data_7LNX # _model_server_result.job_id ZLSjeHYW76H6Vwlk6yi3rw _model_server_result.datetime_utc '2025-02-23 16:32:07' _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 7lnx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 7LNX # _exptl.entry_id 7LNX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 288.172 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2Z)-3-methylhept-2-en-1-yl trihydrogen 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 7LNX _cell.length_a 40.565 _cell.length_b 73.277 _cell.length_c 166.93 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LNX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _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,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 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C8 H18 O7 P2' _chem_comp.formula_weight 288.172 _chem_comp.id Y7D _chem_comp.mon_nstd_flag . _chem_comp.name '(2Z)-3-methylhept-2-en-1-yl trihydrogen 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 C01 C02 Y7D sing 434 n n C02 C03 Y7D sing 435 n n C02 C08 Y7D doub 436 z n C03 C04 Y7D sing 437 n n C04 C05 Y7D sing 438 n n C08 C09 Y7D sing 439 n n C05 C06 Y7D sing 440 n n C09 O10 Y7D sing 441 n n O10 P11 Y7D sing 442 n n O13 P11 Y7D sing 443 n n O13 P32 Y7D sing 444 n n P11 O12 Y7D doub 445 n n P11 O14 Y7D sing 446 n n O40 P32 Y7D doub 447 n n O36 P32 Y7D sing 448 n n P32 O39 Y7D sing 449 n n C09 H1 Y7D sing 450 n n C09 H2 Y7D sing 451 n n O14 H3 Y7D sing 452 n n C01 H4 Y7D sing 453 n n C01 H5 Y7D sing 454 n n C01 H6 Y7D sing 455 n n C03 H7 Y7D sing 456 n n C03 H8 Y7D sing 457 n n C04 H9 Y7D sing 458 n n C04 H10 Y7D sing 459 n n C05 H11 Y7D sing 460 n n C05 H12 Y7D sing 461 n n C06 H13 Y7D sing 462 n n C06 H14 Y7D sing 463 n n C06 H15 Y7D sing 464 n n C08 H16 Y7D sing 465 n n O36 H17 Y7D sing 466 n n O39 H18 Y7D sing 467 n n # _atom_sites.entry_id 7LNX _atom_sites.fract_transf_matrix[1][1] 0.024652 _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] 0.013647 _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] 0.005991 _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 ADP A 1 501 501 ADP ADP . D 3 Y7D A 1 502 502 Y7D Y7D . E 2 ADP B 1 301 301 ADP ADP . F 4 GOL B 1 302 302 GOL GOL . G 5 WOG B 1 303 303 WOG WOG . H 6 HOH A 1 601 601 HOH HOH . H 6 HOH A 2 602 602 HOH HOH . H 6 HOH A 3 603 605 HOH HOH . H 6 HOH A 4 604 603 HOH HOH . H 6 HOH A 5 605 604 HOH HOH . H 6 HOH A 6 606 606 HOH HOH . H 6 HOH A 7 607 607 HOH HOH . H 6 HOH A 8 608 608 HOH HOH . H 6 HOH A 9 609 407 HOH HOH . H 6 HOH A 10 610 610 HOH HOH . H 6 HOH A 11 611 609 HOH HOH . H 6 HOH A 12 612 410 HOH HOH . H 6 HOH A 13 613 611 HOH HOH . H 6 HOH A 14 614 612 HOH HOH . H 6 HOH A 15 615 613 HOH HOH . H 6 HOH A 16 616 614 HOH HOH . H 6 HOH A 17 617 615 HOH HOH . H 6 HOH A 18 618 616 HOH HOH . H 6 HOH A 19 619 617 HOH HOH . H 6 HOH A 20 620 619 HOH HOH . H 6 HOH A 21 621 620 HOH HOH . H 6 HOH A 22 622 618 HOH HOH . H 6 HOH A 23 623 621 HOH HOH . H 6 HOH A 24 624 622 HOH HOH . H 6 HOH A 25 625 624 HOH HOH . H 6 HOH A 26 626 422 HOH HOH . H 6 HOH A 27 627 625 HOH HOH . H 6 HOH A 28 628 623 HOH HOH . H 6 HOH A 29 629 626 HOH HOH . H 6 HOH A 30 630 627 HOH HOH . I 6 HOH B 1 401 404 HOH HOH . I 6 HOH B 2 402 403 HOH HOH . I 6 HOH B 3 403 402 HOH HOH . I 6 HOH B 4 404 405 HOH HOH . I 6 HOH B 5 405 401 HOH HOH . I 6 HOH B 6 406 417 HOH HOH . I 6 HOH B 7 407 406 HOH HOH . I 6 HOH B 8 408 409 HOH HOH . I 6 HOH B 9 409 408 HOH HOH . I 6 HOH B 10 410 412 HOH HOH . I 6 HOH B 11 411 411 HOH HOH . I 6 HOH B 12 412 413 HOH HOH . I 6 HOH B 13 413 414 HOH HOH . I 6 HOH B 14 414 415 HOH HOH . I 6 HOH B 15 415 418 HOH HOH . I 6 HOH B 16 416 420 HOH HOH . I 6 HOH B 17 417 419 HOH HOH . I 6 HOH B 18 418 423 HOH HOH . I 6 HOH B 19 419 421 HOH HOH . I 6 HOH B 20 420 424 HOH HOH . I 6 HOH B 21 421 426 HOH HOH . I 6 HOH B 22 422 425 HOH HOH . I 6 HOH B 23 423 427 HOH HOH . I 6 HOH B 24 424 428 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 C02 Y7D . . . D 3 -3.672 -0.06 31.662 1 51.75 ? C02 Y7D 502 A 1 HETATM 2 C C09 Y7D . . . D 3 -4.895 -1.817 32.925 1 42.23 ? C09 Y7D 502 A 1 HETATM 3 O O14 Y7D . . . D 3 -4.801 -2.919 36.626 1 59.35 ? O14 Y7D 502 A 1 HETATM 4 C C01 Y7D . . . D 3 -4.817 0.014 30.695 1 36.06 ? C01 Y7D 502 A 1 HETATM 5 C C03 Y7D . . . D 3 -2.472 0.833 31.466 1 45.2 ? C03 Y7D 502 A 1 HETATM 6 C C04 Y7D . . . D 3 -2.811 2.263 31.87 1 47.22 ? C04 Y7D 502 A 1 HETATM 7 C C05 Y7D . . . D 3 -2.798 2.449 33.382 1 55.27 ? C05 Y7D 502 A 1 HETATM 8 C C06 Y7D . . . D 3 -2.63 3.911 33.739 1 58.57 ? C06 Y7D 502 A 1 HETATM 9 C C08 Y7D . . . D 3 -3.71 -0.91 32.698 1 52.07 ? C08 Y7D 502 A 1 HETATM 10 O O10 Y7D . . . D 3 -5.13 -1.921 34.326 1 47.55 ? O10 Y7D 502 A 1 HETATM 11 O O12 Y7D . . . D 3 -5.863 -4.3 34.866 1 50.84 ? O12 Y7D 502 A 1 HETATM 12 O O13 Y7D . . . D 3 -3.362 -3.856 34.758 1 46.76 ? O13 Y7D 502 A 1 HETATM 13 O O36 Y7D . . . D 3 -3.596 -6.247 35.598 1 49.2 ? O36 Y7D 502 A 1 HETATM 14 O O39 Y7D . . . D 3 -2.584 -4.54 37.074 1 56.42 ? O39 Y7D 502 A 1 HETATM 15 O O40 Y7D . . . D 3 -1.338 -5.362 35.108 1 39.08 ? O40 Y7D 502 A 1 HETATM 16 P P11 Y7D . . . D 3 -4.805 -3.263 35.156 1 43.02 ? P11 Y7D 502 A 1 HETATM 17 P P32 Y7D . . . D 3 -2.706 -5.027 35.65 1 69.34 ? P32 Y7D 502 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 1026 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 17 #