data_5JD7 # _model_server_result.job_id M18YW0VoDlOXwfSh8wh_pw _model_server_result.datetime_utc '2024-12-26 23:19:27' _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 5jd7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5JD7 # _exptl.entry_id 5JD7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 445.323 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-6-phenyl-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one _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 5JD7 _cell.length_a 46.29 _cell.length_b 46.29 _cell.length_c 102.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JD7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _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 'C18 H16 N5 O7 P' _chem_comp.formula_weight 445.323 _chem_comp.id 6JR _chem_comp.mon_nstd_flag . _chem_comp.name 3-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-6-phenyl-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms PET-cGMP # 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 N12 C22 6JR sing 1 n n N12 C24 6JR sing 2 n y N12 C23 6JR sing 3 n y C15 O02 6JR sing 4 n n C15 C18 6JR sing 5 n n C20 N09 6JR sing 6 n y C20 N10 6JR doub 7 n y C21 C22 6JR sing 8 n n C21 N10 6JR sing 9 n y C21 C19 6JR doub 10 n y C22 O08 6JR doub 11 n n C24 C25 6JR doub 12 n y C26 C28 6JR doub 13 n y C26 C25 6JR sing 14 n n C26 C27 6JR sing 15 n y C28 C30 6JR sing 16 n y P01 O03 6JR sing 17 n n P01 O04 6JR sing 18 n n P01 O06 6JR sing 19 n n P01 O07 6JR doub 20 n n O02 C17 6JR sing 21 n n O03 C14 6JR sing 22 n n O04 C18 6JR sing 23 n n O05 C16 6JR sing 24 n n N09 C17 6JR sing 25 n n N09 C19 6JR sing 26 n y N11 C19 6JR sing 27 n n N11 C23 6JR sing 28 n n N13 C23 6JR doub 29 n y N13 C25 6JR sing 30 n y C14 C16 6JR sing 31 n n C16 C17 6JR sing 32 n n C27 C29 6JR doub 33 n y C29 C31 6JR sing 34 n y C30 C31 6JR doub 35 n y C15 H151 6JR sing 36 n n C20 H201 6JR sing 37 n n C24 H241 6JR sing 38 n n C28 H281 6JR sing 39 n n O05 H051 6JR sing 40 n n O06 H061 6JR sing 41 n n N11 H3 6JR sing 42 n n C14 H141 6JR sing 43 n n C16 H161 6JR sing 44 n n C17 H171 6JR sing 45 n n C18 H181 6JR sing 46 n n C18 H182 6JR sing 47 n n C27 H271 6JR sing 48 n n C29 H291 6JR sing 49 n n C30 H301 6JR sing 50 n n C31 H311 6JR sing 51 n n C15 C14 6JR sing 52 n n # _atom_sites.entry_id 5JD7 _atom_sites.fract_transf_matrix[1][1] 0.021603 _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] 0.021603 _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] 0.00976 _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 6JR A 1 401 1 6JR L02 . C 3 HOH A 1 501 46 HOH HOH . C 3 HOH A 2 502 63 HOH HOH . C 3 HOH A 3 503 66 HOH HOH . C 3 HOH A 4 504 9 HOH HOH . C 3 HOH A 5 505 12 HOH HOH . C 3 HOH A 6 506 75 HOH HOH . C 3 HOH A 7 507 51 HOH HOH . C 3 HOH A 8 508 44 HOH HOH . C 3 HOH A 9 509 16 HOH HOH . C 3 HOH A 10 510 38 HOH HOH . C 3 HOH A 11 511 68 HOH HOH . C 3 HOH A 12 512 49 HOH HOH . C 3 HOH A 13 513 30 HOH HOH . C 3 HOH A 14 514 20 HOH HOH . C 3 HOH A 15 515 56 HOH HOH . C 3 HOH A 16 516 77 HOH HOH . C 3 HOH A 17 517 4 HOH HOH . C 3 HOH A 18 518 24 HOH HOH . C 3 HOH A 19 519 7 HOH HOH . C 3 HOH A 20 520 29 HOH HOH . C 3 HOH A 21 521 15 HOH HOH . C 3 HOH A 22 522 78 HOH HOH . C 3 HOH A 23 523 22 HOH HOH . C 3 HOH A 24 524 36 HOH HOH . C 3 HOH A 25 525 59 HOH HOH . C 3 HOH A 26 526 5 HOH HOH . C 3 HOH A 27 527 40 HOH HOH . C 3 HOH A 28 528 28 HOH HOH . C 3 HOH A 29 529 19 HOH HOH . C 3 HOH A 30 530 2 HOH HOH . C 3 HOH A 31 531 8 HOH HOH . C 3 HOH A 32 532 72 HOH HOH . C 3 HOH A 33 533 67 HOH HOH . C 3 HOH A 34 534 35 HOH HOH . C 3 HOH A 35 535 55 HOH HOH . C 3 HOH A 36 536 3 HOH HOH . C 3 HOH A 37 537 62 HOH HOH . C 3 HOH A 38 538 23 HOH HOH . C 3 HOH A 39 539 1 HOH HOH . C 3 HOH A 40 540 13 HOH HOH . C 3 HOH A 41 541 48 HOH HOH . C 3 HOH A 42 542 18 HOH HOH . C 3 HOH A 43 543 10 HOH HOH . C 3 HOH A 44 544 43 HOH HOH . C 3 HOH A 45 545 33 HOH HOH . C 3 HOH A 46 546 65 HOH HOH . C 3 HOH A 47 547 14 HOH HOH . C 3 HOH A 48 548 31 HOH HOH . C 3 HOH A 49 549 11 HOH HOH . C 3 HOH A 50 550 39 HOH HOH . C 3 HOH A 51 551 71 HOH HOH . C 3 HOH A 52 552 42 HOH HOH . C 3 HOH A 53 553 32 HOH HOH . C 3 HOH A 54 554 64 HOH HOH . C 3 HOH A 55 555 69 HOH HOH . C 3 HOH A 56 556 61 HOH HOH . C 3 HOH A 57 557 54 HOH HOH . C 3 HOH A 58 558 27 HOH HOH . C 3 HOH A 59 559 80 HOH HOH . C 3 HOH A 60 560 26 HOH HOH . C 3 HOH A 61 561 34 HOH HOH . C 3 HOH A 62 562 21 HOH HOH . C 3 HOH A 63 563 52 HOH HOH . C 3 HOH A 64 564 74 HOH HOH . C 3 HOH A 65 565 6 HOH HOH . C 3 HOH A 66 566 17 HOH HOH . C 3 HOH A 67 567 37 HOH HOH . C 3 HOH A 68 568 25 HOH HOH . C 3 HOH A 69 569 57 HOH HOH . C 3 HOH A 70 570 45 HOH HOH . C 3 HOH A 71 571 76 HOH HOH . C 3 HOH A 72 572 70 HOH HOH . C 3 HOH A 73 573 58 HOH HOH . C 3 HOH A 74 574 41 HOH HOH . C 3 HOH A 75 575 73 HOH HOH . C 3 HOH A 76 576 79 HOH HOH . C 3 HOH A 77 577 53 HOH HOH . C 3 HOH A 78 578 50 HOH HOH . C 3 HOH A 79 579 47 HOH HOH . C 3 HOH A 80 580 60 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 N12 6JR . . . B 2 -8.189 5.716 9.729 1 44.04 ? N12 6JR 401 A 1 HETATM 2 C C15 6JR . . . B 2 -3.199 9.034 10.961 1 29.16 ? C15 6JR 401 A 1 HETATM 3 C C20 6JR . . . B 2 -5.295 5.876 13.384 1 34.36 ? C20 6JR 401 A 1 HETATM 4 C C21 6JR . . . B 2 -6.893 5.587 11.925 1 31.04 ? C21 6JR 401 A 1 HETATM 5 C C22 6JR . . . B 2 -8.128 5.252 11.076 1 44.55 ? C22 6JR 401 A 1 HETATM 6 C C24 6JR . . . B 2 -9.133 5.594 8.738 1 36.19 ? C24 6JR 401 A 1 HETATM 7 C C26 6JR . . . B 2 -9.319 6.411 6.256 1 31.25 ? C26 6JR 401 A 1 HETATM 8 C C28 6JR . . . B 2 -8.485 6.855 5.148 1 39.17 ? C28 6JR 401 A 1 HETATM 9 P P01 6JR . . . B 2 -1.967 9.35 8.134 1 19.89 ? P01 6JR 401 A 1 HETATM 10 O O02 6JR . . . B 2 -4.09 8.682 11.785 1 27.93 ? O02 6JR 401 A 1 HETATM 11 O O03 6JR . . . B 2 -1.886 7.868 8.941 1 19.13 ? O03 6JR 401 A 1 HETATM 12 O O04 6JR . . . B 2 -2.183 10.553 9.31 1 18.68 ? O04 6JR 401 A 1 HETATM 13 O O05 6JR . . . B 2 -1.746 6.282 11.205 1 19.59 ? O05 6JR 401 A 1 HETATM 14 O O06 6JR . . . B 2 -3.098 9.381 7.173 1 16.37 ? O06 6JR 401 A 1 HETATM 15 O O07 6JR . . . B 2 -0.61 9.642 7.469 1 15.95 ? O07 6JR 401 A 1 HETATM 16 O O08 6JR . . . B 2 -9.05 4.6 11.527 1 47.1 ? O08 6JR 401 A 1 HETATM 17 N N09 6JR . . . B 2 -4.92 6.496 12.227 1 35.71 ? N09 6JR 401 A 1 HETATM 18 N N10 6JR . . . B 2 -6.503 5.305 13.207 1 30.45 ? N10 6JR 401 A 1 HETATM 19 N N11 6JR . . . B 2 -5.998 6.746 9.994 1 24.23 ? N11 6JR 401 A 1 HETATM 20 N N13 6JR . . . B 2 -7.406 6.799 7.898 1 36.31 ? N13 6JR 401 A 1 HETATM 21 C C14 6JR . . . B 2 -2.989 7.682 9.884 1 22.86 ? C14 6JR 401 A 1 HETATM 22 C C16 6JR . . . B 2 -3.056 6.642 10.666 1 18.77 ? C16 6JR 401 A 1 HETATM 23 C C17 6JR . . . B 2 -3.878 7.101 12.006 1 19.37 ? C17 6JR 401 A 1 HETATM 24 C C18 6JR . . . B 2 -3.411 10.326 10.212 1 20.56 ? C18 6JR 401 A 1 HETATM 25 C C19 6JR . . . B 2 -5.912 6.308 11.362 1 23.46 ? C19 6JR 401 A 1 HETATM 26 C C23 6JR . . . B 2 -7.149 6.453 9.192 1 36.81 ? C23 6JR 401 A 1 HETATM 27 C C25 6JR . . . B 2 -8.645 6.256 7.633 1 41.68 ? C25 6JR 401 A 1 HETATM 28 C C27 6JR . . . B 2 -10.805 6.104 6.069 1 39.13 ? C27 6JR 401 A 1 HETATM 29 C C29 6JR . . . B 2 -11.395 6.276 4.705 1 42.5 ? C29 6JR 401 A 1 HETATM 30 C C30 6JR . . . B 2 -9.085 7.028 3.776 1 46.72 ? C30 6JR 401 A 1 HETATM 31 C C31 6JR . . . B 2 -10.563 6.732 3.573 1 47.71 ? C31 6JR 401 A 1 HETATM 32 H H151 6JR . . . B 2 -2.368 9.134 11.464 1 34.26 ? H151 6JR 401 A 1 HETATM 33 H H201 6JR . . . B 2 -4.767 5.842 14.204 1 40.5 ? H201 6JR 401 A 1 HETATM 34 H H241 6JR . . . B 2 -9.987 5.126 8.805 1 42.69 ? H241 6JR 401 A 1 HETATM 35 H H281 6JR . . . B 2 -7.539 7.045 5.294 1 46.27 ? H281 6JR 401 A 1 HETATM 36 H H051 6JR . . . B 2 -1.23 5.977 10.549 1 22.77 ? H051 6JR 401 A 1 HETATM 37 H H061 6JR . . . B 2 -3.588 8.646 7.268 1 18.91 ? H061 6JR 401 A 1 HETATM 38 H H141 6JR . . . B 2 -3.794 7.65 9.335 1 26.7 ? H141 6JR 401 A 1 HETATM 39 H H161 6JR . . . B 2 -3.485 5.885 10.223 1 21.79 ? H161 6JR 401 A 1 HETATM 40 H H171 6JR . . . B 2 -3.292 6.978 12.777 1 22.51 ? H171 6JR 401 A 1 HETATM 41 H H181 6JR . . . B 2 -3.498 11.064 10.844 1 23.94 ? H181 6JR 401 A 1 HETATM 42 H H182 6JR . . . B 2 -4.216 10.262 9.664 1 23.94 ? H182 6JR 401 A 1 HETATM 43 H H271 6JR . . . B 2 -11.354 5.807 6.82 1 46.22 ? H271 6JR 401 A 1 HETATM 44 H H291 6JR . . . B 2 -12.342 6.089 4.562 1 50.26 ? H291 6JR 401 A 1 HETATM 45 H H301 6JR . . . B 2 -8.533 7.327 3.029 1 55.33 ? H301 6JR 401 A 1 HETATM 46 H H311 6JR . . . B 2 -10.962 6.837 2.689 1 56.52 ? H311 6JR 401 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 46 #