HOH . 
E 4 HOH A 52 471 471 HOH HOH . 
E 4 HOH A 53 472 472 HOH HOH . 
E 4 HOH A 54 476 476 HOH HOH . 
E 4 HOH A 55 477 477 HOH HOH . 
E 4 HOH A 56 478 478 HOH HOH . 
E 4 HOH A 57 480 480 HOH HOH . 
E 4 HOH A 58 481 481 HOH HOH . 
E 4 HOH A 59 483 483 HOH HOH . 
E 4 HOH A 60 484 484 HOH HOH . 
E 4 HOH A 61 485 485 HOH HOH . 
E 4 HOH A 62 486 486 HOH HOH . 
E 4 HOH A 63 487 487 HOH HOH . 
E 4 HOH A 64 488 488 HOH HOH . 
E 4 HOH A 65 489 489 HOH HOH . 
E 4 HOH A 66 490 490 HOH HOH . 
E 4 HOH A 67 491 491 HOH HOH . 
E 4 HOH A 68 492 492 HOH HOH . 
E 4 HOH A 69 493 493 HOH HOH . 
E 4 HOH A 70 494 494 HOH HOH . 
E 4 HOH A 71 495 495 HOH HOH . 
E 4 HOH A 72 496 496 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 DMA . . . D 3 4.737 31.264 103.084 1 66.03 ? C1 DMA 401 A 1 
HETATM 2 O O1 DMA . . . D 3 4.703 29.962 103.681 1 67.12 ? O1 DMA 401 A 1 
HETATM 3 C C2 DMA . . . D 3 5.398 31.119 101.745 1 65.65 ? C2 DMA 401 A 1 
HETATM 4 C C3 DMA . . . D 3 4.905 31.586 100.602 1 61.96 ? C3 DMA 401 A 1 
HETATM 5 C C4 DMA . . . D 3 3.637 32.376 100.596 1 48.24 ? C4 DMA 401 A 1 
HETATM 6 C C5 DMA . . . D 3 5.76 31.292 99.334 1 63.61 ? C5 DMA 401 A 1 
HETATM 7 P PA DMA . . . D 3 4.575 29.715 105.278 1 73.98 ? PA DMA 401 A 1 
HETATM 8 O O1A DMA . . . D 3 3.463 30.681 105.909 1 59.6 ? O1A DMA 401 A 1 
HETATM 9 O O2A DMA . . . D 3 4.096 28.176 105.341 1 78.92 ? O2A DMA 401 A 1 
HETATM 10 O O3A DMA . . . D 3 5.906 30.016 106.132 1 79.53 ? O3A DMA 401 A 1 
HETATM 11 P PB DMA . . . D 3 7.387 29.726 105.702 1 79.45 ? PB DMA 401 A 1 
HETATM 12 O O1B DMA . . . D 3 8.229 28.854 106.747 1 85.73 ? O1B DMA 401 A 1 
HETATM 13 O O2B DMA . . . D 3 8.081 31.146 105.413 1 82.81 ? O2B DMA 401 A 1 
HETATM 14 O O3B DMA . . . D 3 7.216 28.875 104.364 1 91.39 ? O3B DMA 401 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#