data_5YNP # _model_server_result.job_id pxfLw4cYfjg7SH8-wLvLoA _model_server_result.datetime_utc '2024-11-23 11:35:11' _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 5ynp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5YNP # _exptl.entry_id 5YNP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 381.387 _entity.id 3 _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 5YNP _cell.length_a 67.88 _cell.length_b 70.045 _cell.length_c 119.72 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YNP _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 2 21' # _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 _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 3 _struct_asym.id C _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 B SG CYS 74 B CYS 74 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc2 B SG CYS 77 B CYS 77 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc3 B NE2 HIS 83 B HIS 83 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc4 B SG CYS 90 B CYS 90 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc5 B SG CYS 117 B CYS 117 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc6 B SG CYS 120 B CYS 120 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc7 B SG CYS 128 B CYS 128 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc8 B SG CYS 130 B CYS 130 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? # _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 376 n n N HN1 SFG sing 377 n n N HN2 SFG sing 378 n n CA C SFG sing 379 n n CA CB SFG sing 380 n n CA HA SFG sing 381 n n C O SFG doub 382 n n C OXT SFG sing 383 n n OXT HXT SFG sing 384 n n CB CG SFG sing 385 n n CB HB1 SFG sing 386 n n CB HB2 SFG sing 387 n n CG CD SFG sing 388 n n CG HG1 SFG sing 389 n n CG HG2 SFG sing 390 n n CD NE SFG sing 391 n n CD C5' SFG sing 392 n n CD HD SFG sing 393 n n NE HNE1 SFG sing 394 n n NE HNE2 SFG sing 395 n n C5' C4' SFG sing 396 n n C5' "H5'1" SFG sing 397 n n C5' "H5'2" SFG sing 398 n n C4' O4' SFG sing 399 n n C4' C3' SFG sing 400 n n C4' H4' SFG sing 401 n n O4' C1' SFG sing 402 n n C3' O3' SFG sing 403 n n C3' C2' SFG sing 404 n n C3' H3' SFG sing 405 n n O3' HO3' SFG sing 406 n n C2' O2' SFG sing 407 n n C2' C1' SFG sing 408 n n C2' H2' SFG sing 409 n n O2' HO2' SFG sing 410 n n C1' N9 SFG sing 411 n n C1' H1' SFG sing 412 n n N9 C8 SFG sing 413 n y N9 C4 SFG sing 414 n y C8 N7 SFG doub 415 n y C8 H8 SFG sing 416 n n N7 C5 SFG sing 417 n y C5 C6 SFG sing 418 n y C5 C4 SFG doub 419 n y C6 N6 SFG sing 420 n n C6 N1 SFG doub 421 n y N6 HN61 SFG sing 422 n n N6 HN62 SFG sing 423 n n N1 C2 SFG sing 424 n y C2 N3 SFG doub 425 n y C2 H2 SFG sing 426 n n N3 C4 SFG sing 427 n y # _atom_sites.entry_id 5YNP _atom_sites.fract_transf_matrix[1][1] 0.014732 _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] 0.014277 _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] 0.008353 _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 3 SFG A 1 401 401 SFG SFG . D 4 GTA A 1 402 451 GTA GTA . E 5 ZN B 1 201 998 ZN ZN . F 5 ZN B 1 202 999 ZN ZN . G 6 HOH A 1 501 47 HOH HOH . G 6 HOH A 2 502 79 HOH HOH . G 6 HOH A 3 503 53 HOH HOH . G 6 HOH A 4 504 42 HOH HOH . G 6 HOH A 5 505 33 HOH HOH . G 6 HOH A 6 506 1 HOH HOH . G 6 HOH A 7 507 5 HOH HOH . G 6 HOH A 8 508 27 HOH HOH . G 6 HOH A 9 509 20 HOH HOH . G 6 HOH A 10 510 17 HOH HOH . G 6 HOH A 11 511 25 HOH HOH . G 6 HOH A 12 512 18 HOH HOH . G 6 HOH A 13 513 31 HOH HOH . G 6 HOH A 14 514 32 HOH HOH . G 6 HOH A 15 515 8 HOH HOH . G 6 HOH A 16 516 6 HOH HOH . G 6 HOH A 17 517 41 HOH HOH . G 6 HOH A 18 518 9 HOH HOH . G 6 HOH A 19 519 63 HOH HOH . G 6 HOH A 20 520 10 HOH HOH . G 6 HOH A 21 521 68 HOH HOH . G 6 HOH A 22 522 40 HOH HOH . G 6 HOH A 23 523 56 HOH HOH . G 6 HOH A 24 524 115 HOH HOH . G 6 HOH A 25 525 66 HOH HOH . G 6 HOH A 26 526 43 HOH HOH . G 6 HOH A 27 527 62 HOH HOH . G 6 HOH A 28 528 52 HOH HOH . G 6 HOH A 29 529 118 HOH HOH . G 6 HOH A 30 530 13 HOH HOH . G 6 HOH A 31 531 21 HOH HOH . G 6 HOH A 32 532 12 HOH HOH . G 6 HOH A 33 533 23 HOH HOH . G 6 HOH A 34 534 4 HOH HOH . G 6 HOH A 35 535 7 HOH HOH . G 6 HOH A 36 536 65 HOH HOH . G 6 HOH A 37 537 37 HOH HOH . G 6 HOH A 38 538 14 HOH HOH . G 6 HOH A 39 539 77 HOH HOH . G 6 HOH A 40 540 3 HOH HOH . G 6 HOH A 41 541 64 HOH HOH . G 6 HOH A 42 542 24 HOH HOH . G 6 HOH A 43 543 2 HOH HOH . G 6 HOH A 44 544 29 HOH HOH . G 6 HOH A 45 545 19 HOH HOH . G 6 HOH A 46 546 30 HOH HOH . G 6 HOH A 47 547 38 HOH HOH . G 6 HOH A 48 548 55 HOH HOH . G 6 HOH A 49 549 80 HOH HOH . G 6 HOH A 50 550 15 HOH HOH . G 6 HOH A 51 551 67 HOH HOH . G 6 HOH A 52 552 50 HOH HOH . G 6 HOH A 53 553 101 HOH HOH . G 6 HOH A 54 554 22 HOH HOH . G 6 HOH A 55 555 99 HOH HOH . G 6 HOH A 56 556 28 HOH HOH . G 6 HOH A 57 557 44 HOH HOH . G 6 HOH A 58 558 49 HOH HOH . G 6 HOH A 59 559 36 HOH HOH . G 6 HOH A 60 560 72 HOH HOH . G 6 HOH A 61 561 54 HOH HOH . G 6 HOH A 62 562 102 HOH HOH . G 6 HOH A 63 563 26 HOH HOH . G 6 HOH A 64 564 74 HOH HOH . G 6 HOH A 65 565 11 HOH HOH . G 6 HOH A 66 566 69 HOH HOH . G 6 HOH A 67 567 104 HOH HOH . G 6 HOH A 68 568 59 HOH HOH . G 6 HOH A 69 569 51 HOH HOH . G 6 HOH A 70 570 92 HOH HOH . G 6 HOH A 71 571 73 HOH HOH . G 6 HOH A 72 572 61 HOH HOH . G 6 HOH A 73 573 81 HOH HOH . G 6 HOH A 74 574 39 HOH HOH . G 6 HOH A 75 575 95 HOH HOH . G 6 HOH A 76 576 83 HOH HOH . G 6 HOH A 77 577 105 HOH HOH . G 6 HOH A 78 578 116 HOH HOH . G 6 HOH A 79 579 93 HOH HOH . G 6 HOH A 80 580 113 HOH HOH . G 6 HOH A 81 581 86 HOH HOH . G 6 HOH A 82 582 96 HOH HOH . G 6 HOH A 83 583 82 HOH HOH . G 6 HOH A 84 584 120 HOH HOH . G 6 HOH A 85 585 109 HOH HOH . G 6 HOH A 86 586 91 HOH HOH . G 6 HOH A 87 587 98 HOH HOH . G 6 HOH A 88 588 108 HOH HOH . G 6 HOH A 89 589 94 HOH HOH . G 6 HOH A 90 590 111 HOH HOH . G 6 HOH A 91 591 78 HOH HOH . G 6 HOH A 92 592 75 HOH HOH . G 6 HOH A 93 593 89 HOH HOH . G 6 HOH A 94 594 70 HOH HOH . G 6 HOH A 95 595 97 HOH HOH . G 6 HOH A 96 596 110 HOH HOH . G 6 HOH A 97 597 117 HOH HOH . G 6 HOH A 98 598 114 HOH HOH . G 6 HOH A 99 599 100 HOH HOH . G 6 HOH A 100 600 85 HOH HOH . G 6 HOH A 101 601 107 HOH HOH . G 6 HOH A 102 602 90 HOH HOH . G 6 HOH A 103 603 84 HOH HOH . G 6 HOH A 104 604 106 HOH HOH . H 6 HOH B 1 301 46 HOH HOH . H 6 HOH B 2 302 34 HOH HOH . H 6 HOH B 3 303 35 HOH HOH . H 6 HOH B 4 304 71 HOH HOH . H 6 HOH B 5 305 76 HOH HOH . H 6 HOH B 6 306 16 HOH HOH . H 6 HOH B 7 307 57 HOH HOH . H 6 HOH B 8 308 45 HOH HOH . H 6 HOH B 9 309 48 HOH HOH . H 6 HOH B 10 310 112 HOH HOH . H 6 HOH B 11 311 60 HOH HOH . H 6 HOH B 12 312 58 HOH HOH . H 6 HOH B 13 313 103 HOH HOH . H 6 HOH B 14 314 87 HOH HOH . H 6 HOH B 15 315 119 HOH HOH . H 6 HOH B 16 316 88 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 . . . C 3 68.76 85.579 151.267 1 40.22 ? N SFG 401 A 1 HETATM 2 C CA SFG . . . C 3 68.736 84.349 150.479 1 43.23 ? CA SFG 401 A 1 HETATM 3 C C SFG . . . C 3 69.941 83.479 150.878 1 51.21 ? C SFG 401 A 1 HETATM 4 O O SFG . . . C 3 70.381 83.615 152.048 1 48.71 ? O SFG 401 A 1 HETATM 5 O OXT SFG . . . C 3 70.371 82.663 150.032 1 49.98 ? OXT SFG 401 A 1 HETATM 6 C CB SFG . . . C 3 68.726 84.653 148.966 1 37.07 ? CB SFG 401 A 1 HETATM 7 C CG SFG . . . C 3 67.472 85.488 148.67 1 39.29 ? CG SFG 401 A 1 HETATM 8 C CD SFG . . . C 3 67.073 85.489 147.207 1 30.73 ? CD SFG 401 A 1 HETATM 9 N NE SFG . . . C 3 68.242 85.636 146.379 1 40.11 ? NE SFG 401 A 1 HETATM 10 C C5' SFG . . . C 3 66.154 86.683 146.956 1 38.24 ? C5' SFG 401 A 1 HETATM 11 C C4' SFG . . . C 3 64.754 86.44 147.548 1 37.57 ? C4' SFG 401 A 1 HETATM 12 O O4' SFG . . . C 3 63.891 87.615 147.511 1 42.1 ? O4' SFG 401 A 1 HETATM 13 C C3' SFG . . . C 3 64.014 85.375 146.721 1 38.8 ? C3' SFG 401 A 1 HETATM 14 O O3' SFG . . . C 3 63.982 84.19 147.518 1 44.36 ? O3' SFG 401 A 1 HETATM 15 C C2' SFG . . . C 3 62.63 85.981 146.611 1 41.89 ? C2' SFG 401 A 1 HETATM 16 O O2' SFG . . . C 3 61.629 84.966 146.8 1 41.93 ? O2' SFG 401 A 1 HETATM 17 C C1' SFG . . . C 3 62.603 87.033 147.73 1 42.65 ? C1' SFG 401 A 1 HETATM 18 N N9 SFG . . . C 3 61.504 88.046 147.518 1 37.82 ? N9 SFG 401 A 1 HETATM 19 C C8 SFG . . . C 3 61.315 88.836 146.452 1 37.81 ? C8 SFG 401 A 1 HETATM 20 N N7 SFG . . . C 3 60.234 89.594 146.648 1 29.94 ? N7 SFG 401 A 1 HETATM 21 C C5 SFG . . . C 3 59.744 89.293 147.839 1 34.17 ? C5 SFG 401 A 1 HETATM 22 C C6 SFG . . . C 3 58.673 89.745 148.519 1 36.32 ? C6 SFG 401 A 1 HETATM 23 N N6 SFG . . . C 3 57.911 90.686 147.944 1 33.29 ? N6 SFG 401 A 1 HETATM 24 N N1 SFG . . . C 3 58.355 89.285 149.733 1 34.11 ? N1 SFG 401 A 1 HETATM 25 C C2 SFG . . . C 3 59.169 88.298 150.289 1 44.17 ? C2 SFG 401 A 1 HETATM 26 N N3 SFG . . . C 3 60.277 87.826 149.576 1 36.33 ? N3 SFG 401 A 1 HETATM 27 C C4 SFG . . . C 3 60.53 88.338 148.374 1 36.45 ? C4 SFG 401 A 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #