data_1YI1 # _model_server_result.job_id hoKKR-0ZuQeuOlJYhLysuw _model_server_result.datetime_utc '2024-11-28 12:28:32' _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 1yi1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":700}' # _entry.id 1YI1 # _exptl.entry_id 1YI1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 206.028 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ETHYL DIHYDROGEN DIPHOSPHATE' _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 1YI1 _cell.length_a 179.06 _cell.length_b 179.06 _cell.length_c 186.145 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YI1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 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 PQS tetrameric 4 author_and_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,C,D,E,F,G 1 1,2,3,4 A,B,C,D,E,F,G 2 1,4 # 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' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 89.53 155.070509 0 3 'crystal symmetry operation' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 62.048333 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 89.53 155.070509 62.048333 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 PRO 254 A PRO 339 1_555 A N CSD 255 A CSD 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C CSD 255 A CSD 340 1_555 A N ASP 256 A ASP 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OD1 ASP 453 A ASP 538 1_555 B MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc2 A OD1 ASN 480 A ASN 565 1_555 B MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc3 A O HIS 482 A HIS 567 1_555 B MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc4 B MG MG . A MG 699 1_555 E O2B P22 . A P22 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc5 B MG MG . A MG 699 1_555 E O2A P22 . A P22 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc6 B MG MG . A MG 699 1_555 G O HOH . A HOH 4113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? # _chem_comp.formula 'C2 H8 O7 P2' _chem_comp.formula_weight 206.028 _chem_comp.id P22 _chem_comp.mon_nstd_flag . _chem_comp.name 'ETHYL DIHYDROGEN DIPHOSPHATE' _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 C6 C7 P22 sing 418 n n C6 H61 P22 sing 419 n n C6 H62 P22 sing 420 n n C6 H63 P22 sing 421 n n C7 O7 P22 sing 422 n n C7 H71 P22 sing 423 n n C7 H72 P22 sing 424 n n O7 PA P22 sing 425 n n PA O1A P22 sing 426 n n PA O2A P22 doub 427 n n PA O3A P22 sing 428 n n O1A H1A P22 sing 429 n n O3A PB P22 sing 430 n n PB O1B P22 sing 431 n n PB O2B P22 doub 432 n n PB O3B P22 sing 433 n n O1B H1B P22 sing 434 n n O3B H3B P22 sing 435 n n # _atom_sites.entry_id 1YI1 _atom_sites.fract_transf_matrix[1][1] 0.005585 _atom_sites.fract_transf_matrix[1][2] 0.003224 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006449 _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] 0.005372 _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 MG A 1 699 699 MG MG . C 3 1TB A 1 695 695 1TB 1TB . D 4 NHE A 1 696 696 NHE NHE . E 5 P22 A 1 700 700 P22 P22 . F 6 FAD A 1 701 701 FAD FAD . G 7 HOH A 1 4000 4000 HOH HOH . G 7 HOH A 2 4001 4001 HOH HOH . G 7 HOH A 3 4002 4002 HOH HOH . G 7 HOH A 4 4003 4003 HOH HOH . G 7 HOH A 5 4004 4004 HOH HOH . G 7 HOH A 6 4005 4005 HOH HOH . G 7 HOH A 7 4006 4006 HOH HOH . G 7 HOH A 8 4007 4007 HOH HOH . G 7 HOH A 9 4008 4008 HOH HOH . G 7 HOH A 10 4009 4009 HOH HOH . G 7 HOH A 11 4010 4010 HOH HOH . G 7 HOH A 12 4011 4011 HOH HOH . G 7 HOH A 13 4012 4012 HOH HOH . G 7 HOH A 14 4013 4013 HOH HOH . G 7 HOH A 15 4014 4014 HOH HOH . G 7 HOH A 16 4015 4015 HOH HOH . G 7 HOH A 17 4016 4016 HOH HOH . G 7 HOH A 18 4017 4017 HOH HOH . G 7 HOH A 19 4018 4018 HOH HOH . G 7 HOH A 20 4019 4019 HOH HOH . G 7 HOH A 21 4020 4020 HOH HOH . G 7 HOH A 22 4021 4021 HOH HOH . G 7 HOH A 23 4022 4022 HOH HOH . G 7 HOH A 24 4023 4023 HOH HOH . G 7 HOH A 25 4024 4024 HOH HOH . G 7 HOH A 26 4025 4025 HOH HOH . G 7 HOH A 27 4026 4026 HOH HOH . G 7 HOH A 28 4027 4027 HOH HOH . G 7 HOH A 29 4028 4028 HOH HOH . G 7 HOH A 30 4029 4029 HOH HOH . G 7 HOH A 31 4030 4030 HOH HOH . G 7 HOH A 32 4031 4031 HOH HOH . G 7 HOH A 33 4032 4032 HOH HOH . G 7 HOH A 34 4033 4033 HOH HOH . G 7 HOH A 35 4034 4034 HOH HOH . G 7 HOH A 36 4035 4035 HOH HOH . G 7 HOH A 37 4036 4036 HOH HOH . G 7 HOH A 38 4037 4037 HOH HOH . G 7 HOH A 39 4038 4038 HOH HOH . G 7 HOH A 40 4039 4039 HOH HOH . G 7 HOH A 41 4040 4040 HOH HOH . G 7 HOH A 42 4041 4041 HOH HOH . G 7 HOH A 43 4042 4042 HOH HOH . G 7 HOH A 44 4043 4043 HOH HOH . G 7 HOH A 45 4044 4044 HOH HOH . G 7 HOH A 46 4045 4045 HOH HOH . G 7 HOH A 47 4046 4046 HOH HOH . G 7 HOH A 48 4047 4047 HOH HOH . G 7 HOH A 49 4048 4048 HOH HOH . G 7 HOH A 50 4049 4049 HOH HOH . G 7 HOH A 51 4050 4050 HOH HOH . G 7 HOH A 52 4051 4051 HOH HOH . G 7 HOH A 53 4052 4052 HOH HOH . G 7 HOH A 54 4053 4053 HOH HOH . G 7 HOH A 55 4054 4054 HOH HOH . G 7 HOH A 56 4055 4055 HOH HOH . G 7 HOH A 57 4056 4056 HOH HOH . G 7 HOH A 58 4057 4057 HOH HOH . G 7 HOH A 59 4058 4058 HOH HOH . G 7 HOH A 60 4059 4059 HOH HOH . G 7 HOH A 61 4060 4060 HOH HOH . G 7 HOH A 62 4061 4061 HOH HOH . G 7 HOH A 63 4062 4062 HOH HOH . G 7 HOH A 64 4063 4063 HOH HOH . G 7 HOH A 65 4064 4064 HOH HOH . G 7 HOH A 66 4065 4065 HOH HOH . G 7 HOH A 67 4066 4066 HOH HOH . G 7 HOH A 68 4067 4067 HOH HOH . G 7 HOH A 69 4068 4068 HOH HOH . G 7 HOH A 70 4069 4069 HOH HOH . G 7 HOH A 71 4070 4070 HOH HOH . G 7 HOH A 72 4071 4071 HOH HOH . G 7 HOH A 73 4072 4072 HOH HOH . G 7 HOH A 74 4073 4073 HOH HOH . G 7 HOH A 75 4074 4074 HOH HOH . G 7 HOH A 76 4075 4075 HOH HOH . G 7 HOH A 77 4076 4076 HOH HOH . G 7 HOH A 78 4077 4077 HOH HOH . G 7 HOH A 79 4078 4078 HOH HOH . G 7 HOH A 80 4079 4079 HOH HOH . G 7 HOH A 81 4080 4080 HOH HOH . G 7 HOH A 82 4081 4081 HOH HOH . G 7 HOH A 83 4082 4082 HOH HOH . G 7 HOH A 84 4083 4083 HOH HOH . G 7 HOH A 85 4084 4084 HOH HOH . G 7 HOH A 86 4085 4085 HOH HOH . G 7 HOH A 87 4086 4086 HOH HOH . G 7 HOH A 88 4087 4087 HOH HOH . G 7 HOH A 89 4088 4088 HOH HOH . G 7 HOH A 90 4089 4089 HOH HOH . G 7 HOH A 91 4090 4090 HOH HOH . G 7 HOH A 92 4091 4091 HOH HOH . G 7 HOH A 93 4092 4092 HOH HOH . G 7 HOH A 94 4093 4093 HOH HOH . G 7 HOH A 95 4094 4094 HOH HOH . G 7 HOH A 96 4095 4095 HOH HOH . G 7 HOH A 97 4096 4096 HOH HOH . G 7 HOH A 98 4097 4097 HOH HOH . G 7 HOH A 99 4098 4098 HOH HOH . G 7 HOH A 100 4099 4099 HOH HOH . G 7 HOH A 101 4100 4100 HOH HOH . G 7 HOH A 102 4101 4101 HOH HOH . G 7 HOH A 103 4102 4102 HOH HOH . G 7 HOH A 104 4103 4103 HOH HOH . G 7 HOH A 105 4104 4104 HOH HOH . G 7 HOH A 106 4105 4105 HOH HOH . G 7 HOH A 107 4106 4106 HOH HOH . G 7 HOH A 108 4107 4107 HOH HOH . G 7 HOH A 109 4108 4108 HOH HOH . G 7 HOH A 110 4109 4109 HOH HOH . G 7 HOH A 111 4110 4110 HOH HOH . G 7 HOH A 112 4111 4111 HOH HOH . G 7 HOH A 113 4112 4112 HOH HOH . G 7 HOH A 114 4113 4113 HOH HOH . G 7 HOH A 115 4114 4114 HOH HOH . G 7 HOH A 116 4115 4115 HOH HOH . G 7 HOH A 117 4116 4116 HOH HOH . G 7 HOH A 118 4117 4117 HOH HOH . G 7 HOH A 119 4118 4118 HOH HOH . G 7 HOH A 120 4119 4119 HOH HOH . G 7 HOH A 121 4120 4120 HOH HOH . G 7 HOH A 122 4121 4121 HOH HOH . G 7 HOH A 123 4122 4122 HOH HOH . G 7 HOH A 124 4123 4123 HOH HOH . G 7 HOH A 125 4124 4124 HOH HOH . G 7 HOH A 126 4125 4125 HOH HOH . G 7 HOH A 127 4126 4126 HOH HOH . G 7 HOH A 128 4127 4127 HOH HOH . G 7 HOH A 129 4128 4128 HOH HOH . G 7 HOH A 130 4129 4129 HOH HOH . G 7 HOH A 131 4130 4130 HOH HOH . G 7 HOH A 132 4131 4131 HOH HOH . G 7 HOH A 133 4132 4132 HOH HOH . G 7 HOH A 134 4133 4133 HOH HOH . G 7 HOH A 135 4134 4134 HOH HOH . G 7 HOH A 136 4135 4135 HOH HOH . G 7 HOH A 137 4136 4136 HOH HOH . G 7 HOH A 138 4137 4137 HOH HOH . G 7 HOH A 139 4138 4138 HOH HOH . G 7 HOH A 140 4139 4139 HOH HOH . G 7 HOH A 141 4140 4140 HOH HOH . G 7 HOH A 142 4141 4141 HOH HOH . G 7 HOH A 143 4142 4142 HOH HOH . G 7 HOH A 144 4143 4143 HOH HOH . G 7 HOH A 145 4144 4144 HOH HOH . G 7 HOH A 146 4145 4145 HOH HOH . G 7 HOH A 147 4146 4146 HOH HOH . G 7 HOH A 148 4147 4147 HOH HOH . G 7 HOH A 149 4148 4148 HOH HOH . G 7 HOH A 150 4149 4149 HOH HOH . G 7 HOH A 151 4150 4150 HOH HOH . G 7 HOH A 152 4151 4151 HOH HOH . G 7 HOH A 153 4152 4152 HOH HOH . G 7 HOH A 154 4153 4153 HOH HOH . G 7 HOH A 155 4154 4154 HOH HOH . G 7 HOH A 156 4155 4155 HOH HOH . G 7 HOH A 157 4156 4156 HOH HOH . G 7 HOH A 158 4157 4157 HOH HOH . G 7 HOH A 159 4158 4158 HOH HOH . G 7 HOH A 160 4159 4159 HOH HOH . G 7 HOH A 161 4160 4160 HOH HOH . G 7 HOH A 162 4161 4161 HOH HOH . G 7 HOH A 163 4162 4162 HOH HOH . G 7 HOH A 164 4163 4163 HOH HOH . G 7 HOH A 165 4164 4164 HOH HOH . G 7 HOH A 166 4165 4165 HOH HOH . G 7 HOH A 167 4166 4166 HOH HOH . G 7 HOH A 168 4167 4167 HOH HOH . G 7 HOH A 169 4168 4168 HOH HOH . G 7 HOH A 170 4169 4169 HOH HOH . G 7 HOH A 171 4170 4170 HOH HOH . G 7 HOH A 172 4171 4171 HOH HOH . G 7 HOH A 173 4172 4172 HOH HOH . G 7 HOH A 174 4173 4173 HOH HOH . G 7 HOH A 175 4174 4174 HOH HOH . G 7 HOH A 176 4175 4175 HOH HOH . G 7 HOH A 177 4176 4176 HOH HOH . G 7 HOH A 178 4177 4177 HOH HOH . G 7 HOH A 179 4178 4178 HOH HOH . G 7 HOH A 180 4179 4179 HOH HOH . G 7 HOH A 181 4180 4180 HOH HOH . G 7 HOH A 182 4181 4181 HOH HOH . G 7 HOH A 183 4182 4182 HOH HOH . G 7 HOH A 184 4183 4183 HOH HOH . G 7 HOH A 185 4184 4184 HOH HOH . G 7 HOH A 186 4185 4185 HOH HOH . G 7 HOH A 187 4186 4186 HOH HOH . G 7 HOH A 188 4187 4187 HOH HOH . G 7 HOH A 189 4188 4188 HOH HOH . G 7 HOH A 190 4189 4189 HOH HOH . G 7 HOH A 191 4190 4190 HOH HOH . G 7 HOH A 192 4191 4191 HOH HOH . G 7 HOH A 193 4192 4192 HOH HOH . G 7 HOH A 194 4193 4193 HOH HOH . G 7 HOH A 195 4194 4194 HOH HOH . G 7 HOH A 196 4195 4195 HOH HOH . G 7 HOH A 197 4196 4196 HOH HOH . G 7 HOH A 198 4197 4197 HOH HOH . G 7 HOH A 199 4198 4198 HOH HOH . G 7 HOH A 200 4199 4199 HOH HOH . G 7 HOH A 201 4200 4200 HOH HOH . G 7 HOH A 202 4201 4201 HOH HOH . G 7 HOH A 203 4202 4202 HOH HOH . G 7 HOH A 204 4203 4203 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 C C6 P22 . . . E 5 65.594 53.274 42.794 1 71.85 ? C6 P22 700 A 1 HETATM 2 C C7 P22 . . . E 5 67.037 53.638 43.089 1 73.44 ? C7 P22 700 A 1 HETATM 3 O O7 P22 . . . E 5 67.994 52.77 42.671 1 73.75 ? O7 P22 700 A 1 HETATM 4 P PA P22 . . . E 5 69.557 53.134 42.987 1 71.46 ? PA P22 700 A 1 HETATM 5 O O1A P22 . . . E 5 69.937 54.415 42.329 1 70.7 ? O1A P22 700 A 1 HETATM 6 O O2A P22 . . . E 5 70.444 52.062 42.444 1 69.12 ? O2A P22 700 A 1 HETATM 7 O O3A P22 . . . E 5 69.812 53.261 44.572 1 68.9 ? O3A P22 700 A 1 HETATM 8 P PB P22 . . . E 5 69.264 52.071 45.505 1 64.81 ? PB P22 700 A 1 HETATM 9 O O1B P22 . . . E 5 67.799 52.225 45.756 1 62.24 ? O1B P22 700 A 1 HETATM 10 O O2B P22 . . . E 5 69.576 50.741 44.914 1 64.2 ? O2B P22 700 A 1 HETATM 11 O O3B P22 . . . E 5 69.978 52.178 46.805 1 66.76 ? O3B P22 700 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 11 #