data_6YDX # _model_server_result.job_id uKGcPjcaZ6Qre9PLNyxd2A _model_server_result.datetime_utc '2024-11-16 07:21:10' _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 6ydx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":1120}' # _entry.id 6YDX # _exptl.entry_id 6YDX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.173 _entity.id 9 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 'TRIETHYLENE GLYCOL' _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 102.767 _cell.angle_gamma 90 _cell.entry_id 6YDX _cell.length_a 73.419 _cell.length_b 118.631 _cell.length_c 141.389 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YDX _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,J,K,L,M,N,O,P,Q,R,S,T,U,V,HA 1 1 B,G,H,I,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,IA 2 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 9 _struct_asym.id T _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . 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 NAG 1 C 1 NAG A 1115 NAG 2 n C NAG 2 C 2 NAG A 1303 NAG 3 n D NAG 1 D 1 NAG A 1120 NAG 3 n D NAG 2 D 2 NAG A 1125 NAG 3 n D BMA 3 D 3 BMA A 1144 BMA 2 n E NAG 1 E 1 NAG A 1126 NAG 2 n E NAG 2 E 2 NAG A 1145 NAG 2 n F NAG 1 F 1 NAG A 1141 NAG 2 n F NAG 2 F 2 NAG A 1142 NAG 2 n G NAG 1 G 1 NAG B 1117 NAG 2 n G NAG 2 G 2 NAG B 1136 NAG 3 n H NAG 1 H 1 NAG B 1140 NAG 3 n H NAG 2 H 2 NAG B 1141 NAG 3 n H BMA 3 H 3 BMA B 1142 BMA 2 n I NAG 1 I 1 NAG B 1144 NAG 2 n I NAG 2 I 2 NAG B 1145 NAG # 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 705 A CYS 828 1_555 A SG CYS 712 A CYS 835 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? covale ? covale1 A ND2 ASN 61 A ASN 184 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale2 A ND2 ASN 92 A ASN 215 1_555 L C1 NAG . A NAG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale3 A O GLY 131 A GLY 254 1_555 M C8 NAG . A NAG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale4 A ND2 ASN 133 A ASN 256 1_555 M C1 NAG . A NAG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 A ND2 ASN 143 A ASN 266 1_555 P C1 NAG . A NAG 1116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale6 A ND2 ASN 245 A ASN 368 1_555 N C1 NAG . A NAG 1112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale7 A ND2 ASN 455 A ASN 578 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 A ND2 ASN 541 A ASN 664 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? covale ? covale9 A ND2 ASN 711 A ASN 834 1_555 O C1 NAG . A NAG 1115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 A ND2 ASN 727 A ASN 850 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale11 B ND2 ASN 61 B ASN 184 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale12 B ND2 ASN 133 B ASN 256 1_555 Z C1 NAG . B NAG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale13 B ND2 ASN 143 B ASN 266 1_555 AA C1 NAG . B NAG 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale14 B ND2 ASN 161 B ASN 284 1_555 CA C1 NAG . B NAG 1114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale15 B ND2 ASN 245 B ASN 368 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale16 B ND2 ASN 455 B ASN 578 1_555 Y C1 NAG . B NAG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale17 B ND2 ASN 541 B ASN 664 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale18 B ND2 ASN 727 B ASN 850 1_555 BA C1 NAG . B NAG 1113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale19 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale20 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale21 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale22 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale23 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale24 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale25 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? covale ? covale26 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale27 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? metalc ? metalc1 A NE2 HIS 345 A HIS 468 1_555 K ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc2 A OE1 GLU 364 A GLU 487 1_555 K ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc3 J N34 ONN . A ONN 1101 1_555 K ZN ZN . A ZN 1102 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc4 J O33 ONN . A ONN 1101 1_555 K ZN ZN . A ZN 1102 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc5 J O33 ONN . A ONN 1101 1_555 K ZN ZN . A ZN 1102 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc6 B NE2 HIS 341 B HIS 464 1_555 X ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc7 B NE2 HIS 345 B HIS 468 1_555 X ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc8 B OE1 GLU 364 B GLU 487 1_555 X ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc9 W O33 ONN . B ONN 1101 1_555 X ZN ZN . B ZN 1102 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc10 W O33 ONN . B ONN 1101 1_555 X ZN ZN . B ZN 1102 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.517 ? # _chem_comp.formula 'C6 H14 O4' _chem_comp.formula_weight 150.173 _chem_comp.id PGE _chem_comp.mon_nstd_flag . _chem_comp.name 'TRIETHYLENE GLYCOL' _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 C1 O1 PGE sing 418 n n C1 C2 PGE sing 419 n n C1 H1 PGE sing 420 n n C1 H12 PGE sing 421 n n O1 HO1 PGE sing 422 n n C2 O2 PGE sing 423 n n C2 H2 PGE sing 424 n n C2 H22 PGE sing 425 n n O2 C3 PGE sing 426 n n C3 C4 PGE sing 427 n n C3 H3 PGE sing 428 n n C3 H32 PGE sing 429 n n C4 O3 PGE sing 430 n n C4 H4 PGE sing 431 n n C4 H42 PGE sing 432 n n O4 C6 PGE sing 433 n n O4 HO4 PGE sing 434 n n C6 C5 PGE sing 435 n n C6 H6 PGE sing 436 n n C6 H62 PGE sing 437 n n C5 O3 PGE sing 438 n n C5 H5 PGE sing 439 n n C5 H52 PGE sing 440 n n # _atom_sites.entry_id 6YDX _atom_sites.fract_transf_matrix[1][1] 0.01362 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003086 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008429 _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] 0.007252 _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 J 4 ONN A 1 1101 1 ONN HA8 . K 5 ZN A 1 1102 2 ZN ZN . L 6 NAG A 1 1105 1118 NAG NAG . M 6 NAG A 1 1106 1119 NAG NAG . N 6 NAG A 1 1112 1132 NAG NAG . O 6 NAG A 1 1115 1143 NAG NAG . P 6 NAG A 1 1116 1402 NAG NAG . Q 7 SIN A 1 1117 22 SIN SIN . R 8 EDO A 1 1118 26 EDO EDO . S 8 EDO A 1 1119 23 EDO EDO . T 9 PGE A 1 1120 1 PGE PGE . U 10 PG4 A 1 1121 2 PG4 PG4 . V 11 PO4 A 1 1122 4 PO4 PO4 . W 4 ONN B 1 1101 1 ONN HA8 . X 5 ZN B 1 1102 2 ZN ZN . Y 6 NAG B 1 1105 1119 NAG NAG . Z 6 NAG B 1 1106 1121 NAG NAG . AA 6 NAG B 1 1110 1143 NAG NAG . BA 6 NAG B 1 1113 1146 NAG NAG . CA 6 NAG B 1 1114 1403 NAG NAG . DA 8 EDO B 1 1115 24 EDO EDO . EA 8 EDO B 1 1116 25 EDO EDO . FA 8 EDO B 1 1117 27 EDO EDO . GA 12 PEG B 1 1118 3 PEG PEG . HA 13 HOH A 1 1201 3 HOH HOH . HA 13 HOH A 2 1202 16 HOH HOH . HA 13 HOH A 3 1203 45 HOH HOH . HA 13 HOH A 4 1204 34 HOH HOH . HA 13 HOH A 5 1205 20 HOH HOH . HA 13 HOH A 6 1206 33 HOH HOH . HA 13 HOH A 7 1207 30 HOH HOH . HA 13 HOH A 8 1208 13 HOH HOH . HA 13 HOH A 9 1209 32 HOH HOH . HA 13 HOH A 10 1210 31 HOH HOH . HA 13 HOH A 11 1211 15 HOH HOH . IA 13 HOH B 1 1201 2 HOH HOH . IA 13 HOH B 2 1202 7 HOH HOH . IA 13 HOH B 3 1203 29 HOH HOH . IA 13 HOH B 4 1204 46 HOH HOH . IA 13 HOH B 5 1205 11 HOH HOH . IA 13 HOH B 6 1206 5 HOH HOH . IA 13 HOH B 7 1207 9 HOH HOH . IA 13 HOH B 8 1208 19 HOH HOH . IA 13 HOH B 9 1209 25 HOH HOH . IA 13 HOH B 10 1210 40 HOH HOH . IA 13 HOH B 11 1211 38 HOH HOH . IA 13 HOH B 12 1212 12 HOH HOH . IA 13 HOH B 13 1213 26 HOH HOH . IA 13 HOH B 14 1214 24 HOH HOH . IA 13 HOH B 15 1215 28 HOH HOH . IA 13 HOH B 16 1216 43 HOH HOH . IA 13 HOH B 17 1217 27 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 PGE . . . T 9 36.773 -51.335 40.913 1 49.18 ? C1 PGE 1120 A 1 HETATM 2 O O1 PGE . . . T 9 37.215 -51.194 39.586 1 41.76 ? O1 PGE 1120 A 1 HETATM 3 C C2 PGE . . . T 9 35.263 -51.615 40.96 1 55.32 ? C2 PGE 1120 A 1 HETATM 4 O O2 PGE . . . T 9 34.91 -52.857 41.528 1 60.5 ? O2 PGE 1120 A 1 HETATM 5 C C3 PGE . . . T 9 34.489 -53.872 40.641 1 54.29 ? C3 PGE 1120 A 1 HETATM 6 C C4 PGE . . . T 9 33.15 -53.574 39.946 1 52.69 ? C4 PGE 1120 A 1 HETATM 7 O O4 PGE . . . T 9 33.258 -50.084 36.872 1 46.25 ? O4 PGE 1120 A 1 HETATM 8 C C6 PGE . . . T 9 33.635 -50.556 38.134 1 49.36 ? C6 PGE 1120 A 1 HETATM 9 C C5 PGE . . . T 9 32.678 -51.65 38.623 1 51.92 ? C5 PGE 1120 A 1 HETATM 10 O O3 PGE . . . T 9 33.369 -52.869 38.75 1 55 ? O3 PGE 1120 A 1 # _model_server_stats.io_time_ms 175 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 474 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #