data_5YLT # _model_server_result.job_id cQ8qTSzudQzJBc-CYklG6A _model_server_result.datetime_utc '2024-11-05 01:25:29' _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 5ylt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5YLT # _exptl.entry_id 5YLT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 381.387 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SINEFUNGIN _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 90 _cell.entry_id 5YLT _cell.length_a 110.176 _cell.length_b 34.963 _cell.length_c 67.872 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YLT _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 16 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 119 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 16 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 119 _struct_conn.ptnr2_symmetry 2_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id B _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id B _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 2.039 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C15 H23 N7 O5' _chem_comp.formula_weight 381.387 _chem_comp.id SFG _chem_comp.mon_nstd_flag . _chem_comp.name SINEFUNGIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ADENOSYL-ORNITHINE # 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 N CA SFG sing 350 n n N HN1 SFG sing 351 n n N HN2 SFG sing 352 n n CA C SFG sing 353 n n CA CB SFG sing 354 n n CA HA SFG sing 355 n n C O SFG doub 356 n n C OXT SFG sing 357 n n OXT HXT SFG sing 358 n n CB CG SFG sing 359 n n CB HB1 SFG sing 360 n n CB HB2 SFG sing 361 n n CG CD SFG sing 362 n n CG HG1 SFG sing 363 n n CG HG2 SFG sing 364 n n CD NE SFG sing 365 n n CD C5' SFG sing 366 n n CD HD SFG sing 367 n n NE HNE1 SFG sing 368 n n NE HNE2 SFG sing 369 n n C5' C4' SFG sing 370 n n C5' "H5'1" SFG sing 371 n n C5' "H5'2" SFG sing 372 n n C4' O4' SFG sing 373 n n C4' C3' SFG sing 374 n n C4' H4' SFG sing 375 n n O4' C1' SFG sing 376 n n C3' O3' SFG sing 377 n n C3' C2' SFG sing 378 n n C3' H3' SFG sing 379 n n O3' HO3' SFG sing 380 n n C2' O2' SFG sing 381 n n C2' C1' SFG sing 382 n n C2' H2' SFG sing 383 n n O2' HO2' SFG sing 384 n n C1' N9 SFG sing 385 n n C1' H1' SFG sing 386 n n N9 C8 SFG sing 387 n y N9 C4 SFG sing 388 n y C8 N7 SFG doub 389 n y C8 H8 SFG sing 390 n n N7 C5 SFG sing 391 n y C5 C6 SFG sing 392 n y C5 C4 SFG doub 393 n y C6 N6 SFG sing 394 n n C6 N1 SFG doub 395 n y N6 HN61 SFG sing 396 n n N6 HN62 SFG sing 397 n n N1 C2 SFG sing 398 n y C2 N3 SFG doub 399 n y C2 H2 SFG sing 400 n n N3 C4 SFG sing 401 n y # _atom_sites.entry_id 5YLT _atom_sites.fract_transf_matrix[1][1] 0.009076 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028602 _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] 0.014734 _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 SFG A 1 401 401 SFG SFG . C 3 C7N A 1 402 402 C7N XOX . D 4 GOL A 1 403 501 GOL GOL . E 4 GOL A 1 404 503 GOL GOL . F 4 GOL A 1 405 504 GOL GOL . G 5 HOH A 1 501 98 HOH HOH . G 5 HOH A 2 502 166 HOH HOH . G 5 HOH A 3 503 155 HOH HOH . G 5 HOH A 4 504 77 HOH HOH . G 5 HOH A 5 505 146 HOH HOH . G 5 HOH A 6 506 203 HOH HOH . G 5 HOH A 7 507 119 HOH HOH . G 5 HOH A 8 508 105 HOH HOH . G 5 HOH A 9 509 52 HOH HOH . G 5 HOH A 10 510 130 HOH HOH . G 5 HOH A 11 511 75 HOH HOH . G 5 HOH A 12 512 53 HOH HOH . G 5 HOH A 13 513 196 HOH HOH . G 5 HOH A 14 514 154 HOH HOH . G 5 HOH A 15 515 93 HOH HOH . G 5 HOH A 16 516 140 HOH HOH . G 5 HOH A 17 517 44 HOH HOH . G 5 HOH A 18 518 63 HOH HOH . G 5 HOH A 19 519 82 HOH HOH . G 5 HOH A 20 520 17 HOH HOH . G 5 HOH A 21 521 9 HOH HOH . G 5 HOH A 22 522 158 HOH HOH . G 5 HOH A 23 523 8 HOH HOH . G 5 HOH A 24 524 20 HOH HOH . G 5 HOH A 25 525 49 HOH HOH . G 5 HOH A 26 526 47 HOH HOH . G 5 HOH A 27 527 124 HOH HOH . G 5 HOH A 28 528 1 HOH HOH . G 5 HOH A 29 529 62 HOH HOH . G 5 HOH A 30 530 10 HOH HOH . G 5 HOH A 31 531 116 HOH HOH . G 5 HOH A 32 532 11 HOH HOH . G 5 HOH A 33 533 58 HOH HOH . G 5 HOH A 34 534 153 HOH HOH . G 5 HOH A 35 535 14 HOH HOH . G 5 HOH A 36 536 209 HOH HOH . G 5 HOH A 37 537 40 HOH HOH . G 5 HOH A 38 538 106 HOH HOH . G 5 HOH A 39 539 7 HOH HOH . G 5 HOH A 40 540 24 HOH HOH . G 5 HOH A 41 541 39 HOH HOH . G 5 HOH A 42 542 147 HOH HOH . G 5 HOH A 43 543 57 HOH HOH . G 5 HOH A 44 544 137 HOH HOH . G 5 HOH A 45 545 16 HOH HOH . G 5 HOH A 46 546 100 HOH HOH . G 5 HOH A 47 547 142 HOH HOH . G 5 HOH A 48 548 41 HOH HOH . G 5 HOH A 49 549 54 HOH HOH . G 5 HOH A 50 550 136 HOH HOH . G 5 HOH A 51 551 55 HOH HOH . G 5 HOH A 52 552 169 HOH HOH . G 5 HOH A 53 553 30 HOH HOH . G 5 HOH A 54 554 74 HOH HOH . G 5 HOH A 55 555 6 HOH HOH . G 5 HOH A 56 556 179 HOH HOH . G 5 HOH A 57 557 70 HOH HOH . G 5 HOH A 58 558 50 HOH HOH . G 5 HOH A 59 559 80 HOH HOH . G 5 HOH A 60 560 69 HOH HOH . G 5 HOH A 61 561 21 HOH HOH . G 5 HOH A 62 562 163 HOH HOH . G 5 HOH A 63 563 13 HOH HOH . G 5 HOH A 64 564 51 HOH HOH . G 5 HOH A 65 565 37 HOH HOH . G 5 HOH A 66 566 36 HOH HOH . G 5 HOH A 67 567 22 HOH HOH . G 5 HOH A 68 568 45 HOH HOH . G 5 HOH A 69 569 61 HOH HOH . G 5 HOH A 70 570 31 HOH HOH . G 5 HOH A 71 571 73 HOH HOH . G 5 HOH A 72 572 92 HOH HOH . G 5 HOH A 73 573 174 HOH HOH . G 5 HOH A 74 574 151 HOH HOH . G 5 HOH A 75 575 2 HOH HOH . G 5 HOH A 76 576 18 HOH HOH . G 5 HOH A 77 577 96 HOH HOH . G 5 HOH A 78 578 112 HOH HOH . G 5 HOH A 79 579 12 HOH HOH . G 5 HOH A 80 580 56 HOH HOH . G 5 HOH A 81 581 48 HOH HOH . G 5 HOH A 82 582 79 HOH HOH . G 5 HOH A 83 583 26 HOH HOH . G 5 HOH A 84 584 3 HOH HOH . G 5 HOH A 85 585 4 HOH HOH . G 5 HOH A 86 586 15 HOH HOH . G 5 HOH A 87 587 176 HOH HOH . G 5 HOH A 88 588 125 HOH HOH . G 5 HOH A 89 589 33 HOH HOH . G 5 HOH A 90 590 208 HOH HOH . G 5 HOH A 91 591 85 HOH HOH . G 5 HOH A 92 592 23 HOH HOH . G 5 HOH A 93 593 71 HOH HOH . G 5 HOH A 94 594 95 HOH HOH . G 5 HOH A 95 595 64 HOH HOH . G 5 HOH A 96 596 35 HOH HOH . G 5 HOH A 97 597 34 HOH HOH . G 5 HOH A 98 598 68 HOH HOH . G 5 HOH A 99 599 167 HOH HOH . G 5 HOH A 100 600 88 HOH HOH . G 5 HOH A 101 601 109 HOH HOH . G 5 HOH A 102 602 76 HOH HOH . G 5 HOH A 103 603 91 HOH HOH . G 5 HOH A 104 604 94 HOH HOH . G 5 HOH A 105 605 5 HOH HOH . G 5 HOH A 106 606 132 HOH HOH . G 5 HOH A 107 607 160 HOH HOH . G 5 HOH A 108 608 84 HOH HOH . G 5 HOH A 109 609 89 HOH HOH . G 5 HOH A 110 610 78 HOH HOH . G 5 HOH A 111 611 156 HOH HOH . G 5 HOH A 112 612 192 HOH HOH . G 5 HOH A 113 613 81 HOH HOH . G 5 HOH A 114 614 32 HOH HOH . G 5 HOH A 115 615 87 HOH HOH . G 5 HOH A 116 616 138 HOH HOH . G 5 HOH A 117 617 43 HOH HOH . G 5 HOH A 118 618 170 HOH HOH . G 5 HOH A 119 619 99 HOH HOH . G 5 HOH A 120 620 122 HOH HOH . G 5 HOH A 121 621 19 HOH HOH . G 5 HOH A 122 622 25 HOH HOH . G 5 HOH A 123 623 101 HOH HOH . G 5 HOH A 124 624 148 HOH HOH . G 5 HOH A 125 625 172 HOH HOH . G 5 HOH A 126 626 83 HOH HOH . G 5 HOH A 127 627 183 HOH HOH . G 5 HOH A 128 628 60 HOH HOH . G 5 HOH A 129 629 190 HOH HOH . G 5 HOH A 130 630 150 HOH HOH . G 5 HOH A 131 631 59 HOH HOH . G 5 HOH A 132 632 199 HOH HOH . G 5 HOH A 133 633 161 HOH HOH . G 5 HOH A 134 634 115 HOH HOH . G 5 HOH A 135 635 27 HOH HOH . G 5 HOH A 136 636 29 HOH HOH . G 5 HOH A 137 637 149 HOH HOH . G 5 HOH A 138 638 108 HOH HOH . G 5 HOH A 139 639 145 HOH HOH . G 5 HOH A 140 640 159 HOH HOH . G 5 HOH A 141 641 90 HOH HOH . G 5 HOH A 142 642 118 HOH HOH . G 5 HOH A 143 643 191 HOH HOH . G 5 HOH A 144 644 104 HOH HOH . G 5 HOH A 145 645 66 HOH HOH . G 5 HOH A 146 646 173 HOH HOH . G 5 HOH A 147 647 46 HOH HOH . G 5 HOH A 148 648 103 HOH HOH . G 5 HOH A 149 649 144 HOH HOH . G 5 HOH A 150 650 28 HOH HOH . G 5 HOH A 151 651 110 HOH HOH . G 5 HOH A 152 652 162 HOH HOH . G 5 HOH A 153 653 152 HOH HOH . G 5 HOH A 154 654 189 HOH HOH . G 5 HOH A 155 655 194 HOH HOH . G 5 HOH A 156 656 86 HOH HOH . G 5 HOH A 157 657 184 HOH HOH . G 5 HOH A 158 658 187 HOH HOH . G 5 HOH A 159 659 195 HOH HOH . G 5 HOH A 160 660 198 HOH HOH . G 5 HOH A 161 661 205 HOH HOH . G 5 HOH A 162 662 121 HOH HOH . G 5 HOH A 163 663 165 HOH HOH . G 5 HOH A 164 664 120 HOH HOH . G 5 HOH A 165 665 42 HOH HOH . G 5 HOH A 166 666 127 HOH HOH . G 5 HOH A 167 667 182 HOH HOH . G 5 HOH A 168 668 117 HOH HOH . G 5 HOH A 169 669 185 HOH HOH . G 5 HOH A 170 670 178 HOH HOH . G 5 HOH A 171 671 168 HOH HOH . G 5 HOH A 172 672 210 HOH HOH . G 5 HOH A 173 673 181 HOH HOH . G 5 HOH A 174 674 186 HOH HOH . G 5 HOH A 175 675 111 HOH HOH . G 5 HOH A 176 676 126 HOH HOH . G 5 HOH A 177 677 97 HOH HOH . G 5 HOH A 178 678 114 HOH HOH . G 5 HOH A 179 679 175 HOH HOH . G 5 HOH A 180 680 38 HOH HOH . G 5 HOH A 181 681 200 HOH HOH . G 5 HOH A 182 682 72 HOH HOH . G 5 HOH A 183 683 102 HOH HOH . G 5 HOH A 184 684 67 HOH HOH . G 5 HOH A 185 685 139 HOH HOH . G 5 HOH A 186 686 113 HOH HOH . G 5 HOH A 187 687 207 HOH HOH . G 5 HOH A 188 688 171 HOH HOH . G 5 HOH A 189 689 177 HOH HOH . G 5 HOH A 190 690 65 HOH HOH . G 5 HOH A 191 691 143 HOH HOH . G 5 HOH A 192 692 135 HOH HOH . G 5 HOH A 193 693 129 HOH HOH . G 5 HOH A 194 694 123 HOH HOH . G 5 HOH A 195 695 188 HOH HOH . G 5 HOH A 196 696 128 HOH HOH . G 5 HOH A 197 697 133 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 N N SFG . . . B 2 -41.624 5.916 -22.545 1 16.02 ? N SFG 401 A 1 HETATM 2 C CA SFG . . . B 2 -40.986 6.604 -21.417 1 15.72 ? CA SFG 401 A 1 HETATM 3 C C SFG . . . B 2 -40.857 8.074 -21.748 1 19.15 ? C SFG 401 A 1 HETATM 4 O O SFG . . . B 2 -41.372 8.511 -22.805 1 19.07 ? O SFG 401 A 1 HETATM 5 O OXT SFG . . . B 2 -40.237 8.821 -20.957 1 19.11 ? OXT SFG 401 A 1 HETATM 6 C CB SFG . . . B 2 -39.609 5.978 -21.114 1 15.05 ? CB SFG 401 A 1 HETATM 7 C CG SFG . . . B 2 -39.69 4.637 -20.353 1 13.54 ? CG SFG 401 A 1 HETATM 8 C CD SFG . . . B 2 -40.093 4.814 -18.879 1 14.28 ? CD SFG 401 A 1 HETATM 9 N NE SFG . . . B 2 -38.952 4.465 -18.026 1 12.75 ? NE SFG 401 A 1 HETATM 10 C C5' SFG . . . B 2 -41.254 3.895 -18.48 1 15.8 ? C5' SFG 401 A 1 HETATM 11 C C4' SFG . . . B 2 -42.613 4.331 -19.026 1 15.42 ? C4' SFG 401 A 1 HETATM 12 O O4' SFG . . . B 2 -42.673 4.129 -20.441 1 15.72 ? O4' SFG 401 A 1 HETATM 13 C C3' SFG . . . B 2 -43.746 3.477 -18.472 1 18.6 ? C3' SFG 401 A 1 HETATM 14 O O3' SFG . . . B 2 -44.227 3.963 -17.213 1 22.14 ? O3' SFG 401 A 1 HETATM 15 C C2' SFG . . . B 2 -44.787 3.555 -19.562 1 19.03 ? C2' SFG 401 A 1 HETATM 16 O O2' SFG . . . B 2 -45.427 4.835 -19.525 1 21 ? O2' SFG 401 A 1 HETATM 17 C C1' SFG . . . B 2 -43.929 3.547 -20.807 1 17.62 ? C1' SFG 401 A 1 HETATM 18 N N9 SFG . . . B 2 -43.621 2.183 -21.299 1 21.11 ? N9 SFG 401 A 1 HETATM 19 C C8 SFG . . . B 2 -42.449 1.522 -21.148 1 17.26 ? C8 SFG 401 A 1 HETATM 20 N N7 SFG . . . B 2 -42.5 0.319 -21.773 1 18.62 ? N7 SFG 401 A 1 HETATM 21 C C5 SFG . . . B 2 -43.732 0.203 -22.318 1 19.7 ? C5 SFG 401 A 1 HETATM 22 C C6 SFG . . . B 2 -44.447 -0.829 -23.102 1 21.03 ? C6 SFG 401 A 1 HETATM 23 N N6 SFG . . . B 2 -43.84 -1.995 -23.43 1 20.27 ? N6 SFG 401 A 1 HETATM 24 N N1 SFG . . . B 2 -45.722 -0.55 -23.476 1 19.57 ? N1 SFG 401 A 1 HETATM 25 C C2 SFG . . . B 2 -46.33 0.616 -23.149 1 20.04 ? C2 SFG 401 A 1 HETATM 26 N N3 SFG . . . B 2 -45.75 1.598 -22.43 1 17.3 ? N3 SFG 401 A 1 HETATM 27 C C4 SFG . . . B 2 -44.46 1.433 -22.011 1 18.97 ? C4 SFG 401 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #