data_2A0Y # _model_server_result.job_id 5_DMmCYV8QL-ZkkuiCt6kg _model_server_result.datetime_utc '2024-11-25 10:28:15' _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 2a0y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":300}' # _entry.id 2A0Y # _exptl.entry_id 2A0Y _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 2A0Y _cell.length_a 142.467 _cell.length_b 142.467 _cell.length_c 166.029 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2A0Y _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 2A0Y _atom_sites.fract_transf_matrix[1][1] 0.007019 _atom_sites.fract_transf_matrix[1][2] 0.004053 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008105 _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] 0.006023 _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 . # 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 1.312 21.854 23.842 1 57.87 ? O5' DIH 300 A 1 HETATM 2 C C5' DIH . . . D 3 1.59 20.566 23.309 1 56.27 ? C5' DIH 300 A 1 HETATM 3 C C4' DIH . . . D 3 2.913 19.986 22.965 1 55.4 ? C4' DIH 300 A 1 HETATM 4 C C6' DIH . . . D 3 3.764 19.949 24.169 1 53.44 ? C6' DIH 300 A 1 HETATM 5 C C3' DIH . . . D 3 2.82 18.596 22.428 1 55.15 ? C3' DIH 300 A 1 HETATM 6 O O3' DIH . . . D 3 3.611 18.293 21.281 1 58.05 ? O3' DIH 300 A 1 HETATM 7 C C2' DIH . . . D 3 3.078 17.918 23.716 1 53.83 ? C2' DIH 300 A 1 HETATM 8 N N1' DIH . . . D 3 4.192 18.58 24.357 1 52.11 ? N1' DIH 300 A 1 HETATM 9 C C10 DIH . . . D 3 4.402 18.279 25.762 1 46.29 ? C10 DIH 300 A 1 HETATM 10 C C9 DIH . . . D 3 3.448 18.44 26.889 1 44.12 ? C9 DIH 300 A 1 HETATM 11 C C8 DIH . . . D 3 3.265 19.52 27.731 1 42.47 ? C8 DIH 300 A 1 HETATM 12 N N7 DIH . . . D 3 2.327 19.361 28.633 1 45.22 ? N7 DIH 300 A 1 HETATM 13 C C5 DIH . . . D 3 1.827 18.091 28.414 1 41.63 ? C5 DIH 300 A 1 HETATM 14 C C6 DIH . . . D 3 0.763 17.363 29.095 1 41.77 ? C6 DIH 300 A 1 HETATM 15 O O6 DIH . . . D 3 0.091 17.762 30.04 1 40.68 ? O6 DIH 300 A 1 HETATM 16 N N1 DIH . . . D 3 0.525 16.052 28.579 1 42.19 ? N1 DIH 300 A 1 HETATM 17 C C2 DIH . . . D 3 1.235 15.478 27.489 1 40.87 ? C2 DIH 300 A 1 HETATM 18 N N3 DIH . . . D 3 2.239 16.17 26.837 1 42.16 ? N3 DIH 300 A 1 HETATM 19 C C4 DIH . . . D 3 2.498 17.485 27.337 1 43.28 ? C4 DIH 300 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 19 #