data_5EGR # _model_server_result.job_id hn2G7rS7t0RzYjUdTYdTPA _model_server_result.datetime_utc '2024-10-18 15:24:53' _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 5egr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":406}' # _entry.id 5EGR # _exptl.entry_id 5EGR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 265.269 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-azanyl-7-[(2~{S},3~{R},5~{S})-5-(hydroxymethyl)-3-oxidanyl-pyrrolidin-2-yl]-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 93.25 _cell.angle_gamma 90 _cell.entry_id 5EGR _cell.length_a 90.458 _cell.length_b 64.485 _cell.length_c 70.978 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EGR _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,H,I _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_755 -x+2,y,-z -1 0 0 0 1 0 0 0 -1 180.916 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id G _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 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc2 A SG CYS 320 A CYS 320 1_555 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc3 A SG CYS 323 A CYS 323 1_555 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc4 A ND1 HIS 349 A HIS 349 1_555 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? # _chem_comp.formula 'C11 H15 N5 O3' _chem_comp.formula_weight 265.269 _chem_comp.id 5NT _chem_comp.mon_nstd_flag . _chem_comp.name 2-azanyl-7-[(2~{S},3~{R},5~{S})-5-(hydroxymethyl)-3-oxidanyl-pyrrolidin-2-yl]-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 O C5 5NT sing 1 n n C5 C4 5NT sing 2 n n C4 C6 5NT sing 3 n n C4 N2 5NT sing 4 n n C6 C7 5NT sing 5 n n N2 C3 5NT sing 6 n n C7 O1 5NT sing 7 n n C7 C3 5NT sing 8 n n C3 C2 5NT sing 9 n n C8 C2 5NT doub 10 n y C8 N3 5NT sing 11 n y C2 C1 5NT sing 12 n y N3 C9 5NT sing 13 n y C1 C9 5NT doub 14 n y C1 N1 5NT sing 15 n n C9 C10 5NT sing 16 n n N1 C 5NT doub 17 n n C10 O2 5NT doub 18 n n C10 N4 5NT sing 19 n n C N4 5NT sing 20 n n C N 5NT sing 21 n n N4 H1 5NT sing 22 n n N H2 5NT sing 23 n n N H3 5NT sing 24 n n N3 H4 5NT sing 25 n n C8 H5 5NT sing 26 n n C3 H6 5NT sing 27 n n C7 H7 5NT sing 28 n n O1 H8 5NT sing 29 n n C6 H9 5NT sing 30 n n C6 H10 5NT sing 31 n n C4 H11 5NT sing 32 n n N2 H12 5NT sing 33 n n C5 H14 5NT sing 34 n n C5 H15 5NT sing 35 n n O H16 5NT sing 36 n n # _atom_sites.entry_id 5EGR _atom_sites.fract_transf_matrix[1][1] 0.011055 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000627 _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] 0.014111 _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 GOL A 1 401 1 GOL GOL . C 2 GOL A 1 402 2 GOL GOL . D 2 GOL A 1 403 3 GOL GOL . E 2 GOL A 1 404 4 GOL GOL . F 3 ZN A 1 405 1 ZN ZN . G 4 5NT A 1 406 1 5NT A72 . H 5 EDO A 1 407 1 EDO EDO . I 6 HOH A 1 501 267 HOH HOH . I 6 HOH A 2 502 102 HOH HOH . I 6 HOH A 3 503 194 HOH HOH . I 6 HOH A 4 504 281 HOH HOH . I 6 HOH A 5 505 144 HOH HOH . I 6 HOH A 6 506 285 HOH HOH . I 6 HOH A 7 507 231 HOH HOH . I 6 HOH A 8 508 143 HOH HOH . I 6 HOH A 9 509 25 HOH HOH . I 6 HOH A 10 510 411 HOH HOH . I 6 HOH A 11 511 303 HOH HOH . I 6 HOH A 12 512 93 HOH HOH . I 6 HOH A 13 513 268 HOH HOH . I 6 HOH A 14 514 24 HOH HOH . I 6 HOH A 15 515 222 HOH HOH . I 6 HOH A 16 516 259 HOH HOH . I 6 HOH A 17 517 131 HOH HOH . I 6 HOH A 18 518 403 HOH HOH . I 6 HOH A 19 519 22 HOH HOH . I 6 HOH A 20 520 407 HOH HOH . I 6 HOH A 21 521 96 HOH HOH . I 6 HOH A 22 522 70 HOH HOH . I 6 HOH A 23 523 60 HOH HOH . I 6 HOH A 24 524 189 HOH HOH . I 6 HOH A 25 525 327 HOH HOH . I 6 HOH A 26 526 207 HOH HOH . I 6 HOH A 27 527 123 HOH HOH . I 6 HOH A 28 528 37 HOH HOH . I 6 HOH A 29 529 34 HOH HOH . I 6 HOH A 30 530 71 HOH HOH . I 6 HOH A 31 531 91 HOH HOH . I 6 HOH A 32 532 40 HOH HOH . I 6 HOH A 33 533 3 HOH HOH . I 6 HOH A 34 534 31 HOH HOH . I 6 HOH A 35 535 26 HOH HOH . I 6 HOH A 36 536 55 HOH HOH . I 6 HOH A 37 537 65 HOH HOH . I 6 HOH A 38 538 167 HOH HOH . I 6 HOH A 39 539 154 HOH HOH . I 6 HOH A 40 540 2 HOH HOH . I 6 HOH A 41 541 110 HOH HOH . I 6 HOH A 42 542 212 HOH HOH . I 6 HOH A 43 543 405 HOH HOH . I 6 HOH A 44 544 39 HOH HOH . I 6 HOH A 45 545 115 HOH HOH . I 6 HOH A 46 546 291 HOH HOH . I 6 HOH A 47 547 151 HOH HOH . I 6 HOH A 48 548 29 HOH HOH . I 6 HOH A 49 549 118 HOH HOH . I 6 HOH A 50 550 111 HOH HOH . I 6 HOH A 51 551 213 HOH HOH . I 6 HOH A 52 552 112 HOH HOH . I 6 HOH A 53 553 188 HOH HOH . I 6 HOH A 54 554 233 HOH HOH . I 6 HOH A 55 555 9 HOH HOH . I 6 HOH A 56 556 270 HOH HOH . I 6 HOH A 57 557 8 HOH HOH . I 6 HOH A 58 558 108 HOH HOH . I 6 HOH A 59 559 253 HOH HOH . I 6 HOH A 60 560 80 HOH HOH . I 6 HOH A 61 561 68 HOH HOH . I 6 HOH A 62 562 73 HOH HOH . I 6 HOH A 63 563 139 HOH HOH . I 6 HOH A 64 564 16 HOH HOH . I 6 HOH A 65 565 17 HOH HOH . I 6 HOH A 66 566 275 HOH HOH . I 6 HOH A 67 567 286 HOH HOH . I 6 HOH A 68 568 109 HOH HOH . I 6 HOH A 69 569 300 HOH HOH . I 6 HOH A 70 570 49 HOH HOH . I 6 HOH A 71 571 15 HOH HOH . I 6 HOH A 72 572 211 HOH HOH . I 6 HOH A 73 573 51 HOH HOH . I 6 HOH A 74 574 59 HOH HOH . I 6 HOH A 75 575 245 HOH HOH . I 6 HOH A 76 576 149 HOH HOH . I 6 HOH A 77 577 121 HOH HOH . I 6 HOH A 78 578 36 HOH HOH . I 6 HOH A 79 579 45 HOH HOH . I 6 HOH A 80 580 52 HOH HOH . I 6 HOH A 81 581 177 HOH HOH . I 6 HOH A 82 582 50 HOH HOH . I 6 HOH A 83 583 27 HOH HOH . I 6 HOH A 84 584 7 HOH HOH . I 6 HOH A 85 585 218 HOH HOH . I 6 HOH A 86 586 46 HOH HOH . I 6 HOH A 87 587 184 HOH HOH . I 6 HOH A 88 588 150 HOH HOH . I 6 HOH A 89 589 72 HOH HOH . I 6 HOH A 90 590 288 HOH HOH . I 6 HOH A 91 591 32 HOH HOH . I 6 HOH A 92 592 89 HOH HOH . I 6 HOH A 93 593 43 HOH HOH . I 6 HOH A 94 594 101 HOH HOH . I 6 HOH A 95 595 42 HOH HOH . I 6 HOH A 96 596 103 HOH HOH . I 6 HOH A 97 597 88 HOH HOH . I 6 HOH A 98 598 297 HOH HOH . I 6 HOH A 99 599 35 HOH HOH . I 6 HOH A 100 600 192 HOH HOH . I 6 HOH A 101 601 216 HOH HOH . I 6 HOH A 102 602 165 HOH HOH . I 6 HOH A 103 603 277 HOH HOH . I 6 HOH A 104 604 38 HOH HOH . I 6 HOH A 105 605 18 HOH HOH . I 6 HOH A 106 606 138 HOH HOH . I 6 HOH A 107 607 107 HOH HOH . I 6 HOH A 108 608 176 HOH HOH . I 6 HOH A 109 609 221 HOH HOH . I 6 HOH A 110 610 162 HOH HOH . I 6 HOH A 111 611 33 HOH HOH . I 6 HOH A 112 612 81 HOH HOH . I 6 HOH A 113 613 295 HOH HOH . I 6 HOH A 114 614 145 HOH HOH . I 6 HOH A 115 615 122 HOH HOH . I 6 HOH A 116 616 140 HOH HOH . I 6 HOH A 117 617 287 HOH HOH . I 6 HOH A 118 618 61 HOH HOH . I 6 HOH A 119 619 113 HOH HOH . I 6 HOH A 120 620 134 HOH HOH . I 6 HOH A 121 621 63 HOH HOH . I 6 HOH A 122 622 174 HOH HOH . I 6 HOH A 123 623 69 HOH HOH . I 6 HOH A 124 624 10 HOH HOH . I 6 HOH A 125 625 11 HOH HOH . I 6 HOH A 126 626 56 HOH HOH . I 6 HOH A 127 627 77 HOH HOH . I 6 HOH A 128 628 226 HOH HOH . I 6 HOH A 129 629 182 HOH HOH . I 6 HOH A 130 630 116 HOH HOH . I 6 HOH A 131 631 304 HOH HOH . I 6 HOH A 132 632 196 HOH HOH . I 6 HOH A 133 633 315 HOH HOH . I 6 HOH A 134 634 58 HOH HOH . I 6 HOH A 135 635 257 HOH HOH . I 6 HOH A 136 636 236 HOH HOH . I 6 HOH A 137 637 14 HOH HOH . I 6 HOH A 138 638 399 HOH HOH . I 6 HOH A 139 639 98 HOH HOH . I 6 HOH A 140 640 19 HOH HOH . I 6 HOH A 141 641 227 HOH HOH . I 6 HOH A 142 642 190 HOH HOH . I 6 HOH A 143 643 234 HOH HOH . I 6 HOH A 144 644 105 HOH HOH . I 6 HOH A 145 645 183 HOH HOH . I 6 HOH A 146 646 6 HOH HOH . I 6 HOH A 147 647 82 HOH HOH . I 6 HOH A 148 648 361 HOH HOH . I 6 HOH A 149 649 117 HOH HOH . I 6 HOH A 150 650 141 HOH HOH . I 6 HOH A 151 651 97 HOH HOH . I 6 HOH A 152 652 135 HOH HOH . I 6 HOH A 153 653 130 HOH HOH . I 6 HOH A 154 654 147 HOH HOH . I 6 HOH A 155 655 64 HOH HOH . I 6 HOH A 156 656 99 HOH HOH . I 6 HOH A 157 657 66 HOH HOH . I 6 HOH A 158 658 178 HOH HOH . I 6 HOH A 159 659 106 HOH HOH . I 6 HOH A 160 660 220 HOH HOH . I 6 HOH A 161 661 87 HOH HOH . I 6 HOH A 162 662 13 HOH HOH . I 6 HOH A 163 663 299 HOH HOH . I 6 HOH A 164 664 41 HOH HOH . I 6 HOH A 165 665 1 HOH HOH . I 6 HOH A 166 666 371 HOH HOH . I 6 HOH A 167 667 269 HOH HOH . I 6 HOH A 168 668 200 HOH HOH . I 6 HOH A 169 669 235 HOH HOH . I 6 HOH A 170 670 119 HOH HOH . I 6 HOH A 171 671 84 HOH HOH . I 6 HOH A 172 672 276 HOH HOH . I 6 HOH A 173 673 199 HOH HOH . I 6 HOH A 174 674 62 HOH HOH . I 6 HOH A 175 675 215 HOH HOH . I 6 HOH A 176 676 225 HOH HOH . I 6 HOH A 177 677 369 HOH HOH . I 6 HOH A 178 678 262 HOH HOH . I 6 HOH A 179 679 279 HOH HOH . I 6 HOH A 180 680 249 HOH HOH . I 6 HOH A 181 681 163 HOH HOH . I 6 HOH A 182 682 127 HOH HOH . I 6 HOH A 183 683 79 HOH HOH . I 6 HOH A 184 684 349 HOH HOH . I 6 HOH A 185 685 133 HOH HOH . I 6 HOH A 186 686 195 HOH HOH . I 6 HOH A 187 687 54 HOH HOH . I 6 HOH A 188 688 244 HOH HOH . I 6 HOH A 189 689 255 HOH HOH . I 6 HOH A 190 690 344 HOH HOH . I 6 HOH A 191 691 242 HOH HOH . I 6 HOH A 192 692 312 HOH HOH . I 6 HOH A 193 693 83 HOH HOH . I 6 HOH A 194 694 363 HOH HOH . I 6 HOH A 195 695 318 HOH HOH . I 6 HOH A 196 696 284 HOH HOH . I 6 HOH A 197 697 114 HOH HOH . I 6 HOH A 198 698 232 HOH HOH . I 6 HOH A 199 699 325 HOH HOH . I 6 HOH A 200 700 86 HOH HOH . I 6 HOH A 201 701 311 HOH HOH . I 6 HOH A 202 702 283 HOH HOH . I 6 HOH A 203 703 186 HOH HOH . I 6 HOH A 204 704 321 HOH HOH . I 6 HOH A 205 705 329 HOH HOH . I 6 HOH A 206 706 246 HOH HOH . I 6 HOH A 207 707 100 HOH HOH . I 6 HOH A 208 708 251 HOH HOH . I 6 HOH A 209 709 158 HOH HOH . I 6 HOH A 210 710 354 HOH HOH . I 6 HOH A 211 711 250 HOH HOH . I 6 HOH A 212 712 228 HOH HOH . I 6 HOH A 213 713 169 HOH HOH . I 6 HOH A 214 714 201 HOH HOH . I 6 HOH A 215 715 313 HOH HOH . I 6 HOH A 216 716 161 HOH HOH . I 6 HOH A 217 717 142 HOH HOH . I 6 HOH A 218 718 164 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 O2 5NT . . . G 4 108.658 17.911 23.543 1 28.96 ? O2 5NT 406 A 1 HETATM 2 C C10 5NT . . . G 4 107.541 17.597 23.129 1 29.47 ? C10 5NT 406 A 1 HETATM 3 N N4 5NT . . . G 4 106.533 17.286 24.026 1 29.01 ? N4 5NT 406 A 1 HETATM 4 C C 5NT . . . G 4 105.284 16.85 23.684 1 30.2 ? C 5NT 406 A 1 HETATM 5 N N 5NT . . . G 4 104.443 16.565 24.682 1 28.76 ? N 5NT 406 A 1 HETATM 6 C C9 5NT . . . G 4 107.114 17.433 21.78 1 28.73 ? C9 5NT 406 A 1 HETATM 7 C C1 5NT . . . G 4 105.847 16.971 21.476 1 31.83 ? C1 5NT 406 A 1 HETATM 8 N N1 5NT . . . G 4 104.895 16.671 22.425 1 30.04 ? N1 5NT 406 A 1 HETATM 9 N N3 5NT . . . G 4 107.741 17.648 20.574 1 28.26 ? N3 5NT 406 A 1 HETATM 10 C C8 5NT . . . G 4 106.91 17.321 19.54 1 33.71 ? C8 5NT 406 A 1 HETATM 11 C C2 5NT . . . G 4 105.719 16.868 20.052 1 38.62 ? C2 5NT 406 A 1 HETATM 12 C C3 5NT . . . G 4 104.586 16.243 19.282 1 45.34 ? C3 5NT 406 A 1 HETATM 13 C C7 5NT . . . G 4 103.418 17.184 18.897 1 46.67 ? C7 5NT 406 A 1 HETATM 14 O O1 5NT . . . G 4 102.192 16.472 19.063 1 48.84 ? O1 5NT 406 A 1 HETATM 15 C C6 5NT . . . G 4 103.624 17.394 17.407 1 45.48 ? C6 5NT 406 A 1 HETATM 16 C C4 5NT . . . G 4 104.105 16.026 16.937 1 55.35 ? C4 5NT 406 A 1 HETATM 17 N N2 5NT . . . G 4 105.064 15.689 18.01 1 52.87 ? N2 5NT 406 A 1 HETATM 18 C C5 5NT . . . G 4 104.742 16.057 15.56 1 61.62 ? C5 5NT 406 A 1 HETATM 19 O O 5NT . . . G 4 105.768 17.037 15.479 1 66.79 ? O 5NT 406 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #