data_4HVX # _model_server_result.job_id BJPFikFE1M7sUTpim3VqQw _model_server_result.datetime_utc '2024-10-18 15:25:04' _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 4hvx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 4HVX # _exptl.entry_id 4HVX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 277.279 _entity.id 4 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.18 _cell.angle_gamma 90 _cell.entry_id 4HVX _cell.length_a 91.662 _cell.length_b 64.486 _cell.length_c 71.125 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HVX _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A SG CYS 318 A CYS 318 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc2 A SG CYS 320 A CYS 320 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc3 A SG CYS 323 A CYS 323 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc4 A ND1 HIS 349 A HIS 349 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? # _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 290 n n C1 C3 QEI sing 291 n n C1 N1 QEI sing 292 n n C2 C4 QEI sing 293 n n C2 O1 QEI sing 294 n n C3 C5 QEI doub 295 n n C4 C5 QEI sing 296 n n C4 O2 QEI sing 297 n n C6 N1 QEI sing 298 n n C6 C7 QEI sing 299 n n C9 C10 QEI doub 300 n y C9 C11 QEI sing 301 n n C9 C7 QEI sing 302 n y C10 N2 QEI sing 303 n y C10 N3 QEI sing 304 n n C11 N4 QEI sing 305 n n C11 O3 QEI doub 306 n n C7 C8 QEI doub 307 n y C8 N2 QEI sing 308 n y N3 C12 QEI doub 309 n n C12 N5 QEI sing 310 n n C12 N4 QEI sing 311 n n C1 H1 QEI sing 312 n n C2 H2 QEI sing 313 n n C3 H3 QEI sing 314 n n C4 H4 QEI sing 315 n n C5 H5 QEI sing 316 n n C6 H6 QEI sing 317 n n C6 H6A QEI sing 318 n n O1 HO1 QEI sing 319 n n O2 HO2 QEI sing 320 n n N1 HN1 QEI sing 321 n n C8 H8 QEI sing 322 n n N2 HN2 QEI sing 323 n n N5 HN5 QEI sing 324 n n N5 HN5A QEI sing 325 n n N4 HN4 QEI sing 326 n n # _atom_sites.entry_id 4HVX _atom_sites.fract_transf_matrix[1][1] 0.01091 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001181 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015507 _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] 0.014142 _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 ZN A 1 401 1 ZN ZN . C 3 GOL A 1 402 1 GOL GOL . D 3 GOL A 1 403 2 GOL GOL . E 3 GOL A 1 404 4 GOL GOL . F 4 QEI A 1 405 1 QEI Q . G 5 HOH A 1 501 2 HOH HOH . G 5 HOH A 2 502 3 HOH HOH . G 5 HOH A 3 503 4 HOH HOH . G 5 HOH A 4 504 5 HOH HOH . G 5 HOH A 5 505 6 HOH HOH . G 5 HOH A 6 506 7 HOH HOH . G 5 HOH A 7 507 8 HOH HOH . G 5 HOH A 8 508 10 HOH HOH . G 5 HOH A 9 509 11 HOH HOH . G 5 HOH A 10 510 12 HOH HOH . G 5 HOH A 11 511 13 HOH HOH . G 5 HOH A 12 512 14 HOH HOH . G 5 HOH A 13 513 15 HOH HOH . G 5 HOH A 14 514 16 HOH HOH . G 5 HOH A 15 515 17 HOH HOH . G 5 HOH A 16 516 18 HOH HOH . G 5 HOH A 17 517 19 HOH HOH . G 5 HOH A 18 518 20 HOH HOH . G 5 HOH A 19 519 21 HOH HOH . G 5 HOH A 20 520 22 HOH HOH . G 5 HOH A 21 521 24 HOH HOH . G 5 HOH A 22 522 25 HOH HOH . G 5 HOH A 23 523 26 HOH HOH . G 5 HOH A 24 524 27 HOH HOH . G 5 HOH A 25 525 28 HOH HOH . G 5 HOH A 26 526 29 HOH HOH . G 5 HOH A 27 527 30 HOH HOH . G 5 HOH A 28 528 31 HOH HOH . G 5 HOH A 29 529 32 HOH HOH . G 5 HOH A 30 530 33 HOH HOH . G 5 HOH A 31 531 34 HOH HOH . G 5 HOH A 32 532 35 HOH HOH . G 5 HOH A 33 533 36 HOH HOH . G 5 HOH A 34 534 37 HOH HOH . G 5 HOH A 35 535 38 HOH HOH . G 5 HOH A 36 536 39 HOH HOH . G 5 HOH A 37 537 40 HOH HOH . G 5 HOH A 38 538 41 HOH HOH . G 5 HOH A 39 539 42 HOH HOH . G 5 HOH A 40 540 43 HOH HOH . G 5 HOH A 41 541 44 HOH HOH . G 5 HOH A 42 542 45 HOH HOH . G 5 HOH A 43 543 46 HOH HOH . G 5 HOH A 44 544 47 HOH HOH . G 5 HOH A 45 545 49 HOH HOH . G 5 HOH A 46 546 50 HOH HOH . G 5 HOH A 47 547 51 HOH HOH . G 5 HOH A 48 548 52 HOH HOH . G 5 HOH A 49 549 53 HOH HOH . G 5 HOH A 50 550 54 HOH HOH . G 5 HOH A 51 551 55 HOH HOH . G 5 HOH A 52 552 58 HOH HOH . G 5 HOH A 53 553 59 HOH HOH . G 5 HOH A 54 554 60 HOH HOH . G 5 HOH A 55 555 61 HOH HOH . G 5 HOH A 56 556 63 HOH HOH . G 5 HOH A 57 557 64 HOH HOH . G 5 HOH A 58 558 65 HOH HOH . G 5 HOH A 59 559 66 HOH HOH . G 5 HOH A 60 560 67 HOH HOH . G 5 HOH A 61 561 68 HOH HOH . G 5 HOH A 62 562 69 HOH HOH . G 5 HOH A 63 563 70 HOH HOH . G 5 HOH A 64 564 71 HOH HOH . G 5 HOH A 65 565 72 HOH HOH . G 5 HOH A 66 566 73 HOH HOH . G 5 HOH A 67 567 74 HOH HOH . G 5 HOH A 68 568 76 HOH HOH . G 5 HOH A 69 569 77 HOH HOH . G 5 HOH A 70 570 78 HOH HOH . G 5 HOH A 71 571 79 HOH HOH . G 5 HOH A 72 572 80 HOH HOH . G 5 HOH A 73 573 81 HOH HOH . G 5 HOH A 74 574 83 HOH HOH . G 5 HOH A 75 575 84 HOH HOH . G 5 HOH A 76 576 85 HOH HOH . G 5 HOH A 77 577 86 HOH HOH . G 5 HOH A 78 578 87 HOH HOH . G 5 HOH A 79 579 88 HOH HOH . G 5 HOH A 80 580 89 HOH HOH . G 5 HOH A 81 581 90 HOH HOH . G 5 HOH A 82 582 93 HOH HOH . G 5 HOH A 83 583 94 HOH HOH . G 5 HOH A 84 584 95 HOH HOH . G 5 HOH A 85 585 96 HOH HOH . G 5 HOH A 86 586 97 HOH HOH . G 5 HOH A 87 587 98 HOH HOH . G 5 HOH A 88 588 99 HOH HOH . G 5 HOH A 89 589 101 HOH HOH . G 5 HOH A 90 590 102 HOH HOH . G 5 HOH A 91 591 105 HOH HOH . G 5 HOH A 92 592 106 HOH HOH . G 5 HOH A 93 593 107 HOH HOH . G 5 HOH A 94 594 110 HOH HOH . G 5 HOH A 95 595 112 HOH HOH . G 5 HOH A 96 596 114 HOH HOH . G 5 HOH A 97 597 115 HOH HOH . G 5 HOH A 98 598 116 HOH HOH . G 5 HOH A 99 599 119 HOH HOH . G 5 HOH A 100 600 121 HOH HOH . G 5 HOH A 101 601 122 HOH HOH . G 5 HOH A 102 602 123 HOH HOH . G 5 HOH A 103 603 125 HOH HOH . G 5 HOH A 104 604 127 HOH HOH . G 5 HOH A 105 605 128 HOH HOH . G 5 HOH A 106 606 130 HOH HOH . G 5 HOH A 107 607 131 HOH HOH . G 5 HOH A 108 608 132 HOH HOH . G 5 HOH A 109 609 133 HOH HOH . G 5 HOH A 110 610 135 HOH HOH . G 5 HOH A 111 611 136 HOH HOH . G 5 HOH A 112 612 137 HOH HOH . G 5 HOH A 113 613 138 HOH HOH . G 5 HOH A 114 614 140 HOH HOH . G 5 HOH A 115 615 141 HOH HOH . G 5 HOH A 116 616 142 HOH HOH . G 5 HOH A 117 617 144 HOH HOH . G 5 HOH A 118 618 151 HOH HOH . G 5 HOH A 119 619 152 HOH HOH . G 5 HOH A 120 620 154 HOH HOH . G 5 HOH A 121 621 158 HOH HOH . G 5 HOH A 122 622 163 HOH HOH . G 5 HOH A 123 623 164 HOH HOH . G 5 HOH A 124 624 166 HOH HOH . G 5 HOH A 125 625 168 HOH HOH . G 5 HOH A 126 626 169 HOH HOH . G 5 HOH A 127 627 170 HOH HOH . G 5 HOH A 128 628 173 HOH HOH . G 5 HOH A 129 629 176 HOH HOH . G 5 HOH A 130 630 178 HOH HOH . G 5 HOH A 131 631 180 HOH HOH . G 5 HOH A 132 632 182 HOH HOH . G 5 HOH A 133 633 183 HOH HOH . G 5 HOH A 134 634 188 HOH HOH . G 5 HOH A 135 635 191 HOH HOH . G 5 HOH A 136 636 196 HOH HOH . G 5 HOH A 137 637 198 HOH HOH . G 5 HOH A 138 638 205 HOH HOH . G 5 HOH A 139 639 209 HOH HOH . G 5 HOH A 140 640 211 HOH HOH . G 5 HOH A 141 641 218 HOH HOH . G 5 HOH A 142 642 219 HOH HOH . G 5 HOH A 143 643 222 HOH HOH . G 5 HOH A 144 644 227 HOH HOH . G 5 HOH A 145 645 229 HOH HOH . G 5 HOH A 146 646 231 HOH HOH . G 5 HOH A 147 647 234 HOH HOH . G 5 HOH A 148 648 238 HOH HOH . G 5 HOH A 149 649 239 HOH HOH . G 5 HOH A 150 650 240 HOH HOH . G 5 HOH A 151 651 241 HOH HOH . G 5 HOH A 152 652 242 HOH HOH . G 5 HOH A 153 653 246 HOH HOH . G 5 HOH A 154 654 249 HOH HOH . G 5 HOH A 155 655 250 HOH HOH . G 5 HOH A 156 656 251 HOH HOH . G 5 HOH A 157 657 252 HOH HOH . G 5 HOH A 158 658 254 HOH HOH . G 5 HOH A 159 659 255 HOH HOH . G 5 HOH A 160 660 256 HOH HOH . G 5 HOH A 161 661 257 HOH HOH . G 5 HOH A 162 662 258 HOH HOH . G 5 HOH A 163 663 259 HOH HOH . G 5 HOH A 164 664 260 HOH HOH . G 5 HOH A 165 665 261 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 C6 QEI . . . F 4 19.175 17.078 20.128 0.94 34.31 ? C6 QEI 405 A 1 HETATM 2 C C9 QEI . . . F 4 17.152 16.617 21.732 0.94 33.77 ? C9 QEI 405 A 1 HETATM 3 C C10 QEI . . . F 4 15.829 16.257 21.491 0.94 34.21 ? C10 QEI 405 A 1 HETATM 4 C C11 QEI . . . F 4 17.582 16.798 23.058 0.94 33.65 ? C11 QEI 405 A 1 HETATM 5 N N1 QEI . . . F 4 19.287 16.946 18.662 0.94 37.87 ? N1 QEI 405 A 1 HETATM 6 C C7 QEI . . . F 4 17.752 16.722 20.47 0.94 35.02 ? C7 QEI 405 A 1 HETATM 7 C C8 QEI . . . F 4 16.785 16.419 19.517 0.94 34.88 ? C8 QEI 405 A 1 HETATM 8 N N2 QEI . . . F 4 15.632 16.147 20.168 0.94 35.21 ? N2 QEI 405 A 1 HETATM 9 N N3 QEI . . . F 4 14.978 16.092 22.525 0.94 33.67 ? N3 QEI 405 A 1 HETATM 10 C C12 QEI . . . F 4 15.42 16.274 23.788 0.94 33.21 ? C12 QEI 405 A 1 HETATM 11 N N5 QEI . . . F 4 14.446 16.073 24.878 0.94 33.46 ? N5 QEI 405 A 1 HETATM 12 N N4 QEI . . . F 4 16.698 16.613 24.055 0.94 32.11 ? N4 QEI 405 A 1 HETATM 13 O O3 QEI . . . F 4 18.767 17.124 23.337 0.94 31.61 ? O3 QEI 405 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 13 #