data_5YLV # _model_server_result.job_id HNMW7jGEoLjLHIT5U5eEEA _model_server_result.datetime_utc '2024-11-15 03:06:33' _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 5ylv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1103}' # _entry.id 5YLV # _exptl.entry_id 5YLV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 538.755 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'O-DODECANYL OCTAETHYLENE GLYCOL' _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 120 _cell.entry_id 5YLV _cell.length_a 105.05 _cell.length_b 105.05 _cell.length_c 368.54 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YLV _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,J,K,L,M,N,O _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 ? 5 E N N ? 5 M 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 B SG CYS 130 B CYS 131 1_555 B SG CYS 151 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 B SG CYS 161 B CYS 162 1_555 B SG CYS 177 B CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 200 B CYS 201 1_555 B SG CYS 261 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A C SER 385 A SER 384 1_555 A N BFD 386 A BFD 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C BFD 386 A BFD 385 1_555 A N LYS 387 A LYS 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? covale ? covale3 B ND2 ASN 98 B ASN 99 1_555 I C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 B ND2 ASN 129 B ASN 130 1_555 J C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale5 B OE1 GLN 138 B GLN 139 1_555 B CG LYS 148 B LYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.129 ? covale ? covale6 B OE1 GLN 138 B GLN 139 1_555 B CD LYS 148 B LYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.495 ? covale ? covale7 B ND2 ASN 160 B ASN 161 1_555 K C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A O ASP 184 A ASP 183 1_555 H RB RB . A RB 1106 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.068 ? metalc ? metalc2 A OD2 ASP 186 A ASP 185 1_555 H RB RB . A RB 1106 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc3 A O VAL 342 A VAL 341 1_555 F RB RB . A RB 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc4 A OD2 BFD 386 A BFD 385 1_555 D MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc5 A O THR 388 A THR 387 1_555 D MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc6 A O SER 409 A SER 408 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? metalc ? metalc7 A OG SER 409 A SER 408 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc8 A O GLN 419 A GLN 418 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.166 ? metalc ? metalc9 A O THR 420 A THR 419 1_555 H RB RB . A RB 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.129 ? metalc ? metalc10 A OD1 ASP 727 A ASP 726 1_555 D MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc11 A O LYS 736 A LYS 735 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc12 A O ALA 738 A ALA 737 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? metalc ? metalc13 A OD1 ASP 757 A ASP 756 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? # _chem_comp.formula 'C28 H58 O9' _chem_comp.formula_weight 538.755 _chem_comp.id CE1 _chem_comp.mon_nstd_flag . _chem_comp.name 'O-DODECANYL OCTAETHYLENE GLYCOL' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms THESIT # 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 CE1 sing 126 n n C1 H11 CE1 sing 127 n n C1 H12 CE1 sing 128 n n C1 H13 CE1 sing 129 n n C2 C3 CE1 sing 130 n n C2 H21 CE1 sing 131 n n C2 H22 CE1 sing 132 n n C3 C4 CE1 sing 133 n n C3 H31 CE1 sing 134 n n C3 H32 CE1 sing 135 n n C4 C5 CE1 sing 136 n n C4 H41 CE1 sing 137 n n C4 H42 CE1 sing 138 n n C5 C6 CE1 sing 139 n n C5 H51 CE1 sing 140 n n C5 H52 CE1 sing 141 n n C6 C7 CE1 sing 142 n n C6 H61 CE1 sing 143 n n C6 H62 CE1 sing 144 n n C7 C8 CE1 sing 145 n n C7 H71 CE1 sing 146 n n C7 H72 CE1 sing 147 n n C8 C9 CE1 sing 148 n n C8 H81 CE1 sing 149 n n C8 H82 CE1 sing 150 n n C9 C10 CE1 sing 151 n n C9 H91 CE1 sing 152 n n C9 H92 CE1 sing 153 n n C10 C11 CE1 sing 154 n n C10 H101 CE1 sing 155 n n C10 H102 CE1 sing 156 n n C11 C12 CE1 sing 157 n n C11 H111 CE1 sing 158 n n C11 H112 CE1 sing 159 n n C12 O13 CE1 sing 160 n n C12 H121 CE1 sing 161 n n C12 H122 CE1 sing 162 n n O13 C14 CE1 sing 163 n n C14 C15 CE1 sing 164 n n C14 H141 CE1 sing 165 n n C14 H142 CE1 sing 166 n n C15 O16 CE1 sing 167 n n C15 H151 CE1 sing 168 n n C15 H152 CE1 sing 169 n n O16 C17 CE1 sing 170 n n C17 C18 CE1 sing 171 n n C17 H171 CE1 sing 172 n n C17 H172 CE1 sing 173 n n C18 O19 CE1 sing 174 n n C18 H181 CE1 sing 175 n n C18 H182 CE1 sing 176 n n O19 C20 CE1 sing 177 n n C20 C21 CE1 sing 178 n n C20 H201 CE1 sing 179 n n C20 H202 CE1 sing 180 n n C21 O22 CE1 sing 181 n n C21 H211 CE1 sing 182 n n C21 H212 CE1 sing 183 n n O22 C23 CE1 sing 184 n n C23 C24 CE1 sing 185 n n C23 H231 CE1 sing 186 n n C23 H232 CE1 sing 187 n n C24 O25 CE1 sing 188 n n C24 H241 CE1 sing 189 n n C24 H242 CE1 sing 190 n n O25 C26 CE1 sing 191 n n C26 C27 CE1 sing 192 n n C26 H261 CE1 sing 193 n n C26 H262 CE1 sing 194 n n C27 O28 CE1 sing 195 n n C27 H271 CE1 sing 196 n n C27 H272 CE1 sing 197 n n O28 C29 CE1 sing 198 n n C29 C30 CE1 sing 199 n n C29 H291 CE1 sing 200 n n C29 H292 CE1 sing 201 n n C30 O31 CE1 sing 202 n n C30 H301 CE1 sing 203 n n C30 H302 CE1 sing 204 n n O31 C32 CE1 sing 205 n n C32 C33 CE1 sing 206 n n C32 H321 CE1 sing 207 n n C32 H322 CE1 sing 208 n n C33 O34 CE1 sing 209 n n C33 H331 CE1 sing 210 n n C33 H332 CE1 sing 211 n n O34 C35 CE1 sing 212 n n C35 C36 CE1 sing 213 n n C35 H351 CE1 sing 214 n n C35 H352 CE1 sing 215 n n C36 O37 CE1 sing 216 n n C36 H361 CE1 sing 217 n n C36 H362 CE1 sing 218 n n O37 H37 CE1 sing 219 n n # _atom_sites.entry_id 5YLV _atom_sites.fract_transf_matrix[1][1] 0.009519 _atom_sites.fract_transf_matrix[1][2] 0.005496 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010992 _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] 0.002713 _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 C 3 8WX A 1 1101 1101 8WX 8WX . D 4 MG A 1 1102 1102 MG MG . E 5 CE1 A 1 1103 1103 CE1 CE1 . F 6 RB A 1 1104 1104 RB RB . G 6 RB A 1 1105 1105 RB RB . H 6 RB A 1 1106 1106 RB RB . I 7 NAG B 1 301 301 NAG NAG . J 7 NAG B 1 302 302 NAG NAG . K 7 NAG B 1 303 303 NAG NAG . L 8 PCW B 1 304 304 PCW PCW . M 5 CE1 B 1 305 305 CE1 CE1 . N 9 HOH A 1 1201 1201 HOH HOH . N 9 HOH A 2 1202 1202 HOH HOH . N 9 HOH A 3 1203 1203 HOH HOH . N 9 HOH A 4 1204 1204 HOH HOH . N 9 HOH A 5 1205 1205 HOH HOH . N 9 HOH A 6 1206 1206 HOH HOH . N 9 HOH A 7 1207 1207 HOH HOH . N 9 HOH A 8 1208 1208 HOH HOH . N 9 HOH A 9 1209 1209 HOH HOH . N 9 HOH A 10 1210 1210 HOH HOH . N 9 HOH A 11 1211 1211 HOH HOH . N 9 HOH A 12 1212 1212 HOH HOH . N 9 HOH A 13 1213 1213 HOH HOH . N 9 HOH A 14 1214 1214 HOH HOH . N 9 HOH A 15 1215 1215 HOH HOH . N 9 HOH A 16 1216 1216 HOH HOH . N 9 HOH A 17 1217 1217 HOH HOH . N 9 HOH A 18 1218 1218 HOH HOH . N 9 HOH A 19 1219 1219 HOH HOH . N 9 HOH A 20 1220 1220 HOH HOH . N 9 HOH A 21 1221 1221 HOH HOH . N 9 HOH A 22 1222 1222 HOH HOH . O 9 HOH B 1 401 401 HOH HOH . O 9 HOH B 2 402 402 HOH HOH . O 9 HOH B 3 403 403 HOH HOH . O 9 HOH B 4 404 404 HOH HOH . O 9 HOH B 5 405 405 HOH HOH . O 9 HOH B 6 406 406 HOH HOH . O 9 HOH B 7 407 407 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 C1 CE1 . . . E 5 54.128 10.405 -7.624 1 106.94 ? C1 CE1 1103 A 1 HETATM 2 C C2 CE1 . . . E 5 53.96 11.803 -7.073 1 106.36 ? C2 CE1 1103 A 1 HETATM 3 C C3 CE1 . . . E 5 55.155 12.217 -6.224 1 111.53 ? C3 CE1 1103 A 1 HETATM 4 C C4 CE1 . . . E 5 56.283 12.809 -7.069 1 116.03 ? C4 CE1 1103 A 1 HETATM 5 C C5 CE1 . . . E 5 57.366 11.784 -7.412 1 116.5 ? C5 CE1 1103 A 1 HETATM 6 C C6 CE1 . . . E 5 58.377 12.321 -8.422 1 117.12 ? C6 CE1 1103 A 1 HETATM 7 C C7 CE1 . . . E 5 59.547 11.357 -8.583 1 115.68 ? C7 CE1 1103 A 1 HETATM 8 C C8 CE1 . . . E 5 60.291 11.62 -9.885 1 116.31 ? C8 CE1 1103 A 1 HETATM 9 C C9 CE1 . . . E 5 61.193 12.837 -9.756 1 123.91 ? C9 CE1 1103 A 1 HETATM 10 C C10 CE1 . . . E 5 61.506 13.43 -11.128 1 129.4 ? C10 CE1 1103 A 1 HETATM 11 C C11 CE1 . . . E 5 62.253 14.763 -11.043 1 138.64 ? C11 CE1 1103 A 1 HETATM 12 C C12 CE1 . . . E 5 63.281 14.866 -12.168 1 136.8 ? C12 CE1 1103 A 1 HETATM 13 O O13 CE1 . . . E 5 64.535 14.392 -11.678 1 134.59 ? O13 CE1 1103 A 1 HETATM 14 C C14 CE1 . . . E 5 64.873 13.101 -12.18 1 131.68 ? C14 CE1 1103 A 1 HETATM 15 C C15 CE1 . . . E 5 65.616 12.343 -11.089 1 133.44 ? C15 CE1 1103 A 1 HETATM 16 O O16 CE1 . . . E 5 66.119 11.102 -11.584 1 130.87 ? O16 CE1 1103 A 1 HETATM 17 C C17 CE1 . . . E 5 67.423 10.862 -11.05 1 133.08 ? C17 CE1 1103 A 1 HETATM 18 C C18 CE1 . . . E 5 67.912 9.442 -11.318 1 126.11 ? C18 CE1 1103 A 1 HETATM 19 O O19 CE1 . . . E 5 68.626 9.386 -12.554 1 129.07 ? O19 CE1 1103 A 1 HETATM 20 C C20 CE1 . . . E 5 69.922 8.806 -12.371 1 131.17 ? C20 CE1 1103 A 1 HETATM 21 C C21 CE1 . . . E 5 69.794 7.31 -12.631 1 127.74 ? C21 CE1 1103 A 1 HETATM 22 O O22 CE1 . . . E 5 70.983 6.721 -13.153 1 127.14 ? O22 CE1 1103 A 1 HETATM 23 C C23 CE1 . . . E 5 70.615 5.912 -14.273 1 123.34 ? C23 CE1 1103 A 1 HETATM 24 C C24 CE1 . . . E 5 69.905 4.636 -13.827 1 107.95 ? C24 CE1 1103 A 1 HETATM 25 O O25 CE1 . . . E 5 70.775 3.533 -14.068 1 110.45 ? O25 CE1 1103 A 1 HETATM 26 C C26 CE1 . . . E 5 70.064 2.359 -14.448 1 104.81 ? C26 CE1 1103 A 1 HETATM 27 C C27 CE1 . . . E 5 70.988 1.502 -15.307 1 95.86 ? C27 CE1 1103 A 1 HETATM 28 O O28 CE1 . . . E 5 70.236 0.986 -16.408 1 101.64 ? O28 CE1 1103 A 1 HETATM 29 C C29 CE1 . . . E 5 71.031 0.731 -17.572 1 85.03 ? C29 CE1 1103 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 26 _model_server_stats.element_count 29 #