data_1YPL # _model_server_result.job_id XmUkyNeYAfttfTWqiYufSQ _model_server_result.datetime_utc '2024-10-25 20:23:26' _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 1ypl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":7778}' # _entry.id 1YPL # _exptl.entry_id 1YPL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 100.45 _cell.angle_gamma 90 _cell.entry_id 1YPL _cell.length_a 70.131 _cell.length_b 71.63 _cell.length_c 72.198 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YPL _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N 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 3 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 D NA NA . H NA 7777 1_555 B O ARG 233 H ARG 221 1_555 ? ? ? A ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc2 D NA NA . H NA 7777 1_555 J O HOH . H HOH 9100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc3 D NA NA . H NA 7777 1_555 J O HOH . H HOH 9053 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc4 D NA NA . H NA 7777 1_555 B O LYS 236 H LYS 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc5 E NA NA . H NA 7778 1_555 B O LYS 174 H LYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc6 E NA NA . H NA 7778 1_555 B O THR 177 H THR 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc7 E NA NA . H NA 7778 1_555 J O HOH . H HOH 9095 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? covale ? covale1 C C GLU 8 I GLU 8 1_555 C N TYS 9 I TYS 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale2 C C TYS 9 I TYS 9 1_555 C N LEU 10 I LEU 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? metalc ? metalc8 E NA NA . H NA 7778 1_555 B O PHE 215 H PHE 204 4_546 ? ? ? A ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc9 E NA NA . H NA 7778 1_555 J O HOH . H HOH 9065 4_546 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc10 D NA NA . H NA 7777 1_555 J O HOH . H HOH 9048 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc11 D NA NA . H NA 7777 1_555 J O HOH . H HOH 9096 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc12 E NA NA . H NA 7778 1_555 J O HOH . H HOH 9067 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.882 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1YPL _atom_sites.fract_transf_matrix[1][1] 0.014259 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00263 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013961 _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] 0.014084 _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 4 NA H 1 7777 7777 NA NA . E 4 NA H 1 7778 7778 NA NA . F 5 RA8 H 1 5555 5555 RA8 RA8 . G 6 GOL H 1 6666 6666 GOL GOL . H 6 GOL H 1 6667 6667 GOL GOL . I 7 HOH L 1 9002 9002 HOH HOH . I 7 HOH L 2 9012 9012 HOH HOH . I 7 HOH L 3 9031 9031 HOH HOH . I 7 HOH L 4 9058 9058 HOH HOH . I 7 HOH L 5 9063 9063 HOH HOH . I 7 HOH L 6 9070 9070 HOH HOH . I 7 HOH L 7 9078 9078 HOH HOH . I 7 HOH L 8 9089 9089 HOH HOH . I 7 HOH L 9 9090 9090 HOH HOH . I 7 HOH L 10 9101 9101 HOH HOH . I 7 HOH L 11 9103 9103 HOH HOH . I 7 HOH L 12 9110 9110 HOH HOH . I 7 HOH L 13 9114 9114 HOH HOH . I 7 HOH L 14 9117 9117 HOH HOH . I 7 HOH L 15 9120 9120 HOH HOH . I 7 HOH L 16 9127 9127 HOH HOH . I 7 HOH L 17 9146 9146 HOH HOH . I 7 HOH L 18 9147 9147 HOH HOH . I 7 HOH L 19 9156 9156 HOH HOH . I 7 HOH L 20 9162 9162 HOH HOH . I 7 HOH L 21 9177 9177 HOH HOH . I 7 HOH L 22 9181 9181 HOH HOH . I 7 HOH L 23 9185 9185 HOH HOH . J 7 HOH H 1 9001 9001 HOH HOH . J 7 HOH H 2 9003 9003 HOH HOH . J 7 HOH H 3 9004 9004 HOH HOH . J 7 HOH H 4 9005 9005 HOH HOH . J 7 HOH H 5 9006 9006 HOH HOH . J 7 HOH H 6 9007 9007 HOH HOH . J 7 HOH H 7 9008 9008 HOH HOH . J 7 HOH H 8 9009 9009 HOH HOH . J 7 HOH H 9 9010 9010 HOH HOH . J 7 HOH H 10 9011 9011 HOH HOH . J 7 HOH H 11 9013 9013 HOH HOH . J 7 HOH H 12 9014 9014 HOH HOH . J 7 HOH H 13 9015 9015 HOH HOH . J 7 HOH H 14 9016 9016 HOH HOH . J 7 HOH H 15 9017 9017 HOH HOH . J 7 HOH H 16 9018 9018 HOH HOH . J 7 HOH H 17 9019 9019 HOH HOH . J 7 HOH H 18 9020 9020 HOH HOH . J 7 HOH H 19 9021 9021 HOH HOH . J 7 HOH H 20 9022 9022 HOH HOH . J 7 HOH H 21 9023 9023 HOH HOH . J 7 HOH H 22 9024 9024 HOH HOH . J 7 HOH H 23 9025 9025 HOH HOH . J 7 HOH H 24 9026 9026 HOH HOH . J 7 HOH H 25 9027 9027 HOH HOH . J 7 HOH H 26 9028 9028 HOH HOH . J 7 HOH H 27 9029 9029 HOH HOH . J 7 HOH H 28 9030 9030 HOH HOH . J 7 HOH H 29 9032 9032 HOH HOH . J 7 HOH H 30 9033 9033 HOH HOH . J 7 HOH H 31 9034 9034 HOH HOH . J 7 HOH H 32 9035 9035 HOH HOH . J 7 HOH H 33 9036 9036 HOH HOH . J 7 HOH H 34 9037 9037 HOH HOH . J 7 HOH H 35 9038 9038 HOH HOH . J 7 HOH H 36 9039 9039 HOH HOH . J 7 HOH H 37 9040 9040 HOH HOH . J 7 HOH H 38 9041 9041 HOH HOH . J 7 HOH H 39 9042 9042 HOH HOH . J 7 HOH H 40 9043 9043 HOH HOH . J 7 HOH H 41 9044 9044 HOH HOH . J 7 HOH H 42 9045 9045 HOH HOH . J 7 HOH H 43 9046 9046 HOH HOH . J 7 HOH H 44 9047 9047 HOH HOH . J 7 HOH H 45 9048 9048 HOH HOH . J 7 HOH H 46 9049 9049 HOH HOH . J 7 HOH H 47 9050 9050 HOH HOH . J 7 HOH H 48 9052 9052 HOH HOH . J 7 HOH H 49 9053 9053 HOH HOH . J 7 HOH H 50 9054 9054 HOH HOH . J 7 HOH H 51 9055 9055 HOH HOH . J 7 HOH H 52 9056 9056 HOH HOH . J 7 HOH H 53 9057 9057 HOH HOH . J 7 HOH H 54 9059 9059 HOH HOH . J 7 HOH H 55 9060 9060 HOH HOH . J 7 HOH H 56 9061 9061 HOH HOH . J 7 HOH H 57 9062 9062 HOH HOH . J 7 HOH H 58 9064 9064 HOH HOH . J 7 HOH H 59 9065 9065 HOH HOH . J 7 HOH H 60 9066 9066 HOH HOH . J 7 HOH H 61 9067 9067 HOH HOH . J 7 HOH H 62 9068 9068 HOH HOH . J 7 HOH H 63 9069 9069 HOH HOH . J 7 HOH H 64 9071 9071 HOH HOH . J 7 HOH H 65 9072 9072 HOH HOH . J 7 HOH H 66 9073 9073 HOH HOH . J 7 HOH H 67 9074 9074 HOH HOH . J 7 HOH H 68 9075 9075 HOH HOH . J 7 HOH H 69 9076 9076 HOH HOH . J 7 HOH H 70 9077 9077 HOH HOH . J 7 HOH H 71 9079 9079 HOH HOH . J 7 HOH H 72 9080 9080 HOH HOH . J 7 HOH H 73 9081 9081 HOH HOH . J 7 HOH H 74 9082 9082 HOH HOH . J 7 HOH H 75 9083 9083 HOH HOH . J 7 HOH H 76 9084 9084 HOH HOH . J 7 HOH H 77 9085 9085 HOH HOH . J 7 HOH H 78 9086 9086 HOH HOH . J 7 HOH H 79 9087 9087 HOH HOH . J 7 HOH H 80 9088 9088 HOH HOH . J 7 HOH H 81 9091 9091 HOH HOH . J 7 HOH H 82 9092 9092 HOH HOH . J 7 HOH H 83 9093 9093 HOH HOH . J 7 HOH H 84 9094 9094 HOH HOH . J 7 HOH H 85 9095 9095 HOH HOH . J 7 HOH H 86 9096 9096 HOH HOH . J 7 HOH H 87 9097 9097 HOH HOH . J 7 HOH H 88 9098 9098 HOH HOH . J 7 HOH H 89 9099 9099 HOH HOH . J 7 HOH H 90 9100 9100 HOH HOH . J 7 HOH H 91 9102 9102 HOH HOH . J 7 HOH H 92 9104 9104 HOH HOH . J 7 HOH H 93 9105 9105 HOH HOH . J 7 HOH H 94 9106 9106 HOH HOH . J 7 HOH H 95 9108 9108 HOH HOH . J 7 HOH H 96 9109 9109 HOH HOH . J 7 HOH H 97 9112 9112 HOH HOH . J 7 HOH H 98 9113 9113 HOH HOH . J 7 HOH H 99 9115 9115 HOH HOH . J 7 HOH H 100 9116 9116 HOH HOH . J 7 HOH H 101 9118 9118 HOH HOH . J 7 HOH H 102 9119 9119 HOH HOH . J 7 HOH H 103 9121 9121 HOH HOH . J 7 HOH H 104 9122 9122 HOH HOH . J 7 HOH H 105 9123 9123 HOH HOH . J 7 HOH H 106 9124 9124 HOH HOH . J 7 HOH H 107 9125 9125 HOH HOH . J 7 HOH H 108 9126 9126 HOH HOH . J 7 HOH H 109 9128 9128 HOH HOH . J 7 HOH H 110 9129 9129 HOH HOH . J 7 HOH H 111 9130 9130 HOH HOH . J 7 HOH H 112 9131 9131 HOH HOH . J 7 HOH H 113 9132 9132 HOH HOH . J 7 HOH H 114 9133 9133 HOH HOH . J 7 HOH H 115 9134 9134 HOH HOH . J 7 HOH H 116 9135 9135 HOH HOH . J 7 HOH H 117 9136 9136 HOH HOH . J 7 HOH H 118 9137 9137 HOH HOH . J 7 HOH H 119 9138 9138 HOH HOH . J 7 HOH H 120 9139 9139 HOH HOH . J 7 HOH H 121 9140 9140 HOH HOH . J 7 HOH H 122 9141 9141 HOH HOH . J 7 HOH H 123 9142 9142 HOH HOH . J 7 HOH H 124 9143 9143 HOH HOH . J 7 HOH H 125 9144 9144 HOH HOH . J 7 HOH H 126 9145 9145 HOH HOH . J 7 HOH H 127 9148 9148 HOH HOH . J 7 HOH H 128 9149 9149 HOH HOH . J 7 HOH H 129 9150 9150 HOH HOH . J 7 HOH H 130 9151 9151 HOH HOH . J 7 HOH H 131 9152 9152 HOH HOH . J 7 HOH H 132 9153 9153 HOH HOH . J 7 HOH H 133 9154 9154 HOH HOH . J 7 HOH H 134 9155 9155 HOH HOH . J 7 HOH H 135 9157 9157 HOH HOH . J 7 HOH H 136 9158 9158 HOH HOH . J 7 HOH H 137 9159 9159 HOH HOH . J 7 HOH H 138 9161 9161 HOH HOH . J 7 HOH H 139 9163 9163 HOH HOH . J 7 HOH H 140 9164 9164 HOH HOH . J 7 HOH H 141 9165 9165 HOH HOH . J 7 HOH H 142 9166 9166 HOH HOH . J 7 HOH H 143 9167 9167 HOH HOH . J 7 HOH H 144 9168 9168 HOH HOH . J 7 HOH H 145 9169 9169 HOH HOH . J 7 HOH H 146 9170 9170 HOH HOH . J 7 HOH H 147 9171 9171 HOH HOH . J 7 HOH H 148 9172 9172 HOH HOH . J 7 HOH H 149 9173 9173 HOH HOH . J 7 HOH H 150 9174 9174 HOH HOH . J 7 HOH H 151 9175 9175 HOH HOH . J 7 HOH H 152 9176 9176 HOH HOH . J 7 HOH H 153 9178 9178 HOH HOH . J 7 HOH H 154 9179 9179 HOH HOH . J 7 HOH H 155 9180 9180 HOH HOH . J 7 HOH H 156 9182 9182 HOH HOH . J 7 HOH H 157 9184 9184 HOH HOH . J 7 HOH H 158 9187 9187 HOH HOH . J 7 HOH H 159 9193 9193 HOH HOH . J 7 HOH H 160 9195 9195 HOH HOH . J 7 HOH H 161 9197 9197 HOH HOH . J 7 HOH H 162 9198 9198 HOH HOH . J 7 HOH H 163 9200 9200 HOH HOH . J 7 HOH H 164 9204 9204 HOH HOH . J 7 HOH H 165 9205 9205 HOH HOH . K 7 HOH I 1 9111 9111 HOH HOH . K 7 HOH I 2 9160 9160 HOH HOH . K 7 HOH I 3 9183 9183 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id E _atom_site.label_entity_id 4 _atom_site.Cartn_x 18.255 _atom_site.Cartn_y -15.536 _atom_site.Cartn_z 38.069 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 22.66 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 7778 _atom_site.auth_asym_id H _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #