data_5U19
#
_model_server_result.job_id            tz957BD1H5_fco10aMS_eQ 
_model_server_result.datetime_utc      '2024-10-10 04:17:00' 
_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          5u19 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":403}' 
#
_entry.id    5U19 
#
_exptl.entry_id    5U19 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              482.526 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2-deoxy-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            5U19 
_cell.length_a            65.725 
_cell.length_b            67.383 
_cell.length_c            69.571 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5U19 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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 
_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                      4 
_struct_asym.id                             D 
_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 OE2 GLU 118 A GLU 98 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc2 A OD2 ASP 226 A ASP 206 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? 
metalc ? metalc3 C MG MG . A MG 402 1_555 E O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc4 C MG MG . A MG 402 1_555 E O HOH . A HOH 584 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc5 C MG MG . A MG 402 1_555 E O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? 
#
_chem_comp.formula           'C19 H38 N4 O10' 
_chem_comp.formula_weight    482.526 
_chem_comp.id                827 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside' 
_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
N28 C27 827 sing 1 n n 
O30 C29 827 sing 2 n n 
C27 C26 827 sing 3 n n 
C27 C08 827 sing 4 n n 
C26 C24 827 sing 5 n n 
C29 C06 827 sing 6 n n 
C29 C31 827 sing 7 n n 
N32 C33 827 sing 8 n n 
N32 C31 827 sing 9 n n 
C06 O07 827 sing 10 n n 
C06 O05 827 sing 11 n n 
O07 C08 827 sing 12 n n 
C24 N25 827 sing 13 n n 
C24 C11 827 sing 14 n n 
C08 C09 827 sing 15 n n 
C31 C02 827 sing 16 n n 
O05 C04 827 sing 17 n n 
C09 C11 827 sing 18 n n 
C09 O10 827 sing 19 n n 
C11 O12 827 sing 20 n n 
C02 O03 827 sing 21 n n 
C02 C04 827 sing 22 n n 
C02 C01 827 sing 23 n n 
O12 C13 827 sing 24 n n 
C16 C15 827 sing 25 n n 
C16 O17 827 sing 26 n n 
O14 C15 827 sing 27 n n 
O14 C13 827 sing 28 n n 
C15 C18 827 sing 29 n n 
C13 C22 827 sing 30 n n 
C18 C20 827 sing 31 n n 
C18 O19 827 sing 32 n n 
C22 C20 827 sing 33 n n 
C22 N23 827 sing 34 n n 
C20 O21 827 sing 35 n n 
C13 H1 827 sing 36 n n 
C15 H2 827 sing 37 n n 
C20 H3 827 sing 38 n n 
C22 H4 827 sing 39 n n 
C24 H5 827 sing 40 n n 
C04 H6 827 sing 41 n n 
C04 H7 827 sing 42 n n 
C06 H8 827 sing 43 n n 
C11 H9 827 sing 44 n n 
O17 H10 827 sing 45 n n 
C18 H11 827 sing 46 n n 
C27 H12 827 sing 47 n n 
C09 H13 827 sing 48 n n 
C31 H14 827 sing 49 n n 
C01 H15 827 sing 50 n n 
C01 H16 827 sing 51 n n 
C01 H17 827 sing 52 n n 
C16 H18 827 sing 53 n n 
C16 H19 827 sing 54 n n 
C26 H20 827 sing 55 n n 
C26 H21 827 sing 56 n n 
C08 H22 827 sing 57 n n 
O10 H23 827 sing 58 n n 
C29 H24 827 sing 59 n n 
O03 H25 827 sing 60 n n 
N32 H26 827 sing 61 n n 
C33 H28 827 sing 62 n n 
C33 H29 827 sing 63 n n 
C33 H30 827 sing 64 n n 
O30 H31 827 sing 65 n n 
N28 H32 827 sing 66 n n 
N28 H33 827 sing 67 n n 
N25 H35 827 sing 68 n n 
N25 H36 827 sing 69 n n 
N23 H38 827 sing 70 n n 
N23 H39 827 sing 71 n n 
O21 H41 827 sing 72 n n 
O19 H42 827 sing 73 n n 
#
_atom_sites.entry_id                     5U19 
_atom_sites.fract_transf_matrix[1][1]    0.015215 
_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]    0.014841 
_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]    0.014374 
_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 SAH A 1 401 1 SAH SAH . 
C 3 MG A 1 402 1 MG MG . 
D 4 827 A 1 403 1 827 LIG . 
E 5 HOH A 1 501 131 HOH HOH . 
E 5 HOH A 2 502 56 HOH HOH . 
E 5 HOH A 3 503 66 HOH HOH . 
E 5 HOH A 4 504 115 HOH HOH . 
E 5 HOH A 5 505 99 HOH HOH . 
E 5 HOH A 6 506 139 HOH HOH . 
E 5 HOH A 7 507 65 HOH HOH . 
E 5 HOH A 8 508 138 HOH HOH . 
E 5 HOH A 9 509 27 HOH HOH . 
E 5 HOH A 10 510 133 HOH HOH . 
E 5 HOH A 11 511 10 HOH HOH . 
E 5 HOH A 12 512 155 HOH HOH . 
E 5 HOH A 13 513 67 HOH HOH . 
E 5 HOH A 14 514 73 HOH HOH . 
E 5 HOH A 15 515 63 HOH HOH . 
E 5 HOH A 16 516 57 HOH HOH . 
E 5 HOH A 17 517 124 HOH HOH . 
E 5 HOH A 18 518 31 HOH HOH . 
E 5 HOH A 19 519 159 HOH HOH . 
E 5 HOH A 20 520 102 HOH HOH . 
E 5 HOH A 21 521 88 HOH HOH . 
E 5 HOH A 22 522 47 HOH HOH . 
E 5 HOH A 23 523 74 HOH HOH . 
E 5 HOH A 24 524 128 HOH HOH . 
E 5 HOH A 25 525 52 HOH HOH . 
E 5 HOH A 26 526 45 HOH HOH . 
E 5 HOH A 27 527 23 HOH HOH . 
E 5 HOH A 28 528 158 HOH HOH . 
E 5 HOH A 29 529 140 HOH HOH . 
E 5 HOH A 30 530 34 HOH HOH . 
E 5 HOH A 31 531 39 HOH HOH . 
E 5 HOH A 32 532 80 HOH HOH . 
E 5 HOH A 33 533 46 HOH HOH . 
E 5 HOH A 34 534 95 HOH HOH . 
E 5 HOH A 35 535 48 HOH HOH . 
E 5 HOH A 36 536 26 HOH HOH . 
E 5 HOH A 37 537 11 HOH HOH . 
E 5 HOH A 38 538 54 HOH HOH . 
E 5 HOH A 39 539 136 HOH HOH . 
E 5 HOH A 40 540 20 HOH HOH . 
E 5 HOH A 41 541 126 HOH HOH . 
E 5 HOH A 42 542 89 HOH HOH . 
E 5 HOH A 43 543 24 HOH HOH . 
E 5 HOH A 44 544 82 HOH HOH . 
E 5 HOH A 45 545 72 HOH HOH . 
E 5 HOH A 46 546 42 HOH HOH . 
E 5 HOH A 47 547 134 HOH HOH . 
E 5 HOH A 48 548 146 HOH HOH . 
E 5 HOH A 49 549 9 HOH HOH . 
E 5 HOH A 50 550 25 HOH HOH . 
E 5 HOH A 51 551 93 HOH HOH . 
E 5 HOH A 52 552 81 HOH HOH . 
E 5 HOH A 53 553 117 HOH HOH . 
E 5 HOH A 54 554 43 HOH HOH . 
E 5 HOH A 55 555 135 HOH HOH . 
E 5 HOH A 56 556 114 HOH HOH . 
E 5 HOH A 57 557 58 HOH HOH . 
E 5 HOH A 58 558 49 HOH HOH . 
E 5 HOH A 59 559 53 HOH HOH . 
E 5 HOH A 60 560 13 HOH HOH . 
E 5 HOH A 61 561 64 HOH HOH . 
E 5 HOH A 62 562 62 HOH HOH . 
E 5 HOH A 63 563 132 HOH HOH . 
E 5 HOH A 64 564 125 HOH HOH . 
E 5 HOH A 65 565 50 HOH HOH . 
E 5 HOH A 66 566 44 HOH HOH . 
E 5 HOH A 67 567 70 HOH HOH . 
E 5 HOH A 68 568 91 HOH HOH . 
E 5 HOH A 69 569 35 HOH HOH . 
E 5 HOH A 70 570 2 HOH HOH . 
E 5 HOH A 71 571 92 HOH HOH . 
E 5 HOH A 72 572 86 HOH HOH . 
E 5 HOH A 73 573 75 HOH HOH . 
E 5 HOH A 74 574 150 HOH HOH . 
E 5 HOH A 75 575 145 HOH HOH . 
E 5 HOH A 76 576 85 HOH HOH . 
E 5 HOH A 77 577 68 HOH HOH . 
E 5 HOH A 78 578 84 HOH HOH . 
E 5 HOH A 79 579 157 HOH HOH . 
E 5 HOH A 80 580 142 HOH HOH . 
E 5 HOH A 81 581 100 HOH HOH . 
E 5 HOH A 82 582 32 HOH HOH . 
E 5 HOH A 83 583 77 HOH HOH . 
E 5 HOH A 84 584 161 HOH HOH . 
E 5 HOH A 85 585 96 HOH HOH . 
E 5 HOH A 86 586 156 HOH HOH . 
E 5 HOH A 87 587 40 HOH HOH . 
E 5 HOH A 88 588 18 HOH HOH . 
E 5 HOH A 89 589 151 HOH HOH . 
E 5 HOH A 90 590 98 HOH HOH . 
E 5 HOH A 91 591 153 HOH HOH . 
E 5 HOH A 92 592 119 HOH HOH . 
E 5 HOH A 93 593 59 HOH HOH . 
E 5 HOH A 94 594 55 HOH HOH . 
E 5 HOH A 95 595 127 HOH HOH . 
E 5 HOH A 96 596 130 HOH HOH . 
E 5 HOH A 97 597 149 HOH HOH . 
E 5 HOH A 98 598 79 HOH HOH . 
E 5 HOH A 99 599 101 HOH HOH . 
E 5 HOH A 100 600 148 HOH HOH . 
E 5 HOH A 101 601 141 HOH HOH . 
E 5 HOH A 102 602 36 HOH HOH . 
E 5 HOH A 103 603 116 HOH HOH . 
E 5 HOH A 104 604 143 HOH HOH . 
E 5 HOH A 105 605 160 HOH HOH . 
E 5 HOH A 106 606 118 HOH HOH . 
E 5 HOH A 107 607 110 HOH HOH . 
E 5 HOH A 108 608 6 HOH HOH . 
E 5 HOH A 109 609 90 HOH HOH . 
E 5 HOH A 110 610 111 HOH HOH . 
E 5 HOH A 111 611 154 HOH HOH . 
E 5 HOH A 112 612 69 HOH HOH . 
E 5 HOH A 113 613 152 HOH HOH . 
E 5 HOH A 114 614 112 HOH HOH . 
E 5 HOH A 115 615 51 HOH HOH . 
E 5 HOH A 116 616 103 HOH HOH . 
E 5 HOH A 117 617 147 HOH HOH . 
E 5 HOH A 118 618 83 HOH HOH . 
E 5 HOH A 119 619 33 HOH HOH . 
E 5 HOH A 120 620 129 HOH HOH . 
E 5 HOH A 121 621 120 HOH HOH . 
E 5 HOH A 122 622 94 HOH HOH . 
E 5 HOH A 123 623 144 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 C C13 827 . . . D 4 -4.508 -18.085 17.724 1 33.43 ? C13 827 403 A 1 
HETATM 2 C C15 827 . . . D 4 -2.295 -19.122 17.57 1 37.28 ? C15 827 403 A 1 
HETATM 3 C C20 827 . . . D 4 -2.717 -17.441 19.328 1 30.51 ? C20 827 403 A 1 
HETATM 4 C C22 827 . . . D 4 -4.168 -17.617 19.138 1 37.88 ? C22 827 403 A 1 
HETATM 5 C C24 827 . . . D 4 -4.759 -17.553 14.503 1 34.95 ? C24 827 403 A 1 
HETATM 6 C C02 827 . . . D 4 -7.28 -10.804 16.128 1 31.06 ? C02 827 403 A 1 
HETATM 7 C C04 827 . . . D 4 -7.485 -12.281 16.57 1 29.91 ? C04 827 403 A 1 
HETATM 8 C C06 827 . . . D 4 -7.538 -13.045 14.296 1 29.93 ? C06 827 403 A 1 
HETATM 9 C C11 827 . . . D 4 -5.168 -16.933 15.819 1 29.76 ? C11 827 403 A 1 
HETATM 10 O O17 827 . . . D 4 -2.214 -21.501 17.612 1 49.99 ? O17 827 403 A 1 
HETATM 11 C C18 827 . . . D 4 -2.016 -18.755 19.037 1 35.9 ? C18 827 403 A 1 
HETATM 12 C C27 827 . . . D 4 -5.921 -15.688 13.239 1 32.87 ? C27 827 403 A 1 
HETATM 13 C C09 827 . . . D 4 -5.359 -15.43 15.693 1 25.58 ? C09 827 403 A 1 
HETATM 14 C C31 827 . . . D 4 -6.808 -10.639 14.742 1 27.04 ? C31 827 403 A 1 
HETATM 15 C C01 827 . . . D 4 -6.298 -10.247 17.198 1 32.8 ? C01 827 403 A 1 
HETATM 16 C C16 827 . . . D 4 -1.547 -20.335 17.146 1 43.24 ? C16 827 403 A 1 
HETATM 17 O O14 827 . . . D 4 -3.734 -19.336 17.37 1 32.39 ? O14 827 403 A 1 
HETATM 18 O O12 827 . . . D 4 -4.145 -17.136 16.811 1 31.64 ? O12 827 403 A 1 
HETATM 19 C C26 827 . . . D 4 -5.749 -17.19 13.393 1 33.87 ? C26 827 403 A 1 
HETATM 20 C C08 827 . . . D 4 -6.306 -15.028 14.559 1 28.96 ? C08 827 403 A 1 
HETATM 21 O O10 827 . . . D 4 -5.843 -14.956 16.937 1 28.93 ? O10 827 403 A 1 
HETATM 22 O O07 827 . . . D 4 -6.251 -13.592 14.428 1 28.67 ? O07 827 403 A 1 
HETATM 23 C C29 827 . . . D 4 -7.437 -11.587 13.774 1 29.81 ? C29 827 403 A 1 
HETATM 24 O O05 827 . . . D 4 -8.217 -13.068 15.573 1 28.18 ? O05 827 403 A 1 
HETATM 25 O O03 827 . . . D 4 -8.517 -10.156 16.293 1 36.6 ? O03 827 403 A 1 
HETATM 26 N N32 827 . . . D 4 -7.191 -9.313 14.156 1 22.84 ? N32 827 403 A 1 
HETATM 27 C C33 827 . . . D 4 -6.321 -8.23 14.636 1 23.61 ? C33 827 403 A 1 
HETATM 28 O O30 827 . . . D 4 -6.694 -11.56 12.575 1 25.81 ? O30 827 403 A 1 
HETATM 29 N N28 827 . . . D 4 -6.939 -15.448 12.207 1 28.68 ? N28 827 403 A 1 
HETATM 30 N N25 827 . . . D 4 -4.707 -18.986 14.644 1 38.09 ? N25 827 403 A 1 
HETATM 31 N N23 827 . . . D 4 -4.883 -16.385 19.442 1 32.66 ? N23 827 403 A 1 
HETATM 32 O O21 827 . . . D 4 -2.444 -16.984 20.688 1 32.84 ? O21 827 403 A 1 
HETATM 33 O O19 827 . . . D 4 -0.598 -18.712 19.335 1 31.01 ? O19 827 403 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           33 
#