data_7RD2 # _model_server_result.job_id 1WdJRMDb0BqyzLh-JzC-nw _model_server_result.datetime_utc '2024-11-24 01:10:21' _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":"D","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 . . . D 3 -42.334 -26.442 -62.191 1 100.68 ? N1 5X7 901 A 1 HETATM 2 N N3 5X7 . . . D 3 -39.255 -31.056 -63.114 1 73.96 ? N3 5X7 901 A 1 HETATM 3 C C4 5X7 . . . D 3 -42.359 -22.874 -63.181 1 89.18 ? C4 5X7 901 A 1 HETATM 4 C C5 5X7 . . . D 3 -42.254 -25.23 -63.035 1 96.74 ? C5 5X7 901 A 1 HETATM 5 C C6 5X7 . . . D 3 -41.496 -27.625 -62.434 1 92.84 ? C6 5X7 901 A 1 HETATM 6 C C7 5X7 . . . D 3 -42.129 -28.775 -62.751 1 91.68 ? C7 5X7 901 A 1 HETATM 7 C C8 5X7 . . . D 3 -41.409 -29.895 -62.981 1 101.21 ? C8 5X7 901 A 1 HETATM 8 C C10 5X7 . . . D 3 -37.821 -30.907 -63.254 1 56.95 ? C10 5X7 901 A 1 HETATM 9 C C13 5X7 . . . D 3 -37.552 -30.747 -67.085 1 60.77 ? C13 5X7 901 A 1 HETATM 10 C C15 5X7 . . . D 3 -35.932 -29.301 -66.124 1 52.24 ? C15 5X7 901 A 1 HETATM 11 C C17 5X7 . . . D 3 -35.9 -29.375 -68.66 1 50.11 ? C17 5X7 901 A 1 HETATM 12 C C20 5X7 . . . D 3 -32.611 -30.713 -69.322 1 38.89 ? C20 5X7 901 A 1 HETATM 13 C C21 5X7 . . . D 3 -33.032 -32.041 -69.521 1 38.79 ? C21 5X7 901 A 1 HETATM 14 C C22 5X7 . . . D 3 -34.272 -32.089 -70.159 1 39.39 ? C22 5X7 901 A 1 HETATM 15 C C24 5X7 . . . D 3 -39.393 -28.7 -62.542 1 79.86 ? C24 5X7 901 A 1 HETATM 16 C C26 5X7 . . . D 3 -43.71 -26.552 -61.612 1 96.05 ? C26 5X7 901 A 1 HETATM 17 C C1 5X7 . . . D 3 -45.697 -25.311 -60.897 1 95.36 ? C1 5X7 901 A 1 HETATM 18 C C11 5X7 . . . D 3 -37.422 -30.576 -64.719 1 54.77 ? C11 5X7 901 A 1 HETATM 19 C C12 5X7 . . . D 3 -38.02 -31.133 -65.811 1 52.77 ? C12 5X7 901 A 1 HETATM 20 C C14 5X7 . . . D 3 -36.492 -29.832 -67.238 1 55.17 ? C14 5X7 901 A 1 HETATM 21 C C16 5X7 . . . D 3 -36.385 -29.678 -64.873 1 50.09 ? C16 5X7 901 A 1 HETATM 22 C C18 5X7 . . . D 3 -33.698 -29.925 -68.541 1 39.96 ? C18 5X7 901 A 1 HETATM 23 C C19 5X7 . . . D 3 -33.321 -28.502 -68.465 1 35.43 ? C19 5X7 901 A 1 HETATM 24 C C2 5X7 . . . D 3 -44.18 -25.24 -61.052 1 98.4 ? C2 5X7 901 A 1 HETATM 25 C C23 5X7 . . . D 3 -35.287 -31.473 -69.169 1 42.86 ? C23 5X7 901 A 1 HETATM 26 C C25 5X7 . . . D 3 -40.127 -27.562 -62.32 1 86.05 ? C25 5X7 901 A 1 HETATM 27 C C3 5X7 . . . D 3 -42.563 -24.126 -62.282 1 96.06 ? C3 5X7 901 A 1 HETATM 28 C C9 5X7 . . . D 3 -40.032 -29.842 -62.865 1 87.22 ? C9 5X7 901 A 1 HETATM 29 N N2 5X7 . . . D 3 -42.096 -31.112 -63.294 1 140.1 1 N2 5X7 901 A 1 HETATM 30 N N4 5X7 . . . D 3 -34.998 -30.1 -69.083 1 49.47 ? N4 5X7 901 A 1 HETATM 31 O O1 5X7 . . . D 3 -43.947 -24.238 -61.954 1 103.26 ? O1 5X7 901 A 1 HETATM 32 O O2 5X7 . . . D 3 -43.451 -31.285 -62.957 1 182.33 1 O2 5X7 901 A 1 HETATM 33 O O3 5X7 . . . D 3 -41.446 -32.166 -63.891 1 164.29 ? O3 5X7 901 A 1 HETATM 34 O O4 5X7 . . . D 3 -33.55 -27.998 -69.695 1 37.13 ? O4 5X7 901 A 1 HETATM 35 O O5 5X7 . . . D 3 -31.579 -30.892 -68.432 1 36.43 ? O5 5X7 901 A 1 HETATM 36 O O6 5X7 . . . D 3 -32.066 -32.695 -70.377 1 37.17 ? O6 5X7 901 A 1 HETATM 37 O O7 5X7 . . . D 3 -34.591 -33.43 -70.332 1 36.43 ? O7 5X7 901 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 227 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 37 #