data_5U0N
#
_model_server_result.job_id            IZ4ysguTAo0nf1Vo2COBGA 
_model_server_result.datetime_utc      '2024-11-13 20:37:27' 
_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          5u0n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":403}' 
#
_entry.id    5U0N 
#
_exptl.entry_id    5U0N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              454.473 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-xylopyranosyl)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            5U0N 
_cell.length_a            57.975 
_cell.length_b            67.385 
_cell.length_c            69.974 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5U0N 
_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 OE1 GLU 118 A GLU 98 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc2 A OD2 ASP 226 A ASP 206 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc3 C MG MG . A MG 402 1_555 E O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc4 C MG MG . A MG 402 1_555 E O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc5 C MG MG . A MG 402 1_555 E O HOH . A HOH 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? 
#
_chem_comp.formula           'C17 H34 N4 O10' 
_chem_comp.formula_weight    454.473 
_chem_comp.id                7XP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-xylopyranosyl)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
NAB CAS 7XP sing 1 n n 
OAH CAX 7XP sing 2 n n 
CAS CAM 7XP sing 3 n n 
CAS CBE 7XP sing 4 n n 
CAM CAR 7XP sing 5 n n 
CAX CBC 7XP sing 6 n n 
CAX CAU 7XP sing 7 n n 
CBC OAQ 7XP sing 8 n n 
CBC OAN 7XP sing 9 n n 
NAC CAU 7XP sing 10 n n 
OAQ CBE 7XP sing 11 n n 
CBE CAZ 7XP sing 12 n n 
CAU CAT 7XP sing 13 n n 
CAR NAA 7XP sing 14 n n 
CAR CBD 7XP sing 15 n n 
OAN CAL 7XP sing 16 n n 
CAZ CBD 7XP sing 17 n n 
CAZ OAJ 7XP sing 18 n n 
CAT CAL 7XP sing 19 n n 
CAT OAF 7XP sing 20 n n 
CBD O1 7XP sing 21 n n 
O6 C6 7XP sing 22 n n 
O1 C1 7XP sing 23 n n 
O5 C1 7XP sing 24 n n 
O5 C5 7XP sing 25 n n 
C6 C5 7XP sing 26 n n 
C1 C2 7XP sing 27 n n 
C5 C4 7XP sing 28 n n 
C2 N2 7XP sing 29 n n 
C2 C3 7XP sing 30 n n 
C4 C3 7XP sing 31 n n 
C4 O4 7XP sing 32 n n 
C3 O3 7XP sing 33 n n 
C4 H1 7XP sing 34 n n 
C5 H2 7XP sing 35 n n 
C6 H3 7XP sing 36 n n 
C6 H4 7XP sing 37 n n 
N2 H5 7XP sing 38 n n 
N2 H6 7XP sing 39 n n 
C3 H8 7XP sing 40 n n 
OAH H9 7XP sing 41 n n 
CAX H10 7XP sing 42 n n 
CAU H11 7XP sing 43 n n 
NAC H12 7XP sing 44 n n 
NAC H13 7XP sing 45 n n 
CAT H15 7XP sing 46 n n 
OAF H16 7XP sing 47 n n 
CAL H17 7XP sing 48 n n 
CAL H18 7XP sing 49 n n 
CBC H19 7XP sing 50 n n 
CBE H20 7XP sing 51 n n 
CAZ H21 7XP sing 52 n n 
OAJ H22 7XP sing 53 n n 
CAS H23 7XP sing 54 n n 
NAB H24 7XP sing 55 n n 
NAB H25 7XP sing 56 n n 
CAM H27 7XP sing 57 n n 
CAM H28 7XP sing 58 n n 
CAR H29 7XP sing 59 n n 
NAA H30 7XP sing 60 n n 
NAA H31 7XP sing 61 n n 
CBD H33 7XP sing 62 n n 
C1 H34 7XP sing 63 n n 
O6 H35 7XP sing 64 n n 
O4 H36 7XP sing 65 n n 
O3 H37 7XP sing 66 n n 
C2 H38 7XP sing 67 n n 
#
_atom_sites.entry_id                     5U0N 
_atom_sites.fract_transf_matrix[1][1]    0.017249 
_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]    0.01484 
_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]    0.014291 
_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 7XP A 1 403 1 7XP DRG . 
E 5 HOH A 1 501 107 HOH HOH . 
E 5 HOH A 2 502 86 HOH HOH . 
E 5 HOH A 3 503 121 HOH HOH . 
E 5 HOH A 4 504 37 HOH HOH . 
E 5 HOH A 5 505 18 HOH HOH . 
E 5 HOH A 6 506 122 HOH HOH . 
E 5 HOH A 7 507 80 HOH HOH . 
E 5 HOH A 8 508 3 HOH HOH . 
E 5 HOH A 9 509 137 HOH HOH . 
E 5 HOH A 10 510 90 HOH HOH . 
E 5 HOH A 11 511 117 HOH HOH . 
E 5 HOH A 12 512 78 HOH HOH . 
E 5 HOH A 13 513 24 HOH HOH . 
E 5 HOH A 14 514 28 HOH HOH . 
E 5 HOH A 15 515 75 HOH HOH . 
E 5 HOH A 16 516 32 HOH HOH . 
E 5 HOH A 17 517 30 HOH HOH . 
E 5 HOH A 18 518 56 HOH HOH . 
E 5 HOH A 19 519 26 HOH HOH . 
E 5 HOH A 20 520 4 HOH HOH . 
E 5 HOH A 21 521 102 HOH HOH . 
E 5 HOH A 22 522 97 HOH HOH . 
E 5 HOH A 23 523 125 HOH HOH . 
E 5 HOH A 24 524 72 HOH HOH . 
E 5 HOH A 25 525 123 HOH HOH . 
E 5 HOH A 26 526 89 HOH HOH . 
E 5 HOH A 27 527 120 HOH HOH . 
E 5 HOH A 28 528 39 HOH HOH . 
E 5 HOH A 29 529 106 HOH HOH . 
E 5 HOH A 30 530 19 HOH HOH . 
E 5 HOH A 31 531 16 HOH HOH . 
E 5 HOH A 32 532 17 HOH HOH . 
E 5 HOH A 33 533 8 HOH HOH . 
E 5 HOH A 34 534 65 HOH HOH . 
E 5 HOH A 35 535 76 HOH HOH . 
E 5 HOH A 36 536 25 HOH HOH . 
E 5 HOH A 37 537 101 HOH HOH . 
E 5 HOH A 38 538 85 HOH HOH . 
E 5 HOH A 39 539 1 HOH HOH . 
E 5 HOH A 40 540 73 HOH HOH . 
E 5 HOH A 41 541 135 HOH HOH . 
E 5 HOH A 42 542 31 HOH HOH . 
E 5 HOH A 43 543 5 HOH HOH . 
E 5 HOH A 44 544 111 HOH HOH . 
E 5 HOH A 45 545 22 HOH HOH . 
E 5 HOH A 46 546 113 HOH HOH . 
E 5 HOH A 47 547 15 HOH HOH . 
E 5 HOH A 48 548 58 HOH HOH . 
E 5 HOH A 49 549 6 HOH HOH . 
E 5 HOH A 50 550 35 HOH HOH . 
E 5 HOH A 51 551 67 HOH HOH . 
E 5 HOH A 52 552 46 HOH HOH . 
E 5 HOH A 53 553 54 HOH HOH . 
E 5 HOH A 54 554 81 HOH HOH . 
E 5 HOH A 55 555 112 HOH HOH . 
E 5 HOH A 56 556 140 HOH HOH . 
E 5 HOH A 57 557 38 HOH HOH . 
E 5 HOH A 58 558 13 HOH HOH . 
E 5 HOH A 59 559 130 HOH HOH . 
E 5 HOH A 60 560 42 HOH HOH . 
E 5 HOH A 61 561 70 HOH HOH . 
E 5 HOH A 62 562 7 HOH HOH . 
E 5 HOH A 63 563 119 HOH HOH . 
E 5 HOH A 64 564 9 HOH HOH . 
E 5 HOH A 65 565 139 HOH HOH . 
E 5 HOH A 66 566 96 HOH HOH . 
E 5 HOH A 67 567 104 HOH HOH . 
E 5 HOH A 68 568 40 HOH HOH . 
E 5 HOH A 69 569 83 HOH HOH . 
E 5 HOH A 70 570 60 HOH HOH . 
E 5 HOH A 71 571 62 HOH HOH . 
E 5 HOH A 72 572 79 HOH HOH . 
E 5 HOH A 73 573 129 HOH HOH . 
E 5 HOH A 74 574 68 HOH HOH . 
E 5 HOH A 75 575 126 HOH HOH . 
E 5 HOH A 76 576 51 HOH HOH . 
E 5 HOH A 77 577 114 HOH HOH . 
E 5 HOH A 78 578 34 HOH HOH . 
E 5 HOH A 79 579 55 HOH HOH . 
E 5 HOH A 80 580 82 HOH HOH . 
E 5 HOH A 81 581 128 HOH HOH . 
E 5 HOH A 82 582 87 HOH HOH . 
E 5 HOH A 83 583 103 HOH HOH . 
E 5 HOH A 84 584 91 HOH HOH . 
E 5 HOH A 85 585 133 HOH HOH . 
E 5 HOH A 86 586 118 HOH HOH . 
E 5 HOH A 87 587 132 HOH HOH . 
E 5 HOH A 88 588 116 HOH HOH . 
E 5 HOH A 89 589 98 HOH HOH . 
E 5 HOH A 90 590 45 HOH HOH . 
E 5 HOH A 91 591 48 HOH HOH . 
E 5 HOH A 92 592 108 HOH HOH . 
E 5 HOH A 93 593 47 HOH HOH . 
E 5 HOH A 94 594 105 HOH HOH . 
E 5 HOH A 95 595 41 HOH HOH . 
E 5 HOH A 96 596 115 HOH HOH . 
E 5 HOH A 97 597 12 HOH HOH . 
E 5 HOH A 98 598 50 HOH HOH . 
E 5 HOH A 99 599 94 HOH HOH . 
E 5 HOH A 100 600 138 HOH HOH . 
E 5 HOH A 101 601 44 HOH HOH . 
E 5 HOH A 102 602 99 HOH HOH . 
E 5 HOH A 103 603 71 HOH HOH . 
E 5 HOH A 104 604 131 HOH HOH . 
E 5 HOH A 105 605 93 HOH HOH . 
E 5 HOH A 106 606 59 HOH HOH . 
E 5 HOH A 107 607 109 HOH HOH . 
E 5 HOH A 108 608 49 HOH HOH . 
E 5 HOH A 109 609 52 HOH HOH . 
E 5 HOH A 110 610 141 HOH HOH . 
E 5 HOH A 111 611 74 HOH HOH . 
E 5 HOH A 112 612 69 HOH HOH . 
E 5 HOH A 113 613 110 HOH HOH . 
E 5 HOH A 114 614 100 HOH HOH . 
E 5 HOH A 115 615 36 HOH HOH . 
E 5 HOH A 116 616 92 HOH HOH . 
E 5 HOH A 117 617 134 HOH HOH . 
E 5 HOH A 118 618 127 HOH HOH . 
E 5 HOH A 119 619 124 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 C4 7XP . . . D 4 59.596 85.868 19.293 1 19.39 ? C4 7XP 403 A 1 
HETATM 2 C C5 7XP . . . D 4 59.713 86.244 17.804 1 21.51 ? C5 7XP 403 A 1 
HETATM 3 C C6 7XP . . . D 4 58.974 87.553 17.589 1 22.96 ? C6 7XP 403 A 1 
HETATM 4 N N2 7XP . . . D 4 62.39 83.357 19.104 1 13.5 ? N2 7XP 403 A 1 
HETATM 5 C C3 7XP . . . D 4 60.356 84.584 19.47 1 19.71 ? C3 7XP 403 A 1 
HETATM 6 O OAH 7XP . . . D 4 62.977 78.493 12.299 1 18.13 ? OAH 7XP 403 A 1 
HETATM 7 C CAX 7XP . . . D 4 64.04 78.52 13.249 1 17.56 ? CAX 7XP 403 A 1 
HETATM 8 C CAU 7XP . . . D 4 63.574 77.606 14.357 1 13.87 ? CAU 7XP 403 A 1 
HETATM 9 N NAC 7XP . . . D 4 63.485 76.287 13.773 1 11.91 ? NAC 7XP 403 A 1 
HETATM 10 C CAT 7XP . . . D 4 64.568 77.647 15.504 1 14.11 ? CAT 7XP 403 A 1 
HETATM 11 O OAF 7XP . . . D 4 64.187 76.752 16.564 1 17.49 ? OAF 7XP 403 A 1 
HETATM 12 C CAL 7XP . . . D 4 64.557 79.046 15.999 1 16.69 ? CAL 7XP 403 A 1 
HETATM 13 O OAN 7XP . . . D 4 65.098 79.865 14.929 1 16.6 ? OAN 7XP 403 A 1 
HETATM 14 C CBC 7XP . . . D 4 64.278 79.928 13.756 1 12.88 ? CBC 7XP 403 A 1 
HETATM 15 O OAQ 7XP . . . D 4 63.057 80.582 14.097 1 19.84 ? OAQ 7XP 403 A 1 
HETATM 16 C CBE 7XP . . . D 4 63.17 82.051 14.282 1 19.63 ? CBE 7XP 403 A 1 
HETATM 17 C CAZ 7XP . . . D 4 62.276 82.512 15.428 1 16.99 ? CAZ 7XP 403 A 1 
HETATM 18 O OAJ 7XP . . . D 4 62.63 81.859 16.64 1 18.97 ? OAJ 7XP 403 A 1 
HETATM 19 C CAS 7XP . . . D 4 62.718 82.853 13.005 1 20.86 ? CAS 7XP 403 A 1 
HETATM 20 N NAB 7XP . . . D 4 63.538 82.482 11.85 1 17.6 ? NAB 7XP 403 A 1 
HETATM 21 C CAM 7XP . . . D 4 62.717 84.395 13.19 1 16.51 ? CAM 7XP 403 A 1 
HETATM 22 C CAR 7XP . . . D 4 61.853 84.77 14.393 1 19.81 ? CAR 7XP 403 A 1 
HETATM 23 N NAA 7XP . . . D 4 61.732 86.252 14.573 1 18.17 ? NAA 7XP 403 A 1 
HETATM 24 C CBD 7XP . . . D 4 62.363 84.038 15.659 1 16.88 ? CBD 7XP 403 A 1 
HETATM 25 O O1 7XP . . . D 4 61.505 84.329 16.746 1 20.78 ? O1 7XP 403 A 1 
HETATM 26 C C1 7XP . . . D 4 61.96 85.297 17.692 1 17.68 ? C1 7XP 403 A 1 
HETATM 27 O O5 7XP . . . D 4 61.105 86.447 17.451 1 21.64 ? O5 7XP 403 A 1 
HETATM 28 O O6 7XP . . . D 4 59.106 87.991 16.228 1 22.41 ? O6 7XP 403 A 1 
HETATM 29 O O4 7XP . . . D 4 58.22 85.69 19.781 1 19.3 ? O4 7XP 403 A 1 
HETATM 30 O O3 7XP . . . D 4 60.195 84.072 20.816 1 18.4 ? O3 7XP 403 A 1 
HETATM 31 C C2 7XP . . . D 4 61.829 84.719 19.087 1 16.09 ? C2 7XP 403 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#