data_7RD2
#
_model_server_result.job_id            zg-lPiTbK1Lp97WTO7y7EQ 
_model_server_result.datetime_utc      '2024-11-24 01:06:17' 
_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          7rd2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":901}' 
#
_entry.id    7RD2 
#
_exptl.entry_id    7RD2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              516.587 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2R,3R,4R,5S)-1-{[4-({4-[(2R,6S)-2,6-dimethylmorpholin-4-yl]-2-nitroanilino}methyl)phenyl]methyl}-2-(hydroxymethyl)piperidine-3,4,5-triol 
_entity.pdbx_number_of_molecules    2 
_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            7RD2 
_cell.length_a            134.563 
_cell.length_b            178.393 
_cell.length_c            179.677 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7RD2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,H,I,J,K,L,S 1 1 
B,C,M,N,O,P,Q,R,T 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 M N N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   NAG 
_pdbx_entity_branch_link.comp_id_2                   NAG 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O4 
_pdbx_entity_branch_link.leaving_atom_id_2           HO4 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n C NAG 1 C 1 NAG C 1 NAG 
2 n C NAG 2 C 2 NAG C 2 NAG 
#
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 656 A CYS 654 1_555 A SG CYS 670 A CYS 668 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf2 B SG CYS 656 B CYS 654 1_555 B SG CYS 670 B CYS 668 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
covale ? covale1 B ND2 ASN 47 B ASN 45 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale2 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? 
#
_chem_comp.formula           'C26 H36 N4 O7' 
_chem_comp.formula_weight    516.587 
_chem_comp.id                5X7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2R,3R,4R,5S)-1-{[4-({4-[(2R,6S)-2,6-dimethylmorpholin-4-yl]-2-nitroanilino}methyl)phenyl]methyl}-2-(hydroxymethyl)piperidine-3,4,5-triol 
_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
C1 C2 5X7 sing 1 n n 
O3 N2 5X7 doub 2 n n 
O2 N2 5X7 sing 3 n n 
N2 C8 5X7 sing 4 n n 
C2 C26 5X7 sing 5 n n 
C2 O1 5X7 sing 6 n n 
C26 N1 5X7 sing 7 n n 
C7 C8 5X7 doub 8 n y 
C7 C6 5X7 sing 9 n y 
C8 C9 5X7 sing 10 n y 
N1 C6 5X7 sing 11 n n 
N1 C5 5X7 sing 12 n n 
O1 C3 5X7 sing 13 n n 
C6 C25 5X7 doub 14 n y 
C9 N3 5X7 sing 15 n n 
C9 C24 5X7 doub 16 n y 
N3 C10 5X7 sing 17 n n 
C10 C11 5X7 sing 18 n n 
C25 C24 5X7 sing 19 n y 
C3 C5 5X7 sing 20 n n 
C3 C4 5X7 sing 21 n n 
C11 C12 5X7 doub 22 n y 
C11 C16 5X7 sing 23 n y 
C12 C13 5X7 sing 24 n y 
C16 C15 5X7 doub 25 n y 
C13 C14 5X7 doub 26 n y 
C15 C14 5X7 sing 27 n y 
C14 C17 5X7 sing 28 n n 
O7 C22 5X7 sing 29 n n 
C23 C22 5X7 sing 30 n n 
C23 N4 5X7 sing 31 n n 
C17 N4 5X7 sing 32 n n 
C22 C21 5X7 sing 33 n n 
N4 C18 5X7 sing 34 n n 
C21 C20 5X7 sing 35 n n 
C21 O6 5X7 sing 36 n n 
C18 C20 5X7 sing 37 n n 
C18 C19 5X7 sing 38 n n 
C20 O5 5X7 sing 39 n n 
C19 O4 5X7 sing 40 n n 
N3 H1 5X7 sing 41 n n 
C4 H2 5X7 sing 42 n n 
C4 H3 5X7 sing 43 n n 
C4 H4 5X7 sing 44 n n 
C5 H5 5X7 sing 45 n n 
C5 H6 5X7 sing 46 n n 
C7 H7 5X7 sing 47 n n 
C10 H8 5X7 sing 48 n n 
C10 H9 5X7 sing 49 n n 
C13 H10 5X7 sing 50 n n 
C15 H11 5X7 sing 51 n n 
C17 H12 5X7 sing 52 n n 
C17 H13 5X7 sing 53 n n 
C20 H14 5X7 sing 54 n n 
C21 H15 5X7 sing 55 n n 
C22 H16 5X7 sing 56 n n 
C24 H17 5X7 sing 57 n n 
C26 H18 5X7 sing 58 n n 
C26 H19 5X7 sing 59 n n 
C1 H20 5X7 sing 60 n n 
C1 H21 5X7 sing 61 n n 
C1 H22 5X7 sing 62 n n 
C12 H23 5X7 sing 63 n n 
C16 H24 5X7 sing 64 n n 
C18 H25 5X7 sing 65 n n 
C19 H26 5X7 sing 66 n n 
C19 H27 5X7 sing 67 n n 
C2 H28 5X7 sing 68 n n 
C23 H29 5X7 sing 69 n n 
C23 H30 5X7 sing 70 n n 
C25 H31 5X7 sing 71 n n 
C3 H32 5X7 sing 72 n n 
O4 H34 5X7 sing 73 n n 
O5 H35 5X7 sing 74 n n 
O6 H36 5X7 sing 75 n n 
O7 H37 5X7 sing 76 n n 
#
_atom_sites.entry_id                     7RD2 
_atom_sites.fract_transf_matrix[1][1]    0.007431 
_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]    0.005606 
_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]    0.005566 
_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
D 3 5X7 A 1 901 901 5X7 LIG . 
E 4 SO4 A 1 902 1 SO4 SO4 . 
F 4 SO4 A 1 903 2 SO4 SO4 . 
G 4 SO4 A 1 904 3 SO4 SO4 . 
H 4 SO4 A 1 905 4 SO4 SO4 . 
I 4 SO4 A 1 906 5 SO4 SO4 . 
J 4 SO4 A 1 907 6 SO4 SO4 . 
K 4 SO4 A 1 908 7 SO4 SO4 . 
L 4 SO4 A 1 909 8 SO4 SO4 . 
M 3 5X7 B 1 901 901 5X7 LIG . 
N 5 GOL B 1 902 1001 GOL GOL . 
O 4 SO4 B 1 903 9 SO4 SO4 . 
P 4 SO4 B 1 904 10 SO4 SO4 . 
Q 4 SO4 B 1 905 11 SO4 SO4 . 
R 4 SO4 B 1 906 12 SO4 SO4 . 
S 6 HOH A 1 1001 18 HOH HOH . 
S 6 HOH A 2 1002 21 HOH HOH . 
S 6 HOH A 3 1003 2 HOH HOH . 
S 6 HOH A 4 1004 25 HOH HOH . 
S 6 HOH A 5 1005 1 HOH HOH . 
S 6 HOH A 6 1006 157 HOH HOH . 
S 6 HOH A 7 1007 6 HOH HOH . 
S 6 HOH A 8 1008 23 HOH HOH . 
S 6 HOH A 9 1009 22 HOH HOH . 
S 6 HOH A 10 1010 16 HOH HOH . 
S 6 HOH A 11 1011 142 HOH HOH . 
S 6 HOH A 12 1012 80 HOH HOH . 
S 6 HOH A 13 1013 19 HOH HOH . 
S 6 HOH A 14 1014 110 HOH HOH . 
S 6 HOH A 15 1015 5 HOH HOH . 
S 6 HOH A 16 1016 11 HOH HOH . 
T 6 HOH B 1 1001 7 HOH HOH . 
T 6 HOH B 2 1002 9 HOH HOH . 
T 6 HOH B 3 1003 4 HOH HOH . 
T 6 HOH B 4 1004 12 HOH HOH . 
T 6 HOH B 5 1005 78 HOH HOH . 
T 6 HOH B 6 1006 26 HOH HOH . 
T 6 HOH B 7 1007 24 HOH HOH . 
T 6 HOH B 8 1008 10 HOH HOH . 
T 6 HOH B 9 1009 8 HOH HOH . 
T 6 HOH B 10 1010 28 HOH HOH . 
T 6 HOH B 11 1011 14 HOH HOH . 
T 6 HOH B 12 1012 17 HOH HOH . 
T 6 HOH B 13 1013 3 HOH HOH . 
T 6 HOH B 14 1014 13 HOH HOH . 
T 6 HOH B 15 1015 25 HOH HOH . 
T 6 HOH B 16 1016 29 HOH HOH . 
T 6 HOH B 17 1017 20 HOH HOH . 
T 6 HOH B 18 1018 23 HOH HOH . 
T 6 HOH B 19 1019 15 HOH HOH . 
T 6 HOH B 20 1020 201 HOH HOH . 
T 6 HOH B 21 1021 27 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 N1 5X7 . . . M 3 -13.237 -33.202 -39.276 1 75.32 ? N1 5X7 901 B 1 
HETATM 2 N N3 5X7 . . . M 3 -10.783 -38.451 -38.879 1 70.28 ? N3 5X7 901 B 1 
HETATM 3 C C4 5X7 . . . M 3 -15.637 -31.607 -36.801 1 75.36 ? C4 5X7 901 B 1 
HETATM 4 C C5 5X7 . . . M 3 -13.795 -32.615 -38.007 1 81.05 ? C5 5X7 901 B 1 
HETATM 5 C C6 5X7 . . . M 3 -12.613 -34.541 -39.196 1 76.31 ? C6 5X7 901 B 1 
HETATM 6 C C7 5X7 . . . M 3 -11.46 -34.777 -39.892 1 71.52 ? C7 5X7 901 B 1 
HETATM 7 C C8 5X7 . . . M 3 -10.849 -36.015 -39.81 1 73.85 ? C8 5X7 901 B 1 
HETATM 8 C C10 5X7 . . . M 3 -9.343 -38.772 -38.748 1 55.87 ? C10 5X7 901 B 1 
HETATM 9 C C13 5X7 . . . M 3 -7.341 -38.34 -35.524 1 61.3 ? C13 5X7 901 B 1 
HETATM 10 C C15 5X7 . . . M 3 -9.361 -39.549 -34.918 1 60.93 ? C15 5X7 901 B 1 
HETATM 11 C C17 5X7 . . . M 3 -7.594 -39.047 -32.997 1 68.47 ? C17 5X7 901 B 1 
HETATM 12 C C20 5X7 . . . M 3 -6.644 -42.361 -31.813 1 43.4 ? C20 5X7 901 B 1 
HETATM 13 C C21 5X7 . . . M 3 -5.453 -42.564 -32.619 1 42.37 ? C21 5X7 901 B 1 
HETATM 14 C C22 5X7 . . . M 3 -4.736 -41.315 -32.909 1 43.88 ? C22 5X7 901 B 1 
HETATM 15 C C24 5X7 . . . M 3 -12.523 -36.802 -38.295 1 72.87 ? C24 5X7 901 B 1 
HETATM 16 C C26 5X7 . . . M 3 -13.719 -32.504 -40.516 1 76.87 ? C26 5X7 901 B 1 
HETATM 17 C C1 5X7 . . . M 3 -15.543 -31.233 -41.706 1 68.55 ? C1 5X7 901 B 1 
HETATM 18 C C11 5X7 . . . M 3 -8.929 -38.861 -37.244 1 57.97 ? C11 5X7 901 B 1 
HETATM 19 C C12 5X7 . . . M 3 -7.729 -38.29 -36.882 1 56.21 ? C12 5X7 901 B 1 
HETATM 20 C C14 5X7 . . . M 3 -8.148 -38.969 -34.539 1 61.7 ? C14 5X7 901 B 1 
HETATM 21 C C16 5X7 . . . M 3 -9.765 -39.492 -36.279 1 62.34 ? C16 5X7 901 B 1 
HETATM 22 C C18 5X7 . . . M 3 -7.589 -41.329 -32.512 1 47.5 ? C18 5X7 901 B 1 
HETATM 23 C C19 5X7 . . . M 3 -8.821 -41.168 -31.643 1 46.59 ? C19 5X7 901 B 1 
HETATM 24 C C2 5X7 . . . M 3 -15.11 -32.225 -40.526 1 80.85 ? C2 5X7 901 B 1 
HETATM 25 C C23 5X7 . . . M 3 -5.684 -40.252 -33.568 1 44.59 ? C23 5X7 901 B 1 
HETATM 26 C C25 5X7 . . . M 3 -13.144 -35.547 -38.378 1 78.14 ? C25 5X7 901 B 1 
HETATM 27 C C3 5X7 . . . M 3 -15.288 -32.434 -38.072 1 82.22 ? C3 5X7 901 B 1 
HETATM 28 C C9 5X7 . . . M 3 -11.37 -37.06 -38.997 1 71.58 ? C9 5X7 901 B 1 
HETATM 29 N N2 5X7 . . . M 3 -9.666 -36.095 -40.607 1 87.85 1 N2 5X7 901 B 1 
HETATM 30 N N4 5X7 . . . M 3 -6.858 -40.068 -32.719 1 58.04 ? N4 5X7 901 B 1 
HETATM 31 O O1 5X7 . . . M 3 -15.595 -31.726 -39.242 1 85.16 ? O1 5X7 901 B 1 
HETATM 32 O O2 5X7 . . . M 3 -8.921 -37.286 -40.778 1 100.25 1 O2 5X7 901 B 1 
HETATM 33 O O3 5X7 . . . M 3 -9.27 -34.895 -41.203 1 87.55 ? O3 5X7 901 B 1 
HETATM 34 O O4 5X7 . . . M 3 -8.408 -40.567 -30.448 1 48.15 ? O4 5X7 901 B 1 
HETATM 35 O O5 5X7 . . . M 3 -7.314 -43.615 -31.726 1 44.07 ? O5 5X7 901 B 1 
HETATM 36 O O6 5X7 . . . M 3 -4.636 -43.487 -31.78 1 36.72 ? O6 5X7 901 B 1 
HETATM 37 O O7 5X7 . . . M 3 -3.551 -41.511 -33.693 1 39.32 ? O7 5X7 901 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    59 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           37 
#