data_6E0D # _model_server_result.job_id G0xQ0IciBm-o0-hawwbqsg _model_server_result.datetime_utc '2024-11-08 08:36:45' _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 6e0d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 6E0D # _exptl.entry_id 6E0D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.358 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside' _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 6E0D _cell.length_a 58.654 _cell.length_b 58.654 _cell.length_c 151.586 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6E0D _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 disulf ? disulf1 A SG CYS 31 A CYS 9 1_555 A SG CYS 226 A CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 78 A CYS 56 1_555 A SG CYS 88 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf3 A SG CYS 93 A CYS 71 1_555 A SG CYS 99 A CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf4 A SG CYS 143 A CYS 121 1_555 A SG CYS 215 A CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf5 A SG CYS 148 A CYS 126 1_555 A SG CYS 199 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf6 A SG CYS 156 A CYS 134 1_555 A SG CYS 167 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf7 A SG CYS 171 A CYS 149 1_555 A SG CYS 180 A CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf8 A SG CYS 181 A CYS 159 1_555 A SG CYS 186 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? # _chem_comp.formula 'C12 H26 N4 O6' _chem_comp.formula_weight 322.358 _chem_comp.id XXX _chem_comp.mon_nstd_flag . _chem_comp.name '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms '(2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA N-3,4-DIOL;NEOMYCIN A;NEAMINE;(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucoside;(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-D-glucoside;(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-glucoside' # 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 O3A C4A XXX sing 370 n n O3A HO3A XXX sing 371 n n C4A C5A XXX sing 372 n n C4A C9 XXX sing 373 n n C4A H4A XXX sing 374 n n C5A O4A XXX sing 375 n n C5A C6A XXX sing 376 n n C5A H5A XXX sing 377 n n O4A HO4A XXX sing 378 n n C6A N1 XXX sing 379 n n C6A C7 XXX sing 380 n n C6A H6 XXX sing 381 n n N1 HN11 XXX sing 382 n n N1 HN12 XXX sing 383 n n C7 C8 XXX sing 384 n n C7 H71 XXX sing 385 n n C7 H72 XXX sing 386 n n C8 N2 XXX sing 387 n n C8 C9 XXX sing 388 n n C8 H8 XXX sing 389 n n N2 HN21 XXX sing 390 n n N2 HN22 XXX sing 391 n n C9 O1 XXX sing 392 n n C9 H9 XXX sing 393 n n O1 C1 XXX sing 394 n n C1 O5 XXX sing 395 n n C1 C2 XXX sing 396 n n C1 H1 XXX sing 397 n n O5 C5 XXX sing 398 n n C5 C6 XXX sing 399 n n C5 C4 XXX sing 400 n n C5 H5 XXX sing 401 n n C6 N3 XXX sing 402 n n C6 H61 XXX sing 403 n n C6 H62 XXX sing 404 n n N3 HN31 XXX sing 405 n n N3 HN32 XXX sing 406 n n C4 O4 XXX sing 407 n n C4 C3 XXX sing 408 n n C4 H4 XXX sing 409 n n O4 HO4 XXX sing 410 n n C3 O3 XXX sing 411 n n C3 C2 XXX sing 412 n n C3 H3 XXX sing 413 n n O3 HO3 XXX sing 414 n n C2 N4 XXX sing 415 n n C2 H2 XXX sing 416 n n N4 HN41 XXX sing 417 n n N4 HN42 XXX sing 418 n n # _atom_sites.entry_id 6E0D _atom_sites.fract_transf_matrix[1][1] 0.017049 _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] 0.017049 _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] 0.006597 _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 TLA A 1 501 501 TLA TLA . C 3 XXX A 1 502 1 XXX XXX . D 4 HOH A 1 601 333 HOH HOH . D 4 HOH A 2 602 366 HOH HOH . D 4 HOH A 3 603 393 HOH HOH . D 4 HOH A 4 604 326 HOH HOH . D 4 HOH A 5 605 380 HOH HOH . D 4 HOH A 6 606 377 HOH HOH . D 4 HOH A 7 607 404 HOH HOH . D 4 HOH A 8 608 306 HOH HOH . D 4 HOH A 9 609 386 HOH HOH . D 4 HOH A 10 610 384 HOH HOH . D 4 HOH A 11 611 337 HOH HOH . D 4 HOH A 12 612 307 HOH HOH . D 4 HOH A 13 613 330 HOH HOH . D 4 HOH A 14 614 329 HOH HOH . D 4 HOH A 15 615 320 HOH HOH . D 4 HOH A 16 616 351 HOH HOH . D 4 HOH A 17 617 323 HOH HOH . D 4 HOH A 18 618 399 HOH HOH . D 4 HOH A 19 619 344 HOH HOH . D 4 HOH A 20 620 370 HOH HOH . D 4 HOH A 21 621 341 HOH HOH . D 4 HOH A 22 622 325 HOH HOH . D 4 HOH A 23 623 328 HOH HOH . D 4 HOH A 24 624 359 HOH HOH . D 4 HOH A 25 625 373 HOH HOH . D 4 HOH A 26 626 349 HOH HOH . D 4 HOH A 27 627 364 HOH HOH . D 4 HOH A 28 628 369 HOH HOH . D 4 HOH A 29 629 387 HOH HOH . D 4 HOH A 30 630 372 HOH HOH . D 4 HOH A 31 631 390 HOH HOH . D 4 HOH A 32 632 361 HOH HOH . D 4 HOH A 33 633 324 HOH HOH . D 4 HOH A 34 634 357 HOH HOH . D 4 HOH A 35 635 312 HOH HOH . D 4 HOH A 36 636 303 HOH HOH . D 4 HOH A 37 637 314 HOH HOH . D 4 HOH A 38 638 342 HOH HOH . D 4 HOH A 39 639 343 HOH HOH . D 4 HOH A 40 640 407 HOH HOH . D 4 HOH A 41 641 339 HOH HOH . D 4 HOH A 42 642 318 HOH HOH . D 4 HOH A 43 643 305 HOH HOH . D 4 HOH A 44 644 313 HOH HOH . D 4 HOH A 45 645 340 HOH HOH . D 4 HOH A 46 646 403 HOH HOH . D 4 HOH A 47 647 352 HOH HOH . D 4 HOH A 48 648 302 HOH HOH . D 4 HOH A 49 649 331 HOH HOH . D 4 HOH A 50 650 311 HOH HOH . D 4 HOH A 51 651 350 HOH HOH . D 4 HOH A 52 652 338 HOH HOH . D 4 HOH A 53 653 412 HOH HOH . D 4 HOH A 54 654 385 HOH HOH . D 4 HOH A 55 655 358 HOH HOH . D 4 HOH A 56 656 360 HOH HOH . D 4 HOH A 57 657 391 HOH HOH . D 4 HOH A 58 658 397 HOH HOH . D 4 HOH A 59 659 410 HOH HOH . D 4 HOH A 60 660 354 HOH HOH . D 4 HOH A 61 661 316 HOH HOH . D 4 HOH A 62 662 334 HOH HOH . D 4 HOH A 63 663 347 HOH HOH . D 4 HOH A 64 664 376 HOH HOH . D 4 HOH A 65 665 321 HOH HOH . D 4 HOH A 66 666 394 HOH HOH . D 4 HOH A 67 667 346 HOH HOH . D 4 HOH A 68 668 398 HOH HOH . D 4 HOH A 69 669 336 HOH HOH . D 4 HOH A 70 670 395 HOH HOH . D 4 HOH A 71 671 383 HOH HOH . D 4 HOH A 72 672 381 HOH HOH . D 4 HOH A 73 673 304 HOH HOH . D 4 HOH A 74 674 310 HOH HOH . D 4 HOH A 75 675 411 HOH HOH . D 4 HOH A 76 676 408 HOH HOH . D 4 HOH A 77 677 317 HOH HOH . D 4 HOH A 78 678 309 HOH HOH . D 4 HOH A 79 679 362 HOH HOH . D 4 HOH A 80 680 402 HOH HOH . D 4 HOH A 81 681 368 HOH HOH . D 4 HOH A 82 682 348 HOH HOH . D 4 HOH A 83 683 308 HOH HOH . D 4 HOH A 84 684 319 HOH HOH . D 4 HOH A 85 685 332 HOH HOH . D 4 HOH A 86 686 315 HOH HOH . D 4 HOH A 87 687 378 HOH HOH . D 4 HOH A 88 688 327 HOH HOH . D 4 HOH A 89 689 363 HOH HOH . D 4 HOH A 90 690 375 HOH HOH . D 4 HOH A 91 691 355 HOH HOH . D 4 HOH A 92 692 353 HOH HOH . D 4 HOH A 93 693 301 HOH HOH . D 4 HOH A 94 694 356 HOH HOH . D 4 HOH A 95 695 345 HOH HOH . D 4 HOH A 96 696 374 HOH HOH . D 4 HOH A 97 697 322 HOH HOH . D 4 HOH A 98 698 371 HOH HOH . D 4 HOH A 99 699 382 HOH HOH . D 4 HOH A 100 700 406 HOH HOH . D 4 HOH A 101 701 401 HOH HOH . D 4 HOH A 102 702 379 HOH HOH . D 4 HOH A 103 703 389 HOH HOH . D 4 HOH A 104 704 335 HOH HOH . D 4 HOH A 105 705 388 HOH HOH . D 4 HOH A 106 706 405 HOH HOH . D 4 HOH A 107 707 367 HOH HOH . D 4 HOH A 108 708 409 HOH HOH . D 4 HOH A 109 709 365 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 O3A XXX . . . C 3 20.462 33.696 40.172 0.6 51.92 ? O3A XXX 502 A 1 HETATM 2 C C4A XXX . . . C 3 20.719 33.162 38.871 0.6 40.1 ? C4A XXX 502 A 1 HETATM 3 C C5A XXX . . . C 3 21.049 31.68 38.96 0.6 40.72 ? C5A XXX 502 A 1 HETATM 4 O O4A XXX . . . C 3 19.98 31.034 39.675 0.6 32.79 ? O4A XXX 502 A 1 HETATM 5 C C6A XXX . . . C 3 21.238 31.184 37.513 0.6 39.35 ? C6A XXX 502 A 1 HETATM 6 N N1 XXX . . . C 3 21.428 29.753 37.445 0.6 32.33 ? N1 XXX 502 A 1 HETATM 7 C C7 XXX . . . C 3 22.415 31.893 36.813 0.6 34.97 ? C7 XXX 502 A 1 HETATM 8 C C8 XXX . . . C 3 22.243 33.42 36.781 0.6 30.86 ? C8 XXX 502 A 1 HETATM 9 N N2 XXX . . . C 3 23.469 34.061 36.358 0.6 22.49 ? N2 XXX 502 A 1 HETATM 10 C C9 XXX . . . C 3 21.781 34.034 38.139 0.6 40.65 ? C9 XXX 502 A 1 HETATM 11 O O1 XXX . . . C 3 21.134 35.348 37.993 0.6 46.32 ? O1 XXX 502 A 1 HETATM 12 C C1 XXX . . . C 3 21.708 36.704 38.044 0.6 92.92 ? C1 XXX 502 A 1 HETATM 13 O O5 XXX . . . C 3 22.552 36.822 39.208 0.6 200 ? O5 XXX 502 A 1 HETATM 14 C C5 XXX . . . C 3 23.45 37.935 39.227 0.6 200 ? C5 XXX 502 A 1 HETATM 15 C C6 XXX . . . C 3 22.787 39.316 39.11 0.6 200 ? C6 XXX 502 A 1 HETATM 16 N N3 XXX . . . C 3 21.42 39.276 39.591 0.6 200 ? N3 XXX 502 A 1 HETATM 17 C C4 XXX . . . C 3 24.425 37.646 38.1 0.6 200 ? C4 XXX 502 A 1 HETATM 18 O O4 XXX . . . C 3 24.951 36.318 38.301 0.6 200 ? O4 XXX 502 A 1 HETATM 19 C C3 XXX . . . C 3 23.779 37.687 36.703 0.6 200 ? C3 XXX 502 A 1 HETATM 20 O O3 XXX . . . C 3 23.835 39.02 36.153 0.6 191.82 ? O3 XXX 502 A 1 HETATM 21 C C2 XXX . . . C 3 22.312 37.244 36.695 0.6 200 ? C2 XXX 502 A 1 HETATM 22 N N4 XXX . . . C 3 22.252 36.255 35.629 0.6 195.76 ? N4 XXX 502 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #