data_1UBW
#
_model_server_result.job_id            7ijleykAsX1GF14poyjzlw 
_model_server_result.datetime_utc      '2024-11-15 08:44:16' 
_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          1ubw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    1UBW 
#
_exptl.entry_id    1UBW 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              314.209 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'GERANYL 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            1UBW 
_cell.length_a            88.7 
_cell.length_b            88.7 
_cell.length_c            274.9 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1UBW 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        98 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 41 2 2' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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 88.7 0 
#
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc2 A OD1 ASP 117 A ASP 117 1_555 C MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc3 A OD2 ASP 121 A ASP 121 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? 
metalc ? metalc4 A OD2 ASP 121 A ASP 121 1_555 C MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? 
metalc ? metalc5 D O3A GPP . A GPP 401 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc6 D O1A GPP . A GPP 401 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? 
metalc ? metalc7 D O2B GPP . A GPP 401 1_555 B MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? 
metalc ? metalc8 D O1A GPP . A GPP 401 1_555 C MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc9 B MG MG . A MG 402 1_555 E O HOH . A HOH 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? 
metalc ? metalc10 C MG MG . A MG 403 1_555 E O HOH . A HOH 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.88 ? 
#
_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                     1UBW 
_atom_sites.fract_transf_matrix[1][1]    0.011274 
_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]    0.011274 
_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]    0.003638 
_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 GPP A 1 401 401 GPP GPP . 
E 4 HOH A 1 404 404 HOH HOH . 
E 4 HOH A 2 406 406 HOH HOH . 
E 4 HOH A 3 407 407 HOH HOH . 
E 4 HOH A 4 408 408 HOH HOH . 
E 4 HOH A 5 409 409 HOH HOH . 
E 4 HOH A 6 410 410 HOH HOH . 
E 4 HOH A 7 411 411 HOH HOH . 
E 4 HOH A 8 412 412 HOH HOH . 
E 4 HOH A 9 413 413 HOH HOH . 
E 4 HOH A 10 414 414 HOH HOH . 
E 4 HOH A 11 417 417 HOH HOH . 
E 4 HOH A 12 418 418 HOH HOH . 
E 4 HOH A 13 420 420 HOH HOH . 
E 4 HOH A 14 421 421 HOH HOH . 
E 4 HOH A 15 422 422 HOH HOH . 
E 4 HOH A 16 423 423 HOH HOH . 
E 4 HOH A 17 426 426 HOH HOH . 
E 4 HOH A 18 429 429 HOH HOH . 
E 4 HOH A 19 430 430 HOH HOH . 
E 4 HOH A 20 431 431 HOH HOH . 
E 4 HOH A 21 432 432 HOH HOH . 
E 4 HOH A 22 434 434 HOH HOH . 
E 4 HOH A 23 435 435 HOH HOH . 
E 4 HOH A 24 438 438 HOH HOH . 
E 4 HOH A 25 439 439 HOH HOH . 
E 4 HOH A 26 441 441 HOH HOH . 
E 4 HOH A 27 442 442 HOH HOH . 
E 4 HOH A 28 443 443 HOH HOH . 
E 4 HOH A 29 448 448 HOH HOH . 
E 4 HOH A 30 449 449 HOH HOH . 
E 4 HOH A 31 450 450 HOH HOH . 
E 4 HOH A 32 452 452 HOH HOH . 
E 4 HOH A 33 453 453 HOH HOH . 
E 4 HOH A 34 454 454 HOH HOH . 
E 4 HOH A 35 455 455 HOH HOH . 
E 4 HOH A 36 456 456 HOH HOH . 
E 4 HOH A 37 457 457 HOH HOH . 
E 4 HOH A 38 459 459 HOH HOH . 
E 4 HOH A 39 460 460 HOH HOH . 
E 4 HOH A 40 461 461 HOH HOH . 
E 4 HOH A 41 462 462 HOH HOH . 
E 4 HOH A 42 463 463 HOH HOH . 
E 4 HOH A 43 464 464 HOH HOH . 
E 4 HOH A 44 466 466 HOH HOH . 
E 4 HOH A 45 467 467 HOH HOH . 
E 4 HOH A 46 468 468 HOH HOH . 
E 4 HOH A 47 469 469 HOH HOH . 
E 4 HOH A 48 472 472 HOH HOH . 
E 4 HOH A 49 473 473 HOH HOH . 
E 4 HOH A 50 474 474 HOH HOH . 
E 4 HOH A 51 475 475 HOH HOH . 
E 4 HOH A 52 476 476 HOH HOH . 
E 4 HOH A 53 478 478 HOH HOH . 
E 4 HOH A 54 479 479 HOH HOH . 
E 4 HOH A 55 480 480 HOH HOH . 
E 4 HOH A 56 481 481 HOH HOH . 
E 4 HOH A 57 482 482 HOH HOH . 
E 4 HOH A 58 483 483 HOH HOH . 
E 4 HOH A 59 484 484 HOH HOH . 
E 4 HOH A 60 485 485 HOH HOH . 
E 4 HOH A 61 486 486 HOH HOH . 
E 4 HOH A 62 487 487 HOH HOH . 
E 4 HOH A 63 488 488 HOH HOH . 
E 4 HOH A 64 489 489 HOH HOH . 
E 4 HOH A 65 490 490 HOH HOH . 
E 4 HOH A 66 491 491 HOH HOH . 
E 4 HOH A 67 492 492 HOH HOH . 
E 4 HOH A 68 493 493 HOH HOH . 
E 4 HOH A 69 494 494 HOH HOH . 
E 4 HOH A 70 495 495 HOH HOH . 
E 4 HOH A 71 496 496 HOH HOH . 
E 4 HOH A 72 497 497 HOH HOH . 
E 4 HOH A 73 498 498 HOH HOH . 
E 4 HOH A 74 499 499 HOH HOH . 
E 4 HOH A 75 500 500 HOH HOH . 
E 4 HOH A 76 501 501 HOH HOH . 
E 4 HOH A 77 502 502 HOH HOH . 
E 4 HOH A 78 503 503 HOH HOH . 
E 4 HOH A 79 504 504 HOH HOH . 
E 4 HOH A 80 505 505 HOH HOH . 
E 4 HOH A 81 506 506 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 3 5.12 30.752 102.497 1 48.48 ? C1 GPP 401 A 1 
HETATM 2 O O1 GPP . . . D 3 5.219 30.985 103.892 1 52.57 ? O1 GPP 401 A 1 
HETATM 3 C C2 GPP . . . D 3 4.125 31.651 101.806 1 48.22 ? C2 GPP 401 A 1 
HETATM 4 C C3 GPP . . . D 3 4.348 32.118 100.567 1 39.97 ? C3 GPP 401 A 1 
HETATM 5 C C4 GPP . . . D 3 5.648 31.678 99.905 1 43.12 ? C4 GPP 401 A 1 
HETATM 6 C C5 GPP . . . D 3 3.288 32.981 99.861 1 26.67 ? C5 GPP 401 A 1 
HETATM 7 C C6 GPP . . . D 3 2.749 34.301 100.405 1 27.06 ? C6 GPP 401 A 1 
HETATM 8 C C7 GPP . . . D 3 1.676 34.85 99.5 1 28.24 ? C7 GPP 401 A 1 
HETATM 9 C C8 GPP . . . D 3 1.225 36.083 99.738 1 35.13 ? C8 GPP 401 A 1 
HETATM 10 C C9 GPP . . . D 3 1.876 36.794 100.92 1 34.45 ? C9 GPP 401 A 1 
HETATM 11 C C10 GPP . . . D 3 0.128 36.582 98.775 1 31.68 ? C10 GPP 401 A 1 
HETATM 12 P PA GPP . . . D 3 4.873 29.997 105.146 1 51.71 ? PA GPP 401 A 1 
HETATM 13 O O1A GPP . . . D 3 3.475 30.526 105.838 1 46.75 ? O1A GPP 401 A 1 
HETATM 14 O O2A GPP . . . D 3 4.905 28.44 104.891 1 33.03 ? O2A GPP 401 A 1 
HETATM 15 O O3A GPP . . . D 3 6.001 30.215 106.201 1 50.91 ? O3A GPP 401 A 1 
HETATM 16 P PB GPP . . . D 3 7.497 29.863 105.94 1 45.2 ? PB GPP 401 A 1 
HETATM 17 O O1B GPP . . . D 3 8.784 29.528 105.032 1 60.19 ? O1B GPP 401 A 1 
HETATM 18 O O2B GPP . . . D 3 7.912 31.325 106.399 1 39.02 ? O2B GPP 401 A 1 
HETATM 19 O O3B GPP . . . D 3 7.866 28.809 107.077 1 56.8 ? O3B GPP 401 A 1 
#
_model_server_stats.io_time_ms              63 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           19 
#