data_6E0D
#
_model_server_result.job_id            S1O1r1EezOWaCqeChBL8Bw 
_model_server_result.datetime_utc      '2024-11-24 14:51:59' 
_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              23 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           507 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           22 
#