data_1Y2W # _model_server_result.job_id R-9foqCNWue1kVup-Mnq-Q _model_server_result.datetime_utc '2025-02-27 01:05:15' _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 1y2w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":146}' # _entry.id 1Y2W # _exptl.entry_id 1Y2W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 105.093 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SERINE _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 1Y2W _cell.length_a 91.9 _cell.length_b 96.799 _cell.length_c 75.156 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y2W _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _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,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 91.9 0 37.578 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G 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 GAL _pdbx_entity_branch_link.comp_id_2 NGA _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 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _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 NGA 1 C 1 NGA A 144 NGA 2 n C GAL 2 C 2 GAL A 145 GAL 2 n D NGA 1 D 1 NGA B 144 NGA 2 n D GAL 2 D 2 GAL B 145 GAL # 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 covale ? covale1 F OG SER . A SER 146 1_555 C C1 NGA . C NGA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale2 F OG SER . A SER 146 1_555 C O5 NGA . C NGA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? covale ? covale3 G OG SER . B SER 146 1_555 D C1 NGA . D NGA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale4 G OG SER . B SER 146 1_555 D O5 NGA . D NGA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? covale ? covale5 C O3 NGA . C NGA 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale6 D O3 NGA . D NGA 1 1_555 D C1 GAL . D GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _chem_comp.formula 'C3 H7 N O3' _chem_comp.formula_weight 105.093 _chem_comp.id SER _chem_comp.mon_nstd_flag y _chem_comp.name SERINE _chem_comp.type 'l-peptide linking' _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 N CA SER sing 361 n n N H SER sing 362 n n N H2 SER sing 363 n n CA C SER sing 364 n n CA CB SER sing 365 n n CA HA SER sing 366 n n C O SER doub 367 n n C OXT SER sing 368 n n CB OG SER sing 369 n n CB HB2 SER sing 370 n n CB HB3 SER sing 371 n n OG HG SER sing 372 n n OXT HXT SER sing 373 n n # _atom_sites.entry_id 1Y2W _atom_sites.fract_transf_matrix[1][1] 0.010881 _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] 0.010331 _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] 0.013306 _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 E 3 NAG A 1 147 147 NAG NAG . F 4 SER A 1 146 146 SER SER . G 4 SER B 1 146 146 SER SER . H 5 HOH A 1 148 1 HOH HOH . H 5 HOH A 2 149 2 HOH HOH . H 5 HOH A 3 150 4 HOH HOH . H 5 HOH A 4 151 5 HOH HOH . H 5 HOH A 5 152 6 HOH HOH . H 5 HOH A 6 153 7 HOH HOH . H 5 HOH A 7 154 16 HOH HOH . H 5 HOH A 8 155 17 HOH HOH . H 5 HOH A 9 156 19 HOH HOH . H 5 HOH A 10 157 21 HOH HOH . H 5 HOH A 11 158 24 HOH HOH . H 5 HOH A 12 159 25 HOH HOH . H 5 HOH A 13 160 26 HOH HOH . H 5 HOH A 14 161 27 HOH HOH . H 5 HOH A 15 162 29 HOH HOH . H 5 HOH A 16 163 30 HOH HOH . H 5 HOH A 17 164 31 HOH HOH . H 5 HOH A 18 165 32 HOH HOH . H 5 HOH A 19 166 33 HOH HOH . H 5 HOH A 20 167 38 HOH HOH . H 5 HOH A 21 168 39 HOH HOH . H 5 HOH A 22 169 40 HOH HOH . H 5 HOH A 23 170 41 HOH HOH . H 5 HOH A 24 171 42 HOH HOH . H 5 HOH A 25 172 43 HOH HOH . H 5 HOH A 26 173 44 HOH HOH . H 5 HOH A 27 174 46 HOH HOH . H 5 HOH A 28 175 47 HOH HOH . H 5 HOH A 29 176 49 HOH HOH . H 5 HOH A 30 177 50 HOH HOH . H 5 HOH A 31 178 53 HOH HOH . H 5 HOH A 32 179 55 HOH HOH . H 5 HOH A 33 180 59 HOH HOH . H 5 HOH A 34 181 60 HOH HOH . H 5 HOH A 35 182 61 HOH HOH . H 5 HOH A 36 183 62 HOH HOH . H 5 HOH A 37 184 64 HOH HOH . H 5 HOH A 38 185 70 HOH HOH . H 5 HOH A 39 186 71 HOH HOH . H 5 HOH A 40 187 74 HOH HOH . H 5 HOH A 41 188 78 HOH HOH . H 5 HOH A 42 189 79 HOH HOH . H 5 HOH A 43 190 81 HOH HOH . H 5 HOH A 44 191 85 HOH HOH . H 5 HOH A 45 192 88 HOH HOH . H 5 HOH A 46 193 89 HOH HOH . H 5 HOH A 47 194 90 HOH HOH . H 5 HOH A 48 195 92 HOH HOH . H 5 HOH A 49 196 93 HOH HOH . H 5 HOH A 50 197 94 HOH HOH . H 5 HOH A 51 198 95 HOH HOH . H 5 HOH A 52 199 97 HOH HOH . H 5 HOH A 53 200 98 HOH HOH . H 5 HOH A 54 201 99 HOH HOH . H 5 HOH A 55 202 101 HOH HOH . H 5 HOH A 56 203 102 HOH HOH . H 5 HOH A 57 204 104 HOH HOH . H 5 HOH A 58 205 106 HOH HOH . H 5 HOH A 59 206 108 HOH HOH . H 5 HOH A 60 207 110 HOH HOH . H 5 HOH A 61 208 111 HOH HOH . H 5 HOH A 62 209 113 HOH HOH . H 5 HOH A 63 210 114 HOH HOH . H 5 HOH A 64 211 115 HOH HOH . H 5 HOH A 65 212 117 HOH HOH . H 5 HOH A 66 213 118 HOH HOH . H 5 HOH A 67 214 121 HOH HOH . H 5 HOH A 68 215 122 HOH HOH . H 5 HOH A 69 216 123 HOH HOH . I 5 HOH B 1 147 3 HOH HOH . I 5 HOH B 2 148 8 HOH HOH . I 5 HOH B 3 149 9 HOH HOH . I 5 HOH B 4 150 10 HOH HOH . I 5 HOH B 5 151 11 HOH HOH . I 5 HOH B 6 152 12 HOH HOH . I 5 HOH B 7 153 13 HOH HOH . I 5 HOH B 8 154 14 HOH HOH . I 5 HOH B 9 155 15 HOH HOH . I 5 HOH B 10 156 18 HOH HOH . I 5 HOH B 11 157 20 HOH HOH . I 5 HOH B 12 158 22 HOH HOH . I 5 HOH B 13 159 23 HOH HOH . I 5 HOH B 14 160 28 HOH HOH . I 5 HOH B 15 161 34 HOH HOH . I 5 HOH B 16 162 35 HOH HOH . I 5 HOH B 17 163 36 HOH HOH . I 5 HOH B 18 164 37 HOH HOH . I 5 HOH B 19 165 45 HOH HOH . I 5 HOH B 20 166 48 HOH HOH . I 5 HOH B 21 167 51 HOH HOH . I 5 HOH B 22 168 52 HOH HOH . I 5 HOH B 23 169 54 HOH HOH . I 5 HOH B 24 170 56 HOH HOH . I 5 HOH B 25 171 57 HOH HOH . I 5 HOH B 26 172 58 HOH HOH . I 5 HOH B 27 173 63 HOH HOH . I 5 HOH B 28 174 65 HOH HOH . I 5 HOH B 29 175 66 HOH HOH . I 5 HOH B 30 176 67 HOH HOH . I 5 HOH B 31 177 68 HOH HOH . I 5 HOH B 32 178 69 HOH HOH . I 5 HOH B 33 179 72 HOH HOH . I 5 HOH B 34 180 73 HOH HOH . I 5 HOH B 35 181 75 HOH HOH . I 5 HOH B 36 182 76 HOH HOH . I 5 HOH B 37 183 77 HOH HOH . I 5 HOH B 38 184 80 HOH HOH . I 5 HOH B 39 185 82 HOH HOH . I 5 HOH B 40 186 83 HOH HOH . I 5 HOH B 41 187 84 HOH HOH . I 5 HOH B 42 188 86 HOH HOH . I 5 HOH B 43 189 87 HOH HOH . I 5 HOH B 44 190 91 HOH HOH . I 5 HOH B 45 191 96 HOH HOH . I 5 HOH B 46 192 100 HOH HOH . I 5 HOH B 47 193 103 HOH HOH . I 5 HOH B 48 194 105 HOH HOH . I 5 HOH B 49 195 107 HOH HOH . I 5 HOH B 50 196 109 HOH HOH . I 5 HOH B 51 197 112 HOH HOH . I 5 HOH B 52 198 116 HOH HOH . I 5 HOH B 53 199 119 HOH HOH . I 5 HOH B 54 200 120 HOH HOH . I 5 HOH B 55 201 124 HOH HOH . I 5 HOH B 56 202 125 HOH HOH . I 5 HOH B 57 203 126 HOH HOH . I 5 HOH B 58 204 127 HOH HOH . I 5 HOH B 59 205 128 HOH HOH . I 5 HOH B 60 206 129 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 N SER . . . F 4 42.207 42.051 50.26 1 30.5 ? N SER 146 A 1 HETATM 2 C CA SER . . . F 4 43.462 42.832 50.044 1 30.29 ? CA SER 146 A 1 HETATM 3 C C SER . . . F 4 43.182 44.299 49.732 1 30.7 ? C SER 146 A 1 HETATM 4 O O SER . . . F 4 42.106 44.648 49.247 1 30.77 ? O SER 146 A 1 HETATM 5 C CB SER . . . F 4 44.319 42.206 48.935 1 30.2 ? CB SER 146 A 1 HETATM 6 O OG SER . . . F 4 43.574 41.95 47.746 1 27.86 ? OG SER 146 A 1 HETATM 7 O OXT SER . . . F 4 44.086 45.138 49.773 1 31.15 ? OXT SER 146 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 7 #