data_8DL3 # _model_server_result.job_id xZEf38F6WYFESjh35cjIdw _model_server_result.datetime_utc '2024-11-26 08:56:36' _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 8dl3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 8DL3 # _exptl.entry_id 8DL3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 277.279 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.33 _cell.angle_gamma 90 _cell.entry_id 8DL3 _cell.length_a 42.726 _cell.length_b 136.759 _cell.length_c 52.606 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DL3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C12 H15 N5 O3' _chem_comp.formula_weight 277.279 _chem_comp.id QEI _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms queuine # 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 C1 C2 QEI sing 277 n n C1 C3 QEI sing 278 n n C1 N1 QEI sing 279 n n C2 C4 QEI sing 280 n n C2 O1 QEI sing 281 n n C3 C5 QEI doub 282 n n C4 C5 QEI sing 283 n n C4 O2 QEI sing 284 n n C6 N1 QEI sing 285 n n C6 C7 QEI sing 286 n n C9 C10 QEI doub 287 n y C9 C11 QEI sing 288 n n C9 C7 QEI sing 289 n y C10 N2 QEI sing 290 n y C10 N3 QEI sing 291 n n C11 N4 QEI sing 292 n n C11 O3 QEI doub 293 n n C7 C8 QEI doub 294 n y C8 N2 QEI sing 295 n y N3 C12 QEI doub 296 n n C12 N5 QEI sing 297 n n C12 N4 QEI sing 298 n n C1 H1 QEI sing 299 n n C2 H2 QEI sing 300 n n C3 H3 QEI sing 301 n n C4 H4 QEI sing 302 n n C5 H5 QEI sing 303 n n C6 H6 QEI sing 304 n n C6 H6A QEI sing 305 n n O1 HO1 QEI sing 306 n n O2 HO2 QEI sing 307 n n N1 HN1 QEI sing 308 n n C8 H8 QEI sing 309 n n N2 HN2 QEI sing 310 n n N5 HN5 QEI sing 311 n n N5 HN5A QEI sing 312 n n N4 HN4 QEI sing 313 n n # _atom_sites.entry_id 8DL3 _atom_sites.fract_transf_matrix[1][1] 0.023405 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000137 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007312 _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] 0.01901 _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 QEI A 1 401 401 QEI QEI . D 2 QEI B 1 401 401 QEI QEI . E 3 HOH A 1 501 185 HOH HOH . E 3 HOH A 2 502 85 HOH HOH . E 3 HOH A 3 503 165 HOH HOH . E 3 HOH A 4 504 107 HOH HOH . E 3 HOH A 5 505 48 HOH HOH . E 3 HOH A 6 506 87 HOH HOH . E 3 HOH A 7 507 137 HOH HOH . E 3 HOH A 8 508 106 HOH HOH . E 3 HOH A 9 509 42 HOH HOH . E 3 HOH A 10 510 182 HOH HOH . E 3 HOH A 11 511 22 HOH HOH . E 3 HOH A 12 512 118 HOH HOH . E 3 HOH A 13 513 46 HOH HOH . E 3 HOH A 14 514 68 HOH HOH . E 3 HOH A 15 515 65 HOH HOH . E 3 HOH A 16 516 29 HOH HOH . E 3 HOH A 17 517 83 HOH HOH . E 3 HOH A 18 518 55 HOH HOH . E 3 HOH A 19 519 134 HOH HOH . E 3 HOH A 20 520 58 HOH HOH . E 3 HOH A 21 521 57 HOH HOH . E 3 HOH A 22 522 14 HOH HOH . E 3 HOH A 23 523 49 HOH HOH . E 3 HOH A 24 524 140 HOH HOH . E 3 HOH A 25 525 145 HOH HOH . E 3 HOH A 26 526 6 HOH HOH . E 3 HOH A 27 527 23 HOH HOH . E 3 HOH A 28 528 7 HOH HOH . E 3 HOH A 29 529 19 HOH HOH . E 3 HOH A 30 530 97 HOH HOH . E 3 HOH A 31 531 131 HOH HOH . E 3 HOH A 32 532 61 HOH HOH . E 3 HOH A 33 533 51 HOH HOH . E 3 HOH A 34 534 40 HOH HOH . E 3 HOH A 35 535 32 HOH HOH . E 3 HOH A 36 536 52 HOH HOH . E 3 HOH A 37 537 95 HOH HOH . E 3 HOH A 38 538 187 HOH HOH . E 3 HOH A 39 539 10 HOH HOH . E 3 HOH A 40 540 25 HOH HOH . E 3 HOH A 41 541 111 HOH HOH . E 3 HOH A 42 542 93 HOH HOH . E 3 HOH A 43 543 72 HOH HOH . E 3 HOH A 44 544 128 HOH HOH . E 3 HOH A 45 545 124 HOH HOH . E 3 HOH A 46 546 76 HOH HOH . E 3 HOH A 47 547 84 HOH HOH . E 3 HOH A 48 548 1 HOH HOH . E 3 HOH A 49 549 126 HOH HOH . E 3 HOH A 50 550 24 HOH HOH . E 3 HOH A 51 551 66 HOH HOH . E 3 HOH A 52 552 114 HOH HOH . E 3 HOH A 53 553 125 HOH HOH . E 3 HOH A 54 554 142 HOH HOH . E 3 HOH A 55 555 59 HOH HOH . E 3 HOH A 56 556 186 HOH HOH . E 3 HOH A 57 557 176 HOH HOH . E 3 HOH A 58 558 91 HOH HOH . E 3 HOH A 59 559 34 HOH HOH . E 3 HOH A 60 560 82 HOH HOH . E 3 HOH A 61 561 108 HOH HOH . E 3 HOH A 62 562 71 HOH HOH . E 3 HOH A 63 563 45 HOH HOH . E 3 HOH A 64 564 116 HOH HOH . E 3 HOH A 65 565 27 HOH HOH . E 3 HOH A 66 566 70 HOH HOH . E 3 HOH A 67 567 168 HOH HOH . E 3 HOH A 68 568 150 HOH HOH . E 3 HOH A 69 569 156 HOH HOH . E 3 HOH A 70 570 129 HOH HOH . E 3 HOH A 71 571 139 HOH HOH . E 3 HOH A 72 572 127 HOH HOH . E 3 HOH A 73 573 89 HOH HOH . E 3 HOH A 74 574 21 HOH HOH . E 3 HOH A 75 575 77 HOH HOH . E 3 HOH A 76 576 119 HOH HOH . E 3 HOH A 77 577 94 HOH HOH . E 3 HOH A 78 578 194 HOH HOH . E 3 HOH A 79 579 138 HOH HOH . E 3 HOH A 80 580 41 HOH HOH . E 3 HOH A 81 581 104 HOH HOH . E 3 HOH A 82 582 169 HOH HOH . E 3 HOH A 83 583 175 HOH HOH . E 3 HOH A 84 584 173 HOH HOH . E 3 HOH A 85 585 147 HOH HOH . E 3 HOH A 86 586 183 HOH HOH . E 3 HOH A 87 587 28 HOH HOH . E 3 HOH A 88 588 181 HOH HOH . E 3 HOH A 89 589 153 HOH HOH . E 3 HOH A 90 590 102 HOH HOH . E 3 HOH A 91 591 188 HOH HOH . F 3 HOH B 1 501 159 HOH HOH . F 3 HOH B 2 502 18 HOH HOH . F 3 HOH B 3 503 60 HOH HOH . F 3 HOH B 4 504 74 HOH HOH . F 3 HOH B 5 505 158 HOH HOH . F 3 HOH B 6 506 53 HOH HOH . F 3 HOH B 7 507 193 HOH HOH . F 3 HOH B 8 508 37 HOH HOH . F 3 HOH B 9 509 115 HOH HOH . F 3 HOH B 10 510 110 HOH HOH . F 3 HOH B 11 511 86 HOH HOH . F 3 HOH B 12 512 132 HOH HOH . F 3 HOH B 13 513 62 HOH HOH . F 3 HOH B 14 514 9 HOH HOH . F 3 HOH B 15 515 171 HOH HOH . F 3 HOH B 16 516 31 HOH HOH . F 3 HOH B 17 517 109 HOH HOH . F 3 HOH B 18 518 96 HOH HOH . F 3 HOH B 19 519 38 HOH HOH . F 3 HOH B 20 520 33 HOH HOH . F 3 HOH B 21 521 189 HOH HOH . F 3 HOH B 22 522 144 HOH HOH . F 3 HOH B 23 523 101 HOH HOH . F 3 HOH B 24 524 17 HOH HOH . F 3 HOH B 25 525 11 HOH HOH . F 3 HOH B 26 526 122 HOH HOH . F 3 HOH B 27 527 92 HOH HOH . F 3 HOH B 28 528 47 HOH HOH . F 3 HOH B 29 529 146 HOH HOH . F 3 HOH B 30 530 163 HOH HOH . F 3 HOH B 31 531 67 HOH HOH . F 3 HOH B 32 532 105 HOH HOH . F 3 HOH B 33 533 157 HOH HOH . F 3 HOH B 34 534 20 HOH HOH . F 3 HOH B 35 535 43 HOH HOH . F 3 HOH B 36 536 123 HOH HOH . F 3 HOH B 37 537 16 HOH HOH . F 3 HOH B 38 538 164 HOH HOH . F 3 HOH B 39 539 154 HOH HOH . F 3 HOH B 40 540 143 HOH HOH . F 3 HOH B 41 541 2 HOH HOH . F 3 HOH B 42 542 81 HOH HOH . F 3 HOH B 43 543 167 HOH HOH . F 3 HOH B 44 544 78 HOH HOH . F 3 HOH B 45 545 35 HOH HOH . F 3 HOH B 46 546 190 HOH HOH . F 3 HOH B 47 547 3 HOH HOH . F 3 HOH B 48 548 26 HOH HOH . F 3 HOH B 49 549 133 HOH HOH . F 3 HOH B 50 550 177 HOH HOH . F 3 HOH B 51 551 4 HOH HOH . F 3 HOH B 52 552 180 HOH HOH . F 3 HOH B 53 553 130 HOH HOH . F 3 HOH B 54 554 12 HOH HOH . F 3 HOH B 55 555 113 HOH HOH . F 3 HOH B 56 556 141 HOH HOH . F 3 HOH B 57 557 98 HOH HOH . F 3 HOH B 58 558 5 HOH HOH . F 3 HOH B 59 559 8 HOH HOH . F 3 HOH B 60 560 135 HOH HOH . F 3 HOH B 61 561 50 HOH HOH . F 3 HOH B 62 562 160 HOH HOH . F 3 HOH B 63 563 152 HOH HOH . F 3 HOH B 64 564 192 HOH HOH . F 3 HOH B 65 565 90 HOH HOH . F 3 HOH B 66 566 30 HOH HOH . F 3 HOH B 67 567 39 HOH HOH . F 3 HOH B 68 568 56 HOH HOH . F 3 HOH B 69 569 99 HOH HOH . F 3 HOH B 70 570 103 HOH HOH . F 3 HOH B 71 571 79 HOH HOH . F 3 HOH B 72 572 162 HOH HOH . F 3 HOH B 73 573 170 HOH HOH . F 3 HOH B 74 574 136 HOH HOH . F 3 HOH B 75 575 75 HOH HOH . F 3 HOH B 76 576 73 HOH HOH . F 3 HOH B 77 577 184 HOH HOH . F 3 HOH B 78 578 54 HOH HOH . F 3 HOH B 79 579 69 HOH HOH . F 3 HOH B 80 580 112 HOH HOH . F 3 HOH B 81 581 36 HOH HOH . F 3 HOH B 82 582 166 HOH HOH . F 3 HOH B 83 583 120 HOH HOH . F 3 HOH B 84 584 44 HOH HOH . F 3 HOH B 85 585 13 HOH HOH . F 3 HOH B 86 586 88 HOH HOH . F 3 HOH B 87 587 15 HOH HOH . F 3 HOH B 88 588 179 HOH HOH . F 3 HOH B 89 589 174 HOH HOH . F 3 HOH B 90 590 121 HOH HOH . F 3 HOH B 91 591 148 HOH HOH . F 3 HOH B 92 592 178 HOH HOH . F 3 HOH B 93 593 117 HOH HOH . F 3 HOH B 94 594 191 HOH HOH . F 3 HOH B 95 595 149 HOH HOH . F 3 HOH B 96 596 80 HOH HOH . F 3 HOH B 97 597 100 HOH HOH . F 3 HOH B 98 598 155 HOH HOH . F 3 HOH B 99 599 64 HOH HOH . F 3 HOH B 100 600 172 HOH HOH . F 3 HOH B 101 601 63 HOH HOH . F 3 HOH B 102 602 161 HOH HOH . F 3 HOH B 103 603 151 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 C1 QEI . . . D 2 20.055 39.288 11.558 1 37.81 ? C1 QEI 401 B 1 HETATM 2 C C2 QEI . . . D 2 20.837 39.776 12.77 1 40.84 ? C2 QEI 401 B 1 HETATM 3 C C3 QEI . . . D 2 19.319 40.538 11.131 1 39.77 ? C3 QEI 401 B 1 HETATM 4 C C4 QEI . . . D 2 20.024 40.933 13.343 1 40.58 ? C4 QEI 401 B 1 HETATM 5 C C5 QEI . . . D 2 19.318 41.447 12.102 1 42.26 ? C5 QEI 401 B 1 HETATM 6 C C6 QEI . . . D 2 19.883 36.847 11.895 1 34.47 ? C6 QEI 401 B 1 HETATM 7 C C9 QEI . . . D 2 18.873 35.982 14.243 1 34.35 ? C9 QEI 401 B 1 HETATM 8 C C10 QEI . . . D 2 18.64 34.612 14.757 1 34.18 ? C10 QEI 401 B 1 HETATM 9 C C11 QEI . . . D 2 18.491 37.111 15.101 1 30.84 ? C11 QEI 401 B 1 HETATM 10 O O1 QEI . . . D 2 22.139 40.218 12.394 1 44.98 ? O1 QEI 401 B 1 HETATM 11 O O2 QEI . . . D 2 20.859 41.873 14.02 1 36.92 ? O2 QEI 401 B 1 HETATM 12 N N1 QEI . . . D 2 19.265 38.146 12.006 1 34.88 ? N1 QEI 401 B 1 HETATM 13 C C7 QEI . . . D 2 19.454 35.813 12.905 1 33.43 ? C7 QEI 401 B 1 HETATM 14 C C8 QEI . . . D 2 19.528 34.436 12.728 1 36.89 ? C8 QEI 401 B 1 HETATM 15 N N2 QEI . . . D 2 19.057 33.755 13.821 1 37.36 ? N2 QEI 401 B 1 HETATM 16 N N3 QEI . . . D 2 18.107 34.465 15.994 1 34.53 ? N3 QEI 401 B 1 HETATM 17 C C12 QEI . . . D 2 17.78 35.561 16.742 1 34.13 ? C12 QEI 401 B 1 HETATM 18 N N5 QEI . . . D 2 17.247 35.336 17.975 1 32.47 ? N5 QEI 401 B 1 HETATM 19 N N4 QEI . . . D 2 17.967 36.834 16.3 1 32.73 ? N4 QEI 401 B 1 HETATM 20 O O3 QEI . . . D 2 18.657 38.268 14.689 1 30.79 ? O3 QEI 401 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #