data_2A0W # _model_server_result.job_id dGtNpQMQ_QA5HDI9l0391Q _model_server_result.datetime_utc '2024-11-25 10:59:48' _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 2a0w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":300}' # _entry.id 2A0W # _exptl.entry_id 2A0W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 265.288 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-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 120 _cell.entry_id 2A0W _cell.length_a 141.881 _cell.length_b 141.881 _cell.length_c 166.399 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2A0W _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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 'C12 H17 N4 O3 1' _chem_comp.formula_weight 265.288 _chem_comp.id DIH _chem_comp.mon_nstd_flag . _chem_comp.name 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one _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 O6 C6 DIH doub 83 n n C6 N1 DIH sing 84 n n C6 C5 DIH sing 85 n n N7 C5 DIH sing 86 n y N7 C8 DIH sing 87 n y N1 C2 DIH sing 88 n n C5 C4 DIH doub 89 n y C8 C9 DIH doub 90 n y C2 N3 DIH doub 91 n n C4 C9 DIH sing 92 n y C4 N3 DIH sing 93 n n C9 C10 DIH sing 94 n n C10 N1' DIH sing 95 n n N1' C6' DIH sing 96 n n N1' C2' DIH sing 97 n n C6' C4' DIH sing 98 n n C2' C3' DIH sing 99 n n O5' C5' DIH sing 100 n n C5' C4' DIH sing 101 n n C4' C3' DIH sing 102 n n C3' O3' DIH sing 103 n n O5' H1 DIH sing 104 n n C5' H2 DIH sing 105 n n C5' H3 DIH sing 106 n n C4' H4 DIH sing 107 n n C6' H5 DIH sing 108 n n C6' H6 DIH sing 109 n n C3' H7 DIH sing 110 n n O3' H8 DIH sing 111 n n C2' H9 DIH sing 112 n n C2' H10 DIH sing 113 n n N1' H11 DIH sing 114 n n C10 H12 DIH sing 115 n n C10 H13 DIH sing 116 n n C8 H14 DIH sing 117 n n N7 H15 DIH sing 118 n n N1 H16 DIH sing 119 n n C2 H17 DIH sing 120 n n # _atom_sites.entry_id 2A0W _atom_sites.fract_transf_matrix[1][1] 0.007048 _atom_sites.fract_transf_matrix[1][2] 0.004069 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008139 _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] 0.00601 _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 SO4 A 1 401 401 SO4 SO4 . C 2 SO4 A 1 402 402 SO4 SO4 . D 3 DIH A 1 300 300 DIH DIH . E 4 HOH A 1 501 501 HOH HOH . E 4 HOH A 2 502 502 HOH HOH . E 4 HOH A 3 503 503 HOH HOH . E 4 HOH A 4 504 504 HOH HOH . E 4 HOH A 5 505 505 HOH HOH . E 4 HOH A 6 506 506 HOH HOH . E 4 HOH A 7 507 507 HOH HOH . E 4 HOH A 8 508 508 HOH HOH . E 4 HOH A 9 509 509 HOH HOH . E 4 HOH A 10 510 510 HOH HOH . E 4 HOH A 11 511 511 HOH HOH . E 4 HOH A 12 512 512 HOH HOH . E 4 HOH A 13 513 513 HOH HOH . E 4 HOH A 14 514 514 HOH HOH . E 4 HOH A 15 515 515 HOH HOH . E 4 HOH A 16 516 516 HOH HOH . E 4 HOH A 17 517 517 HOH HOH . E 4 HOH A 18 518 518 HOH HOH . E 4 HOH A 19 519 519 HOH HOH . E 4 HOH A 20 520 520 HOH HOH . E 4 HOH A 21 521 521 HOH HOH . E 4 HOH A 22 522 522 HOH HOH . E 4 HOH A 23 523 523 HOH HOH . E 4 HOH A 24 524 524 HOH HOH . E 4 HOH A 25 525 525 HOH HOH . E 4 HOH A 26 526 526 HOH HOH . E 4 HOH A 27 527 527 HOH HOH . E 4 HOH A 28 528 528 HOH HOH . E 4 HOH A 29 529 529 HOH HOH . E 4 HOH A 30 530 530 HOH HOH . E 4 HOH A 31 531 531 HOH HOH . E 4 HOH A 32 532 532 HOH HOH . E 4 HOH A 33 533 533 HOH HOH . E 4 HOH A 34 534 534 HOH HOH . E 4 HOH A 35 535 535 HOH HOH . E 4 HOH A 36 536 536 HOH HOH . E 4 HOH A 37 537 537 HOH HOH . E 4 HOH A 38 538 538 HOH HOH . E 4 HOH A 39 539 539 HOH HOH . E 4 HOH A 40 540 540 HOH HOH . E 4 HOH A 41 541 541 HOH HOH . E 4 HOH A 42 542 542 HOH HOH . E 4 HOH A 43 543 543 HOH HOH . E 4 HOH A 44 544 544 HOH HOH . E 4 HOH A 45 545 545 HOH HOH . E 4 HOH A 46 546 546 HOH HOH . E 4 HOH A 47 547 547 HOH HOH . E 4 HOH A 48 548 548 HOH HOH . E 4 HOH A 49 549 549 HOH HOH . E 4 HOH A 50 550 550 HOH HOH . E 4 HOH A 51 551 551 HOH HOH . E 4 HOH A 52 552 552 HOH HOH . E 4 HOH A 53 553 553 HOH HOH . E 4 HOH A 54 554 554 HOH HOH . E 4 HOH A 55 555 555 HOH HOH . E 4 HOH A 56 556 556 HOH HOH . E 4 HOH A 57 557 557 HOH HOH . E 4 HOH A 58 558 558 HOH HOH . E 4 HOH A 59 559 559 HOH HOH . E 4 HOH A 60 560 560 HOH HOH . E 4 HOH A 61 561 561 HOH HOH . E 4 HOH A 62 562 562 HOH HOH . E 4 HOH A 63 563 563 HOH HOH . E 4 HOH A 64 564 564 HOH HOH . E 4 HOH A 65 565 565 HOH HOH . E 4 HOH A 66 566 566 HOH HOH . E 4 HOH A 67 567 567 HOH HOH . E 4 HOH A 68 568 568 HOH HOH . E 4 HOH A 69 569 569 HOH HOH . E 4 HOH A 70 570 570 HOH HOH . E 4 HOH A 71 571 571 HOH HOH . E 4 HOH A 72 572 572 HOH HOH . E 4 HOH A 73 573 573 HOH HOH . E 4 HOH A 74 574 574 HOH HOH . E 4 HOH A 75 575 575 HOH HOH . E 4 HOH A 76 576 576 HOH HOH . E 4 HOH A 77 578 578 HOH HOH . E 4 HOH A 78 579 579 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 O O5' DIH . . . D 3 1.637 22.139 23.62 1 58.8 ? O5' DIH 300 A 1 HETATM 2 C C5' DIH . . . D 3 1.813 20.808 23.146 1 54.45 ? C5' DIH 300 A 1 HETATM 3 C C4' DIH . . . D 3 3.09 20.105 22.854 1 53.33 ? C4' DIH 300 A 1 HETATM 4 C C6' DIH . . . D 3 3.907 20.038 24.08 1 51.03 ? C6' DIH 300 A 1 HETATM 5 C C3' DIH . . . D 3 2.907 18.706 22.368 1 51.33 ? C3' DIH 300 A 1 HETATM 6 O O3' DIH . . . D 3 3.735 18.302 21.282 1 51.79 ? O3' DIH 300 A 1 HETATM 7 C C2' DIH . . . D 3 3.051 18.071 23.691 1 51.01 ? C2' DIH 300 A 1 HETATM 8 N N1' DIH . . . D 3 4.216 18.648 24.302 1 50.66 ? N1' DIH 300 A 1 HETATM 9 C C10 DIH . . . D 3 4.431 18.374 25.707 1 45.01 ? C10 DIH 300 A 1 HETATM 10 C C9 DIH . . . D 3 3.512 18.539 26.856 1 42.87 ? C9 DIH 300 A 1 HETATM 11 C C8 DIH . . . D 3 3.38 19.598 27.742 1 39.45 ? C8 DIH 300 A 1 HETATM 12 N N7 DIH . . . D 3 2.461 19.436 28.662 1 40.67 ? N7 DIH 300 A 1 HETATM 13 C C5 DIH . . . D 3 1.916 18.186 28.403 1 39.03 ? C5 DIH 300 A 1 HETATM 14 C C6 DIH . . . D 3 0.853 17.451 29.083 1 39.83 ? C6 DIH 300 A 1 HETATM 15 O O6 DIH . . . D 3 0.211 17.823 30.056 1 40.2 ? O6 DIH 300 A 1 HETATM 16 N N1 DIH . . . D 3 0.566 16.167 28.513 1 40.46 ? N1 DIH 300 A 1 HETATM 17 C C2 DIH . . . D 3 1.238 15.623 27.384 1 39.65 ? C2 DIH 300 A 1 HETATM 18 N N3 DIH . . . D 3 2.243 16.32 26.741 1 39.65 ? N3 DIH 300 A 1 HETATM 19 C C4 DIH . . . D 3 2.547 17.601 27.29 1 40.56 ? C4 DIH 300 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #