data_5KCY
#
_model_server_result.job_id            cab-XQBoevmkYiTrvailxg 
_model_server_result.datetime_utc      '2024-11-23 19:38:49' 
_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          5kcy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":502}' 
#
_entry.id    5KCY 
#
_exptl.entry_id    5KCY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              330.275 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'GERANYL 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         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            5KCY 
_cell.length_a            96.95 
_cell.length_b            134.91 
_cell.length_c            68.69 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KCY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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' 2_755 -x+2,-y,z -1 0 0 0 -1 0 0 0 1 193.9 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F N N 
#
_chem_comp.formula           'C10 H20 O6 P2 S' 
_chem_comp.formula_weight    330.275 
_chem_comp.id                GST 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'GERANYL S-THIOLODIPHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE' 
#
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
PA O1A GST sing 129 n n 
PA O2A GST doub 130 n n 
PA O3A GST sing 131 n n 
PA O1B GST sing 132 n n 
O1A H1A GST sing 133 n n 
O3A H3A GST sing 134 n n 
O1B PB GST sing 135 n n 
PB O2B GST doub 136 n n 
PB O3B GST sing 137 n n 
PB S1 GST sing 138 n n 
O3B H3B GST sing 139 n n 
S1 C1 GST sing 140 n n 
C1 C2 GST sing 141 n n 
C1 H11 GST sing 142 n n 
C1 H12 GST sing 143 n n 
C2 C3 GST doub 144 e n 
C2 H2 GST sing 145 n n 
C3 C10 GST sing 146 n n 
C3 C4 GST sing 147 n n 
C10 H101 GST sing 148 n n 
C10 H102 GST sing 149 n n 
C10 H103 GST sing 150 n n 
C4 C5 GST sing 151 n n 
C4 H41 GST sing 152 n n 
C4 H42 GST sing 153 n n 
C5 C6 GST sing 154 n n 
C5 H51 GST sing 155 n n 
C5 H52 GST sing 156 n n 
C6 C7 GST doub 157 n n 
C6 H6 GST sing 158 n n 
C7 C9 GST sing 159 n n 
C7 C8 GST sing 160 n n 
C9 H91 GST sing 161 n n 
C9 H92 GST sing 162 n n 
C9 H93 GST sing 163 n n 
C8 H81 GST sing 164 n n 
C8 H82 GST sing 165 n n 
C8 H83 GST sing 166 n n 
#
_atom_sites.entry_id                     5KCY 
_atom_sites.fract_transf_matrix[1][1]    0.010315 
_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]    0.007412 
_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]    0.014558 
_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 XBU A 1 501 1 XBU DBU . 
D 3 GST A 1 502 3 GST GPP . 
E 2 XBU B 1 501 2 XBU DBU . 
F 3 GST B 1 502 4 GST GPP . 
G 4 HOH A 1 601 151 HOH HOH . 
G 4 HOH A 2 602 7 HOH HOH . 
G 4 HOH A 3 603 22 HOH HOH . 
G 4 HOH A 4 604 68 HOH HOH . 
G 4 HOH A 5 605 61 HOH HOH . 
G 4 HOH A 6 606 30 HOH HOH . 
G 4 HOH A 7 607 6 HOH HOH . 
G 4 HOH A 8 608 9 HOH HOH . 
G 4 HOH A 9 609 101 HOH HOH . 
G 4 HOH A 10 610 106 HOH HOH . 
G 4 HOH A 11 611 26 HOH HOH . 
G 4 HOH A 12 612 3 HOH HOH . 
G 4 HOH A 13 613 121 HOH HOH . 
G 4 HOH A 14 614 49 HOH HOH . 
G 4 HOH A 15 615 21 HOH HOH . 
G 4 HOH A 16 616 70 HOH HOH . 
G 4 HOH A 17 617 56 HOH HOH . 
G 4 HOH A 18 618 27 HOH HOH . 
G 4 HOH A 19 619 127 HOH HOH . 
G 4 HOH A 20 620 14 HOH HOH . 
G 4 HOH A 21 621 66 HOH HOH . 
G 4 HOH A 22 622 103 HOH HOH . 
G 4 HOH A 23 623 12 HOH HOH . 
G 4 HOH A 24 624 99 HOH HOH . 
G 4 HOH A 25 625 20 HOH HOH . 
G 4 HOH A 26 626 40 HOH HOH . 
G 4 HOH A 27 627 107 HOH HOH . 
G 4 HOH A 28 628 24 HOH HOH . 
G 4 HOH A 29 629 33 HOH HOH . 
G 4 HOH A 30 630 52 HOH HOH . 
G 4 HOH A 31 631 81 HOH HOH . 
G 4 HOH A 32 632 19 HOH HOH . 
G 4 HOH A 33 633 84 HOH HOH . 
G 4 HOH A 34 634 60 HOH HOH . 
G 4 HOH A 35 635 46 HOH HOH . 
G 4 HOH A 36 636 102 HOH HOH . 
H 4 HOH B 1 601 33 HOH HOH . 
H 4 HOH B 2 602 11 HOH HOH . 
H 4 HOH B 3 603 24 HOH HOH . 
H 4 HOH B 4 604 37 HOH HOH . 
H 4 HOH B 5 605 36 HOH HOH . 
H 4 HOH B 6 606 13 HOH HOH . 
H 4 HOH B 7 607 18 HOH HOH . 
H 4 HOH B 8 608 76 HOH HOH . 
H 4 HOH B 9 609 25 HOH HOH . 
H 4 HOH B 10 610 65 HOH HOH . 
H 4 HOH B 11 611 42 HOH HOH . 
H 4 HOH B 12 612 158 HOH HOH . 
H 4 HOH B 13 613 47 HOH HOH . 
H 4 HOH B 14 614 39 HOH HOH . 
H 4 HOH B 15 615 85 HOH HOH . 
H 4 HOH B 16 616 72 HOH HOH . 
H 4 HOH B 17 617 15 HOH HOH . 
H 4 HOH B 18 618 90 HOH HOH . 
H 4 HOH B 19 619 54 HOH HOH . 
H 4 HOH B 20 620 31 HOH HOH . 
H 4 HOH B 21 621 36 HOH HOH . 
H 4 HOH B 22 622 68 HOH HOH . 
H 4 HOH B 23 623 31 HOH HOH . 
H 4 HOH B 24 624 32 HOH HOH . 
H 4 HOH B 25 625 1 HOH HOH . 
H 4 HOH B 26 626 8 HOH HOH . 
H 4 HOH B 27 627 110 HOH HOH . 
H 4 HOH B 28 628 64 HOH HOH . 
H 4 HOH B 29 629 88 HOH HOH . 
H 4 HOH B 30 630 105 HOH HOH . 
H 4 HOH B 31 631 91 HOH HOH . 
H 4 HOH B 32 632 147 HOH HOH . 
H 4 HOH B 33 633 51 HOH HOH . 
H 4 HOH B 34 634 72 HOH HOH . 
H 4 HOH B 35 635 51 HOH HOH . 
H 4 HOH B 36 636 45 HOH HOH . 
H 4 HOH B 37 637 98 HOH HOH . 
H 4 HOH B 38 638 28 HOH HOH . 
H 4 HOH B 39 639 161 HOH HOH . 
H 4 HOH B 40 640 85 HOH HOH . 
H 4 HOH B 41 641 46 HOH HOH . 
H 4 HOH B 42 642 63 HOH HOH . 
H 4 HOH B 43 643 4 HOH HOH . 
H 4 HOH B 44 644 116 HOH HOH . 
H 4 HOH B 45 645 79 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 PA GST . . . F 3 73.288 14.653 26.433 1 43.86 ? PA GST 502 B 1 
HETATM 2 O O1A GST . . . F 3 72.269 15.418 27.338 1 52.06 ? O1A GST 502 B 1 
HETATM 3 O O2A GST . . . F 3 72.888 14.502 24.891 1 45.18 ? O2A GST 502 B 1 
HETATM 4 O O3A GST . . . F 3 74.615 15.425 26.43 1 46.63 ? O3A GST 502 B 1 
HETATM 5 O O1B GST . . . F 3 72.791 13.227 27.017 1 46.94 ? O1B GST 502 B 1 
HETATM 6 P PB GST . . . F 3 72.95 12.596 28.554 1 47.54 ? PB GST 502 B 1 
HETATM 7 O O2B GST . . . F 3 73.61 11.142 28.323 1 38.11 ? O2B GST 502 B 1 
HETATM 8 O O3B GST . . . F 3 73.817 13.457 29.414 1 49.83 ? O3B GST 502 B 1 
HETATM 9 S S1 GST . . . F 3 71.044 12.236 29.367 1 44.03 ? S1 GST 502 B 1 
HETATM 10 C C1 GST . . . F 3 71.373 11.049 30.78 1 50.54 ? C1 GST 502 B 1 
HETATM 11 C C2 GST . . . F 3 69.886 10.818 31.109 1 50.9 ? C2 GST 502 B 1 
HETATM 12 C C3 GST . . . F 3 69.05 9.6 30.71 1 47.81 ? C3 GST 502 B 1 
HETATM 13 C C10 GST . . . F 3 69.581 8.351 30.064 1 53.71 ? C10 GST 502 B 1 
HETATM 14 C C4 GST . . . F 3 67.578 9.697 30.85 1 51.62 ? C4 GST 502 B 1 
HETATM 15 C C5 GST . . . F 3 67.247 9.567 32.256 1 49.59 ? C5 GST 502 B 1 
HETATM 16 C C6 GST . . . F 3 66.56 10.831 32.728 1 46.65 ? C6 GST 502 B 1 
HETATM 17 C C7 GST . . . F 3 65.182 10.84 33.383 1 41.34 ? C7 GST 502 B 1 
HETATM 18 C C9 GST . . . F 3 64.195 9.687 33.439 1 35.73 ? C9 GST 502 B 1 
HETATM 19 C C8 GST . . . F 3 64.789 12.153 33.96 1 47.95 ? C8 GST 502 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           219 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           19 
#