data_1NNB # _model_server_result.job_id V_BSht_4nFl8xxLjzIbuNw _model_server_result.datetime_utc '2024-11-26 14:17:41' _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 1nnb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 1NNB # _exptl.entry_id 1NNB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 291.255 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID' _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 1NNB _cell.length_a 183.78 _cell.length_b 183.78 _cell.length_c 183.78 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NNB _symmetry.cell_setting ? _symmetry.Int_Tables_number 211 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4 3 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 15_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 16_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 disulf ? disulf1 A SG CYS 10 A CYS 93 1_555 A SG CYS 336 A CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf2 A SG CYS 42 A CYS 125 1_555 A SG CYS 47 A CYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 94 A CYS 177 1_555 A SG CYS 112 A CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 102 A CYS 185 1_555 A SG CYS 149 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 151 A CYS 234 1_555 A SG CYS 156 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf6 A SG CYS 197 A CYS 280 1_555 A SG CYS 210 A CYS 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 199 A CYS 282 1_555 A SG CYS 208 A CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf8 A SG CYS 237 A CYS 320 1_555 A SG CYS 255 A CYS 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 A SG CYS 340 A CYS 423 1_555 A SG CYS 366 A CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A O ASP 212 A ASP 295 1_555 B CA CA . A CA 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc2 A O GLY 216 A GLY 299 1_555 B CA CA . A CA 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc3 A OD2 ASP 243 A ASP 326 1_555 B CA CA . A CA 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc4 A O ASN 265 A ASN 348 1_555 B CA CA . A CA 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? # _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 1NNB _atom_sites.fract_transf_matrix[1][1] 0.005441 _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] 0.005441 _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] 0.005441 _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 CA A 1 471 471 CA CA . C 3 DAN A 1 500 500 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 . . . C 3 24.019 20.063 65.682 1 20.19 ? C1 DAN 500 A 1 HETATM 2 C C2 DAN . . . C 3 24.655 18.979 64.805 1 19.32 ? C2 DAN 500 A 1 HETATM 3 C C3 DAN . . . C 3 24.202 17.546 64.591 1 18.46 ? C3 DAN 500 A 1 HETATM 4 C C4 DAN . . . C 3 24.707 16.856 63.362 1 18.13 ? C4 DAN 500 A 1 HETATM 5 C C5 DAN . . . C 3 26.246 17.026 63.502 1 18.25 ? C5 DAN 500 A 1 HETATM 6 C C6 DAN . . . C 3 26.618 18.484 63.266 1 18.82 ? C6 DAN 500 A 1 HETATM 7 C C7 DAN . . . C 3 28.03 18.762 63.817 1 18.96 ? C7 DAN 500 A 1 HETATM 8 C C8 DAN . . . C 3 28.328 20.269 63.489 1 18.21 ? C8 DAN 500 A 1 HETATM 9 C C9 DAN . . . C 3 29.809 20.707 63.886 1 17.95 ? C9 DAN 500 A 1 HETATM 10 C C10 DAN . . . C 3 27.413 14.977 62.594 1 17.75 ? C10 DAN 500 A 1 HETATM 11 C C11 DAN . . . C 3 28.082 14.334 61.376 1 16.46 ? C11 DAN 500 A 1 HETATM 12 N N5 DAN . . . C 3 27.009 16.242 62.528 1 18.83 ? N5 DAN 500 A 1 HETATM 13 O O1A DAN . . . C 3 24.611 21.183 65.665 1 21.87 ? O1A DAN 500 A 1 HETATM 14 O O1B DAN . . . C 3 22.794 19.958 65.975 1 20.99 ? O1B DAN 500 A 1 HETATM 15 O O4 DAN . . . C 3 24.285 15.524 63.01 1 19.24 ? O4 DAN 500 A 1 HETATM 16 O O6 DAN . . . C 3 25.711 19.437 63.94 1 19.35 ? O6 DAN 500 A 1 HETATM 17 O O7 DAN . . . C 3 28.117 18.449 65.235 1 19.88 ? O7 DAN 500 A 1 HETATM 18 O O8 DAN . . . C 3 28.16 20.292 62.088 1 16.36 ? O8 DAN 500 A 1 HETATM 19 O O9 DAN . . . C 3 30.736 19.97 63.069 1 18.07 ? O9 DAN 500 A 1 HETATM 20 O O10 DAN . . . C 3 27.447 14.34 63.648 1 19.27 ? O10 DAN 500 A 1 HETATM 21 H H3 DAN . . . C 3 23.524 16.979 65.286 1 12 ? H3 DAN 500 A 1 HETATM 22 H H4 DAN . . . C 3 24.335 17.482 62.541 1 12 ? H4 DAN 500 A 1 HETATM 23 H H5 DAN . . . C 3 26.618 16.706 64.466 1 12 ? H5 DAN 500 A 1 HETATM 24 H H6 DAN . . . C 3 26.535 18.675 62.173 1 12 ? H6 DAN 500 A 1 HETATM 25 H H7 DAN . . . C 3 28.769 18.146 63.293 1 12 ? H7 DAN 500 A 1 HETATM 26 H H8 DAN . . . C 3 27.573 20.934 63.939 1 12 ? H8 DAN 500 A 1 HETATM 27 H H91 DAN . . . C 3 30.006 21.775 63.738 1 12 ? H91 DAN 500 A 1 HETATM 28 H H92 DAN . . . C 3 30.013 20.525 64.957 1 12 ? H92 DAN 500 A 1 HETATM 29 H HN5 DAN . . . C 3 27.31 16.775 61.763 1 12 ? HN5 DAN 500 A 1 HETATM 30 H HO4 DAN . . . C 3 23.313 15.54 62.986 1 12 ? HO4 DAN 500 A 1 HETATM 31 H HO7 DAN . . . C 3 27.239 18.2 65.561 1 12 ? HO7 DAN 500 A 1 HETATM 32 H HO8 DAN . . . C 3 29.035 20.316 61.671 1 12 ? HO8 DAN 500 A 1 HETATM 33 H HO9 DAN . . . C 3 30.818 20.381 62.188 1 12 ? HO9 DAN 500 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 508 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 33 #