data_3LYR # _model_server_result.job_id JyRWFFdq2JjIi5D3R_TWhg _model_server_result.datetime_utc '2025-02-05 10:59:39' _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 3lyr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":252}' # _entry.id 3LYR # _exptl.entry_id 3LYR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 18.038 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'AMMONIUM ION' _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 120 _cell.entry_id 3LYR _cell.length_a 134.218 _cell.length_b 134.218 _cell.length_c 72.391 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LYR _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 covale ? covale1 A C GLY 16 A GLY 23 1_555 A N MSE 17 A MSE 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C MSE 17 A MSE 24 1_555 A N ASN 18 A ASN 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C TRP 23 A TRP 30 1_555 A N MSE 24 A MSE 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale4 A C MSE 24 A MSE 31 1_555 A N GLN 25 A GLN 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 A C SER 126 A SER 133 1_555 A N MSE 127 A MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale6 A C MSE 127 A MSE 134 1_555 A N THR 128 A THR 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale7 A C GLU 142 A GLU 149 1_555 A N MSE 143 A MSE 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale8 A C MSE 143 A MSE 150 1_555 A N CYS 144 A CYS 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale9 A C ILE 152 A ILE 159 1_555 A N MSE 153 A MSE 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale10 A C MSE 153 A MSE 160 1_555 A N CYS 154 A CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale11 A C ASP 200 A ASP 207 1_555 A N MSE 201 A MSE 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale12 A C MSE 201 A MSE 208 1_555 A N ARG 202 A ARG 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 A C ASN 224 A ASN 231 1_555 A N MSE 225 A MSE 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale14 A C MSE 225 A MSE 232 1_555 A N PHE 226 A PHE 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? metalc ? metalc1 B ZN ZN . A ZN 1 1_555 A NE2 HIS 150 A HIS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc2 B ZN ZN . A ZN 1 1_555 A SG CYS 154 A CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc3 B ZN ZN . A ZN 1 1_555 A SG CYS 157 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc4 B ZN ZN . A ZN 1 1_555 A SG CYS 163 A CYS 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? # _chem_comp.formula 'H4 N 1' _chem_comp.formula_weight 18.038 _chem_comp.id NH4 _chem_comp.mon_nstd_flag . _chem_comp.name 'AMMONIUM ION' _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 N HN1 NH4 sing 237 n n N HN2 NH4 sing 238 n n N HN3 NH4 sing 239 n n N HN4 NH4 sing 240 n n # _atom_sites.entry_id 3LYR _atom_sites.fract_transf_matrix[1][1] 0.007451 _atom_sites.fract_transf_matrix[1][2] 0.004302 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008603 _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] 0.013814 _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 ZN A 1 1 1 ZN ZN . C 3 SO4 A 1 251 1 SO4 SO4 . D 4 NH4 A 1 252 1 NH4 NH4 . E 5 HOH A 1 2 2 HOH HOH . E 5 HOH A 2 3 3 HOH HOH . E 5 HOH A 3 4 4 HOH HOH . E 5 HOH A 4 5 5 HOH HOH . E 5 HOH A 5 6 6 HOH HOH . E 5 HOH A 6 7 7 HOH HOH . E 5 HOH A 7 253 1 HOH HOH . E 5 HOH A 8 254 9 HOH HOH . E 5 HOH A 9 255 10 HOH HOH . E 5 HOH A 10 256 11 HOH HOH . E 5 HOH A 11 257 13 HOH HOH . E 5 HOH A 12 258 14 HOH HOH . E 5 HOH A 13 259 15 HOH HOH . E 5 HOH A 14 260 16 HOH HOH . E 5 HOH A 15 261 17 HOH HOH . E 5 HOH A 16 262 18 HOH HOH . E 5 HOH A 17 263 19 HOH HOH . E 5 HOH A 18 264 20 HOH HOH . E 5 HOH A 19 265 21 HOH HOH . E 5 HOH A 20 266 22 HOH HOH . E 5 HOH A 21 267 23 HOH HOH . E 5 HOH A 22 268 24 HOH HOH . E 5 HOH A 23 269 25 HOH HOH . E 5 HOH A 24 270 26 HOH HOH . E 5 HOH A 25 271 27 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol N _atom_site.label_atom_id N _atom_site.label_comp_id NH4 _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 4 _atom_site.Cartn_x 63.272 _atom_site.Cartn_y 76.821 _atom_site.Cartn_z -28.705 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 35.53 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id N _atom_site.auth_comp_id NH4 _atom_site.auth_seq_id 252 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #