data_2FY5 # _model_server_result.job_id GssdmoDd-lkQV5O22SaeMw _model_server_result.datetime_utc '2025-03-05 01:32:28' _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 2fy5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2000}' # _entry.id 2FY5 # _exptl.entry_id 2FY5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 823.597 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN 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 2FY5 _cell.length_a 55.27 _cell.length_b 74.03 _cell.length_c 165.83 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2FY5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C24 H40 N7 O17 P3 S' _chem_comp.formula_weight 823.597 _chem_comp.id SOP _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'S-(2-OXOPROPYL)-COENZYME A' # 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 N6 C6 SOP sing 290 n n N6 HN61 SOP sing 291 n n N6 HN62 SOP sing 292 n n C6 N1 SOP sing 293 n y C6 C5 SOP doub 294 n y N1 C2 SOP doub 295 n y C2 N3 SOP sing 296 n y C2 H2 SOP sing 297 n n N3 C4 SOP doub 298 n y C4 C5 SOP sing 299 n y C4 N9 SOP sing 300 n y C5 N7 SOP sing 301 n y N7 C8 SOP doub 302 n y C8 N9 SOP sing 303 n y C8 H8 SOP sing 304 n n N9 C1' SOP sing 305 n n C1' O4' SOP sing 306 n n C1' C2' SOP sing 307 n n C1' H1' SOP sing 308 n n O4' C4' SOP sing 309 n n C2' O2' SOP sing 310 n n C2' C3' SOP sing 311 n n C2' H2' SOP sing 312 n n O2' HO2' SOP sing 313 n n C3' O3' SOP sing 314 n n C3' C4' SOP sing 315 n n C3' H3' SOP sing 316 n n O3' P3 SOP sing 317 n n P3 O32 SOP sing 318 n n P3 O33 SOP sing 319 n n P3 O31 SOP doub 320 n n O32 HO32 SOP sing 321 n n O33 HO33 SOP sing 322 n n C4' C5' SOP sing 323 n n C4' H4' SOP sing 324 n n C5' O5' SOP sing 325 n n C5' "H5'1" SOP sing 326 n n C5' "H5'2" SOP sing 327 n n O5' P1 SOP sing 328 n n P1 O11 SOP sing 329 n n P1 O12 SOP doub 330 n n P1 O6 SOP sing 331 n n O11 HO11 SOP sing 332 n n O6 P2 SOP sing 333 n n P2 O21 SOP sing 334 n n P2 O22 SOP doub 335 n n P2 O7 SOP sing 336 n n O21 HO21 SOP sing 337 n n O7 CP9 SOP sing 338 n n CP9 CP8 SOP sing 339 n n CP9 HP91 SOP sing 340 n n CP9 HP92 SOP sing 341 n n CP8 CPB SOP sing 342 n n CP8 CPA SOP sing 343 n n CP8 CP7 SOP sing 344 n n CPB HPB1 SOP sing 345 n n CPB HPB2 SOP sing 346 n n CPB HPB3 SOP sing 347 n n CPA HPA1 SOP sing 348 n n CPA HPA2 SOP sing 349 n n CPA HPA3 SOP sing 350 n n CP7 OP3 SOP sing 351 n n CP7 CP6 SOP sing 352 n n CP7 HP7 SOP sing 353 n n OP3 HOP3 SOP sing 354 n n CP6 OP2 SOP doub 355 n n CP6 NP2 SOP sing 356 n n NP2 CP5 SOP sing 357 n n NP2 HNP2 SOP sing 358 n n CP5 CP4 SOP sing 359 n n CP5 HP51 SOP sing 360 n n CP5 HP52 SOP sing 361 n n CP4 CP3 SOP sing 362 n n CP4 HP41 SOP sing 363 n n CP4 HP42 SOP sing 364 n n CP3 OP1 SOP doub 365 n n CP3 NP1 SOP sing 366 n n NP1 CP2 SOP sing 367 n n NP1 HNP1 SOP sing 368 n n CP2 CP1 SOP sing 369 n n CP2 HP21 SOP sing 370 n n CP2 HP22 SOP sing 371 n n CP1 S SOP sing 372 n n CP1 HP11 SOP sing 373 n n CP1 HP12 SOP sing 374 n n S CA1 SOP sing 375 n n CA1 CA2 SOP sing 376 n n CA1 HA11 SOP sing 377 n n CA1 HA12 SOP sing 378 n n CA2 OA1 SOP doub 379 n n CA2 CA3 SOP sing 380 n n CA3 HA31 SOP sing 381 n n CA3 HA32 SOP sing 382 n n CA3 HA33 SOP sing 383 n n # _atom_sites.entry_id 2FY5 _atom_sites.fract_transf_matrix[1][1] 0.018093 _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] 0.013508 _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] 0.00603 _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 SOP A 1 2000 2000 SOP SOP . C 3 HOH A 1 700 700 HOH HOH . C 3 HOH A 2 702 702 HOH HOH . C 3 HOH A 3 703 703 HOH HOH . C 3 HOH A 4 704 704 HOH HOH . C 3 HOH A 5 706 706 HOH HOH . C 3 HOH A 6 707 707 HOH HOH . C 3 HOH A 7 708 708 HOH HOH . C 3 HOH A 8 709 709 HOH HOH . C 3 HOH A 9 710 710 HOH HOH . C 3 HOH A 10 711 711 HOH HOH . C 3 HOH A 11 712 712 HOH HOH . C 3 HOH A 12 713 713 HOH HOH . C 3 HOH A 13 714 714 HOH HOH . C 3 HOH A 14 715 715 HOH HOH . C 3 HOH A 15 717 717 HOH HOH . C 3 HOH A 16 718 718 HOH HOH . C 3 HOH A 17 719 719 HOH HOH . C 3 HOH A 18 720 720 HOH HOH . C 3 HOH A 19 721 721 HOH HOH . C 3 HOH A 20 722 722 HOH HOH . C 3 HOH A 21 723 723 HOH HOH . C 3 HOH A 22 724 724 HOH HOH . C 3 HOH A 23 725 725 HOH HOH . C 3 HOH A 24 726 726 HOH HOH . C 3 HOH A 25 727 727 HOH HOH . C 3 HOH A 26 728 728 HOH HOH . C 3 HOH A 27 729 729 HOH HOH . C 3 HOH A 28 730 730 HOH HOH . C 3 HOH A 29 733 733 HOH HOH . C 3 HOH A 30 734 734 HOH HOH . C 3 HOH A 31 735 735 HOH HOH . C 3 HOH A 32 736 736 HOH HOH . C 3 HOH A 33 737 737 HOH HOH . C 3 HOH A 34 739 739 HOH HOH . C 3 HOH A 35 740 740 HOH HOH . C 3 HOH A 36 741 741 HOH HOH . C 3 HOH A 37 742 742 HOH HOH . C 3 HOH A 38 743 743 HOH HOH . C 3 HOH A 39 744 744 HOH HOH . C 3 HOH A 40 745 745 HOH HOH . C 3 HOH A 41 746 746 HOH HOH . C 3 HOH A 42 747 747 HOH HOH . C 3 HOH A 43 748 748 HOH HOH . C 3 HOH A 44 749 749 HOH HOH . C 3 HOH A 45 750 750 HOH HOH . C 3 HOH A 46 751 751 HOH HOH . C 3 HOH A 47 752 752 HOH HOH . C 3 HOH A 48 753 753 HOH HOH . C 3 HOH A 49 754 754 HOH HOH . C 3 HOH A 50 756 756 HOH HOH . C 3 HOH A 51 757 757 HOH HOH . C 3 HOH A 52 758 758 HOH HOH . C 3 HOH A 53 759 759 HOH HOH . C 3 HOH A 54 760 760 HOH HOH . C 3 HOH A 55 761 761 HOH HOH . C 3 HOH A 56 762 762 HOH HOH . C 3 HOH A 57 763 763 HOH HOH . C 3 HOH A 58 764 764 HOH HOH . C 3 HOH A 59 765 765 HOH HOH . C 3 HOH A 60 766 766 HOH HOH . C 3 HOH A 61 767 767 HOH HOH . C 3 HOH A 62 768 768 HOH HOH . C 3 HOH A 63 769 769 HOH HOH . C 3 HOH A 64 770 770 HOH HOH . C 3 HOH A 65 771 771 HOH HOH . C 3 HOH A 66 772 772 HOH HOH . C 3 HOH A 67 773 773 HOH HOH . C 3 HOH A 68 775 775 HOH HOH . C 3 HOH A 69 776 776 HOH HOH . C 3 HOH A 70 777 777 HOH HOH . C 3 HOH A 71 779 779 HOH HOH . C 3 HOH A 72 780 780 HOH HOH . C 3 HOH A 73 781 781 HOH HOH . C 3 HOH A 74 782 782 HOH HOH . C 3 HOH A 75 783 783 HOH HOH . C 3 HOH A 76 784 784 HOH HOH . C 3 HOH A 77 785 785 HOH HOH . C 3 HOH A 78 786 786 HOH HOH . C 3 HOH A 79 787 787 HOH HOH . C 3 HOH A 80 788 788 HOH HOH . C 3 HOH A 81 789 789 HOH HOH . C 3 HOH A 82 790 790 HOH HOH . C 3 HOH A 83 791 791 HOH HOH . C 3 HOH A 84 793 793 HOH HOH . C 3 HOH A 85 794 794 HOH HOH . C 3 HOH A 86 795 795 HOH HOH . C 3 HOH A 87 796 796 HOH HOH . C 3 HOH A 88 797 797 HOH HOH . C 3 HOH A 89 798 798 HOH HOH . C 3 HOH A 90 799 799 HOH HOH . C 3 HOH A 91 800 800 HOH HOH . C 3 HOH A 92 801 801 HOH HOH . C 3 HOH A 93 802 802 HOH HOH . C 3 HOH A 94 803 803 HOH HOH . C 3 HOH A 95 804 804 HOH HOH . C 3 HOH A 96 805 805 HOH HOH . C 3 HOH A 97 806 806 HOH HOH . C 3 HOH A 98 807 807 HOH HOH . C 3 HOH A 99 808 808 HOH HOH . C 3 HOH A 100 809 809 HOH HOH . C 3 HOH A 101 810 810 HOH HOH . C 3 HOH A 102 811 811 HOH HOH . C 3 HOH A 103 812 812 HOH HOH . C 3 HOH A 104 813 813 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 N N6 SOP . . . B 2 27.821 -6.2 79.272 1 44.15 ? N6 SOP 2000 A 1 HETATM 2 C C6 SOP . . . B 2 28.405 -6.066 78.092 1 45.45 ? C6 SOP 2000 A 1 HETATM 3 N N1 SOP . . . B 2 29.754 -5.9 77.999 1 45.57 ? N1 SOP 2000 A 1 HETATM 4 C C2 SOP . . . B 2 30.366 -5.759 76.817 1 44.78 ? C2 SOP 2000 A 1 HETATM 5 N N3 SOP . . . B 2 29.638 -5.789 75.672 1 45.28 ? N3 SOP 2000 A 1 HETATM 6 C C4 SOP . . . B 2 28.292 -5.947 75.694 1 47.31 ? C4 SOP 2000 A 1 HETATM 7 C C5 SOP . . . B 2 27.638 -6.099 76.924 1 45.71 ? C5 SOP 2000 A 1 HETATM 8 N N7 SOP . . . B 2 26.352 -6.243 76.686 1 47.65 ? N7 SOP 2000 A 1 HETATM 9 C C8 SOP . . . B 2 26.178 -6.19 75.361 1 49.56 ? C8 SOP 2000 A 1 HETATM 10 N N9 SOP . . . B 2 27.344 -6.016 74.738 1 49.83 ? N9 SOP 2000 A 1 HETATM 11 C C1' SOP . . . B 2 27.548 -5.9 73.264 1 54.48 ? C1' SOP 2000 A 1 HETATM 12 O O4' SOP . . . B 2 26.904 -4.736 72.695 1 57.54 ? O4' SOP 2000 A 1 HETATM 13 C C2' SOP . . . B 2 27.003 -7.048 72.388 1 57.55 ? C2' SOP 2000 A 1 HETATM 14 O O2' SOP . . . B 2 27.838 -8.205 72.469 1 58.13 ? O2' SOP 2000 A 1 HETATM 15 C C3' SOP . . . B 2 27.021 -6.399 71.015 1 60.25 ? C3' SOP 2000 A 1 HETATM 16 O O3' SOP . . . B 2 28.32 -6.446 70.424 1 64.7 ? O3' SOP 2000 A 1 HETATM 17 P P3 SOP . . . B 2 28.459 -6.262 68.829 1 68.46 ? P3 SOP 2000 A 1 HETATM 18 O O32 SOP . . . B 2 28.452 -4.67 68.516 1 67.03 ? O32 SOP 2000 A 1 HETATM 19 O O33 SOP . . . B 2 29.906 -6.853 68.459 1 69.65 ? O33 SOP 2000 A 1 HETATM 20 O O31 SOP . . . B 2 27.36 -6.977 68.116 1 67.99 ? O31 SOP 2000 A 1 HETATM 21 C C4' SOP . . . B 2 26.557 -4.982 71.299 1 58.52 ? C4' SOP 2000 A 1 HETATM 22 C C5' SOP . . . B 2 25.038 -4.919 71.12 1 56.74 ? C5' SOP 2000 A 1 HETATM 23 O O5' SOP . . . B 2 24.53 -3.861 71.915 1 55.32 ? O5' SOP 2000 A 1 HETATM 24 P P1 SOP . . . B 2 23.17 -4.017 72.752 1 51.71 ? P1 SOP 2000 A 1 HETATM 25 O O11 SOP . . . B 2 23.144 -2.887 73.708 1 54.36 ? O11 SOP 2000 A 1 HETATM 26 O O12 SOP . . . B 2 23.132 -5.361 73.355 1 51.61 ? O12 SOP 2000 A 1 HETATM 27 O O6 SOP . . . B 2 22.07 -3.778 71.604 1 52.21 ? O6 SOP 2000 A 1 HETATM 28 P P2 SOP . . . B 2 21.12 -4.91 70.997 1 49.23 ? P2 SOP 2000 A 1 HETATM 29 O O21 SOP . . . B 2 21.078 -6.104 71.838 1 50.56 ? O21 SOP 2000 A 1 HETATM 30 O O22 SOP . . . B 2 21.606 -5.081 69.61 1 52.17 ? O22 SOP 2000 A 1 HETATM 31 O O7 SOP . . . B 2 19.709 -4.186 71.027 1 47.42 ? O7 SOP 2000 A 1 HETATM 32 C CP9 SOP . . . B 2 18.775 -4.401 72.093 1 41.72 ? CP9 SOP 2000 A 1 HETATM 33 C CP8 SOP . . . B 2 17.361 -4.318 71.501 1 41.69 ? CP8 SOP 2000 A 1 HETATM 34 C CPB SOP . . . B 2 17.173 -2.904 70.9 1 40.06 ? CPB SOP 2000 A 1 HETATM 35 C CPA SOP . . . B 2 16.328 -4.539 72.616 1 41.46 ? CPA SOP 2000 A 1 HETATM 36 C CP7 SOP . . . B 2 17.277 -5.424 70.408 1 41.58 ? CP7 SOP 2000 A 1 HETATM 37 O OP3 SOP . . . B 2 17.247 -6.736 70.986 1 42.16 ? OP3 SOP 2000 A 1 HETATM 38 C CP6 SOP . . . B 2 16.059 -5.28 69.499 1 42.8 ? CP6 SOP 2000 A 1 HETATM 39 O OP2 SOP . . . B 2 14.994 -5.879 69.726 1 42.54 ? OP2 SOP 2000 A 1 HETATM 40 N NP2 SOP . . . B 2 16.303 -4.448 68.469 1 42.31 ? NP2 SOP 2000 A 1 HETATM 41 C CP5 SOP . . . B 2 15.293 -4.143 67.457 1 41.92 ? CP5 SOP 2000 A 1 HETATM 42 C CP4 SOP . . . B 2 14.658 -2.806 67.822 1 41.51 ? CP4 SOP 2000 A 1 HETATM 43 C CP3 SOP . . . B 2 13.557 -2.482 66.821 1 41.32 ? CP3 SOP 2000 A 1 HETATM 44 O OP1 SOP . . . B 2 12.565 -3.217 66.751 1 40.8 ? OP1 SOP 2000 A 1 HETATM 45 N NP1 SOP . . . B 2 13.737 -1.391 66.074 1 42.45 ? NP1 SOP 2000 A 1 HETATM 46 C CP2 SOP . . . B 2 12.741 -0.949 65.063 1 42.89 ? CP2 SOP 2000 A 1 HETATM 47 C CP1 SOP . . . B 2 11.454 -0.49 65.787 1 43.99 ? CP1 SOP 2000 A 1 HETATM 48 S S SOP . . . B 2 10.141 0.048 64.671 1 43.6 ? S SOP 2000 A 1 HETATM 49 C CA1 SOP . . . B 2 10.262 1.787 64.401 1 50.07 ? CA1 SOP 2000 A 1 HETATM 50 C CA2 SOP . . . B 2 10.535 2.304 63.011 1 53.34 ? CA2 SOP 2000 A 1 HETATM 51 O OA1 SOP . . . B 2 11.666 2.601 62.688 1 56.98 ? OA1 SOP 2000 A 1 HETATM 52 C CA3 SOP . . . B 2 9.283 2.383 62.172 1 53.68 ? CA3 SOP 2000 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 52 #