data_1USX # _model_server_result.job_id oQdKiGsoDYCN32wjJNqI1A _model_server_result.datetime_utc '2025-03-09 02:32:17' _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 1usx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1572}' # _entry.id 1USX # _exptl.entry_id 1USX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 291.255 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID' _entity.pdbx_number_of_molecules 3 _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 1USX _cell.length_a 115.07 _cell.length_b 115.07 _cell.length_c 283.96 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1USX _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 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 PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,D,E,G,H 1 1 C,F,I 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 141.98 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 G N N ? 3 H N N ? 3 I 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 SIA _pdbx_entity_branch_link.comp_id_2 WIA _pdbx_entity_branch_link.atom_id_1 C2 _pdbx_entity_branch_link.leaving_atom_id_1 O2 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 S6 _pdbx_entity_branch_link.leaving_atom_id_2 HS6 _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 D WIA 1 D 1 WIA A 1572 WIA 2 n D SIA 2 D 2 SIA A 1571 SIA 2 n E WIA 1 E 1 WIA B 1571 WIA 2 n E SIA 2 E 2 SIA B 1570 SIA 2 n F WIA 1 F 1 WIA C 1571 WIA 2 n F SIA 2 F 2 SIA C 1570 SIA # 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 49 A CYS 172 1_555 A SG CYS 73 A CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 63 A CYS 186 1_555 A SG CYS 124 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 A SG CYS 115 A CYS 238 1_555 A SG CYS 128 A CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 A SG CYS 221 A CYS 344 1_555 A SG CYS 338 A CYS 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf5 A SG CYS 332 A CYS 455 1_555 A SG CYS 342 A CYS 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf6 A SG CYS 408 A CYS 531 1_555 A SG CYS 419 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 49 B CYS 172 1_555 B SG CYS 73 B CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf8 B SG CYS 63 B CYS 186 1_555 B SG CYS 124 B CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf9 B SG CYS 115 B CYS 238 1_555 B SG CYS 128 B CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf10 B SG CYS 221 B CYS 344 1_555 B SG CYS 338 B CYS 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf11 B SG CYS 332 B CYS 455 1_555 B SG CYS 342 B CYS 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 B SG CYS 408 B CYS 531 1_555 B SG CYS 419 B CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf13 C SG CYS 49 C CYS 172 1_555 C SG CYS 73 C CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf14 C SG CYS 63 C CYS 186 1_555 C SG CYS 124 C CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf15 C SG CYS 115 C CYS 238 1_555 C SG CYS 128 C CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf16 C SG CYS 221 C CYS 344 1_555 C SG CYS 338 C CYS 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf17 C SG CYS 332 C CYS 455 1_555 C SG CYS 342 C CYS 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf18 C SG CYS 408 C CYS 531 1_555 C SG CYS 419 C CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 D S6 WIA . D WIA 1 1_555 D C2 SIA . D SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.78 ? covale ? covale2 E S6 WIA . E WIA 1 1_555 E C2 SIA . E SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? covale ? covale3 F S6 WIA . F WIA 1 1_555 F C2 SIA . F SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.792 ? # _chem_comp.formula 'C11 H17 N O8' _chem_comp.formula_weight 291.255 _chem_comp.id DAN _chem_comp.mon_nstd_flag . _chem_comp.name '2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms Neu5Ac2en # 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 DAN sing 83 n n C1 O1A DAN doub 84 n n C1 O1B DAN sing 85 n n C2 C3 DAN doub 86 n n C2 O6 DAN sing 87 n n C3 C4 DAN sing 88 n n C3 H3 DAN sing 89 n n C4 C5 DAN sing 90 n n C4 O4 DAN sing 91 n n C4 H4 DAN sing 92 n n C5 C6 DAN sing 93 n n C5 N5 DAN sing 94 n n C5 H5 DAN sing 95 n n C6 C7 DAN sing 96 n n C6 O6 DAN sing 97 n n C6 H6 DAN sing 98 n n C7 C8 DAN sing 99 n n C7 O7 DAN sing 100 n n C7 H7 DAN sing 101 n n C8 C9 DAN sing 102 n n C8 O8 DAN sing 103 n n C8 H8 DAN sing 104 n n C9 O9 DAN sing 105 n n C9 H91 DAN sing 106 n n C9 H92 DAN sing 107 n n C10 C11 DAN sing 108 n n C10 N5 DAN sing 109 n n C10 O10 DAN doub 110 n n C11 H111 DAN sing 111 n n C11 H112 DAN sing 112 n n C11 H113 DAN sing 113 n n N5 HN5 DAN sing 114 n n O1B HO1B DAN sing 115 n n O4 HO4 DAN sing 116 n n O7 HO7 DAN sing 117 n n O8 HO8 DAN sing 118 n n O9 HO9 DAN sing 119 n n # _atom_sites.entry_id 1USX _atom_sites.fract_transf_matrix[1][1] 0.00869 _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] 0.00869 _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] 0.003522 _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 G 3 DAN A 1 1570 1570 DAN DAN . H 3 DAN B 1 1572 1572 DAN DAN . I 3 DAN C 1 1572 1572 DAN DAN . # 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 C1 DAN . . . I 3 25.456 -19.596 50.9 1 19.7 ? C1 DAN 1572 C 1 HETATM 2 C C2 DAN . . . I 3 24.332 -19.337 50.095 1 20.21 ? C2 DAN 1572 C 1 HETATM 3 C C3 DAN . . . I 3 23.036 -19.39 50.611 1 20.97 ? C3 DAN 1572 C 1 HETATM 4 C C4 DAN . . . I 3 21.931 -18.67 49.847 1 19.7 ? C4 DAN 1572 C 1 HETATM 5 C C5 DAN . . . I 3 22.314 -18.563 48.372 1 21.31 ? C5 DAN 1572 C 1 HETATM 6 C C6 DAN . . . I 3 23.701 -17.901 48.238 1 19.51 ? C6 DAN 1572 C 1 HETATM 7 C C7 DAN . . . I 3 24.09 -17.799 46.787 1 19.58 ? C7 DAN 1572 C 1 HETATM 8 C C8 DAN . . . I 3 25.298 -16.85 46.586 1 16.74 ? C8 DAN 1572 C 1 HETATM 9 C C9 DAN . . . I 3 25.895 -17.04 45.18 1 17.99 ? C9 DAN 1572 C 1 HETATM 10 C C10 DAN . . . I 3 20.529 -18.358 46.673 1 22.2 ? C10 DAN 1572 C 1 HETATM 11 C C11 DAN . . . I 3 19.613 -17.407 45.95 1 19.78 ? C11 DAN 1572 C 1 HETATM 12 N N5 DAN . . . I 3 21.283 -17.84 47.641 1 20.89 ? N5 DAN 1572 C 1 HETATM 13 O O1A DAN . . . I 3 26.443 -19.099 50.34 1 19.72 ? O1A DAN 1572 C 1 HETATM 14 O O1B DAN . . . I 3 25.632 -20.108 52.023 1 17.37 ? O1B DAN 1572 C 1 HETATM 15 O O4 DAN . . . I 3 20.869 -19.597 50.01 1 21.15 ? O4 DAN 1572 C 1 HETATM 16 O O6 DAN . . . I 3 24.653 -18.715 48.924 1 20.72 ? O6 DAN 1572 C 1 HETATM 17 O O7 DAN . . . I 3 24.389 -19.074 46.303 1 18.96 ? O7 DAN 1572 C 1 HETATM 18 O O8 DAN . . . I 3 24.89 -15.448 46.78 1 16.58 ? O8 DAN 1572 C 1 HETATM 19 O O9 DAN . . . I 3 24.908 -16.736 44.194 1 17.57 ? O9 DAN 1572 C 1 HETATM 20 O O10 DAN . . . I 3 20.553 -19.539 46.348 1 21.09 ? O10 DAN 1572 C 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #