data_3DPY # _model_server_result.job_id Q3WCOZpcIMbL_LaXI-zpMA _model_server_result.datetime_utc '2024-11-06 02:48:38' _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 3dpy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1002}' # _entry.id 3DPY # _exptl.entry_id 3DPY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 382.326 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FARNESYL 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 120 _cell.entry_id 3DPY _cell.length_a 171.491 _cell.length_b 171.491 _cell.length_c 69.529 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DPY _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 B OD1 ASP 297 B ASP 297 1_555 D ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? metalc ? metalc2 B OD2 ASP 297 B ASP 297 1_555 D ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc3 B SG CYS 299 B CYS 299 1_555 D ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc4 B NE2 HIS 362 B HIS 362 1_555 D ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? # _chem_comp.formula 'C15 H28 O7 P2' _chem_comp.formula_weight 382.326 _chem_comp.id FPP _chem_comp.mon_nstd_flag . _chem_comp.name 'FARNESYL 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 FPP sing 90 n n C1 C2 FPP sing 91 n n C1 H11 FPP sing 92 n n C1 H12A FPP sing 93 n n O1 PA FPP sing 94 n n C2 C3 FPP doub 95 e n C2 H2 FPP sing 96 n n C3 C4 FPP sing 97 n n C3 C5 FPP sing 98 n n C4 H41 FPP sing 99 n n C4 H42 FPP sing 100 n n C4 H43 FPP sing 101 n n C5 C6 FPP sing 102 n n C5 H51 FPP sing 103 n n C5 H52 FPP sing 104 n n C6 C7 FPP sing 105 n n C6 H61 FPP sing 106 n n C6 H62 FPP sing 107 n n C7 C8 FPP doub 108 e n C7 H7 FPP sing 109 n n C8 C10 FPP sing 110 n n C8 C9 FPP sing 111 n n C10 H101 FPP sing 112 n n C10 H102 FPP sing 113 n n C10 H103 FPP sing 114 n n C9 C11 FPP sing 115 n n C9 H91 FPP sing 116 n n C9 H92 FPP sing 117 n n C11 C12 FPP sing 118 n n C11 H111 FPP sing 119 n n C11 H112 FPP sing 120 n n C12 C13 FPP doub 121 n n C12 H12 FPP sing 122 n n C13 C14 FPP sing 123 n n C13 C15 FPP sing 124 n n C14 H141 FPP sing 125 n n C14 H142 FPP sing 126 n n C14 H143 FPP sing 127 n n C15 H151 FPP sing 128 n n C15 H152 FPP sing 129 n n C15 H153 FPP sing 130 n n PA O1A FPP doub 131 n n PA O2A FPP sing 132 n n PA O3A FPP sing 133 n n O2A HOA2 FPP sing 134 n n O3A PB FPP sing 135 n n PB O1B FPP doub 136 n n PB O2B FPP sing 137 n n PB O3B FPP sing 138 n n O2B HOB2 FPP sing 139 n n O3B HOB3 FPP sing 140 n n # _atom_sites.entry_id 3DPY _atom_sites.fract_transf_matrix[1][1] 0.005831 _atom_sites.fract_transf_matrix[1][2] 0.003367 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006733 _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] 0.014382 _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 D 4 ZN B 1 1001 1001 ZN ZN . E 5 FPP B 1 1002 1 FPP FPP . F 6 ACY B 1 3002 3002 ACY ACY . G 7 HOH A 1 378 1 HOH HOH . G 7 HOH A 2 379 2 HOH HOH . G 7 HOH A 3 380 15 HOH HOH . G 7 HOH A 4 381 21 HOH HOH . G 7 HOH A 5 382 28 HOH HOH . G 7 HOH A 6 383 37 HOH HOH . G 7 HOH A 7 384 39 HOH HOH . G 7 HOH A 8 385 75 HOH HOH . G 7 HOH A 9 386 77 HOH HOH . G 7 HOH A 10 387 79 HOH HOH . G 7 HOH A 11 388 88 HOH HOH . G 7 HOH A 12 389 196 HOH HOH . G 7 HOH A 13 390 201 HOH HOH . G 7 HOH A 14 391 211 HOH HOH . G 7 HOH A 15 392 223 HOH HOH . G 7 HOH A 16 393 237 HOH HOH . G 7 HOH A 17 394 238 HOH HOH . G 7 HOH A 18 395 246 HOH HOH . G 7 HOH A 19 396 250 HOH HOH . G 7 HOH A 20 397 253 HOH HOH . G 7 HOH A 21 398 257 HOH HOH . G 7 HOH A 22 399 258 HOH HOH . G 7 HOH A 23 400 265 HOH HOH . G 7 HOH A 24 401 269 HOH HOH . G 7 HOH A 25 402 390 HOH HOH . G 7 HOH A 26 403 395 HOH HOH . G 7 HOH A 27 404 400 HOH HOH . G 7 HOH A 28 405 414 HOH HOH . G 7 HOH A 29 406 418 HOH HOH . G 7 HOH A 30 407 422 HOH HOH . G 7 HOH A 31 408 440 HOH HOH . G 7 HOH A 32 409 508 HOH HOH . G 7 HOH A 33 410 509 HOH HOH . G 7 HOH A 34 411 512 HOH HOH . H 7 HOH B 1 3003 5 HOH HOH . H 7 HOH B 2 3004 9 HOH HOH . H 7 HOH B 3 3005 47 HOH HOH . H 7 HOH B 4 3006 48 HOH HOH . H 7 HOH B 5 3007 54 HOH HOH . H 7 HOH B 6 3008 61 HOH HOH . H 7 HOH B 7 3009 80 HOH HOH . H 7 HOH B 8 3010 108 HOH HOH . H 7 HOH B 9 3011 145 HOH HOH . H 7 HOH B 10 3012 222 HOH HOH . H 7 HOH B 11 3013 224 HOH HOH . H 7 HOH B 12 3014 226 HOH HOH . H 7 HOH B 13 3015 239 HOH HOH . H 7 HOH B 14 3016 243 HOH HOH . H 7 HOH B 15 3017 244 HOH HOH . H 7 HOH B 16 3018 247 HOH HOH . H 7 HOH B 17 3019 249 HOH HOH . H 7 HOH B 18 3020 256 HOH HOH . H 7 HOH B 19 3021 260 HOH HOH . H 7 HOH B 20 3022 264 HOH HOH . H 7 HOH B 21 3023 281 HOH HOH . H 7 HOH B 22 3024 402 HOH HOH . H 7 HOH B 23 3025 409 HOH HOH . H 7 HOH B 24 3026 510 HOH HOH . H 7 HOH B 25 3027 511 HOH HOH . I 7 HOH C 1 234 234 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 FPP . . . E 5 62.957 24.403 -1.822 1 41.97 ? C1 FPP 1002 B 1 HETATM 2 O O1 FPP . . . E 5 62.805 23.07 -1.331 1 41.87 ? O1 FPP 1002 B 1 HETATM 3 C C2 FPP . . . E 5 64.426 24.769 -1.833 1 42.53 ? C2 FPP 1002 B 1 HETATM 4 C C3 FPP . . . E 5 65.123 24.966 -2.968 1 43.22 ? C3 FPP 1002 B 1 HETATM 5 C C4 FPP . . . E 5 64.466 24.814 -4.312 1 44.22 ? C4 FPP 1002 B 1 HETATM 6 C C5 FPP . . . E 5 66.596 25.332 -2.924 1 41.95 ? C5 FPP 1002 B 1 HETATM 7 C C6 FPP . . . E 5 66.894 26.26 -1.755 1 39.61 ? C6 FPP 1002 B 1 HETATM 8 C C7 FPP . . . E 5 68.337 26.726 -1.76 1 37.25 ? C7 FPP 1002 B 1 HETATM 9 C C8 FPP . . . E 5 69.016 26.771 -0.602 1 35.28 ? C8 FPP 1002 B 1 HETATM 10 C C10 FPP . . . E 5 68.349 26.349 0.674 1 34.97 ? C10 FPP 1002 B 1 HETATM 11 C C9 FPP . . . E 5 70.448 27.249 -0.541 1 33.39 ? C9 FPP 1002 B 1 HETATM 12 C C11 FPP . . . E 5 71.058 27.453 -1.921 1 29.99 ? C11 FPP 1002 B 1 HETATM 13 C C12 FPP . . . E 5 72.437 28.007 -1.685 1 28.43 ? C12 FPP 1002 B 1 HETATM 14 C C13 FPP . . . E 5 73.555 27.556 -2.279 1 28.26 ? C13 FPP 1002 B 1 HETATM 15 C C14 FPP . . . E 5 73.543 26.418 -3.256 1 27.4 ? C14 FPP 1002 B 1 HETATM 16 C C15 FPP . . . E 5 74.86 28.221 -1.946 1 27.91 ? C15 FPP 1002 B 1 HETATM 17 P PA FPP . . . E 5 61.581 22.618 -0.391 1 39.11 ? PA FPP 1002 B 1 HETATM 18 O O1A FPP . . . E 5 60.163 23.087 -0.94 1 40.53 ? O1A FPP 1002 B 1 HETATM 19 O O2A FPP . . . E 5 61.586 20.847 -0.289 1 41.03 ? O2A FPP 1002 B 1 HETATM 20 O O3A FPP . . . E 5 61.977 23.374 0.96 1 38.82 ? O3A FPP 1002 B 1 HETATM 21 P PB FPP . . . E 5 61.058 24.501 1.652 1 37.28 ? PB FPP 1002 B 1 HETATM 22 O O1B FPP . . . E 5 59.575 24.005 1.841 1 35.41 ? O1B FPP 1002 B 1 HETATM 23 O O2B FPP . . . E 5 61.069 25.918 0.572 1 39.22 ? O2B FPP 1002 B 1 HETATM 24 O O3B FPP . . . E 5 61.747 24.906 3.239 1 35.9 ? O3B FPP 1002 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #