data_4YDI # _model_server_result.job_id 0DHQyqkDdkythrQNdWG6UQ _model_server_result.datetime_utc '2024-10-17 22:05:40' _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 4ydi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":303}' # _entry.id 4YDI # _exptl.entry_id 4YDI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _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 90 _cell.entry_id 4YDI _cell.length_a 141.738 _cell.length_b 172.253 _cell.length_c 91.782 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 2' # _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,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 6 _struct_asym.id S _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 disulf ? disulf1 A SG CYS 11 G CYS 54 1_555 A SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 A SG CYS 76 G CYS 119 1_555 A SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 102 G CYS 218 1_555 A SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 112 G CYS 228 1_555 A SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 180 G CYS 296 1_555 A SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 A SG CYS 245 G CYS 378 1_555 A SG CYS 312 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf7 A SG CYS 252 G CYS 385 1_555 A SG CYS 285 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf8 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf9 B SG CYS 149 H CYS 140 1_555 B SG CYS 205 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf10 C SG CYS 23 L CYS 23 1_555 C SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf11 C SG CYS 130 L CYS 134 1_555 C SG CYS 190 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 118 G ASN 234 1_555 D C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 125 G ASN 241 1_555 E C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 A ND2 ASN 146 G ASN 262 1_555 F C1 NAG . G NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 A ND2 ASN 160 G ASN 276 1_555 G C1 NAG . G NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale5 A ND2 ASN 200 G ASN 332 1_555 H C1 NAG . G NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 A ND2 ASN 223 G ASN 355 1_555 M C1 NAG . G NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale7 A ND2 ASN 230 G ASN 363 1_555 I C1 NAG . G NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale8 A ND2 ASN 253 G ASN 386 1_555 J C1 NAG . G NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale9 A ND2 ASN 259 G ASN 392 1_555 K C1 NAG . G NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale10 A ND2 ASN 265 G ASN 398 1_555 N C1 NAG . G NAG 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 A ND2 ASN 315 G ASN 448 1_555 L C1 NAG . G NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale12 A ND2 ASN 332 G ASN 465 1_555 O C1 NAG . G NAG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale13 C ND2 ASN 103 L ASN 107 1_555 U C1 NAG . L NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _chem_comp.formula 'C2 H6 O2' _chem_comp.formula_weight 62.068 _chem_comp.id EDO _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-ETHANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ETHYLENE GLYCOL' # 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 EDO sing 83 n n C1 C2 EDO sing 84 n n C1 H11 EDO sing 85 n n C1 H12 EDO sing 86 n n O1 HO1 EDO sing 87 n n C2 O2 EDO sing 88 n n C2 H21 EDO sing 89 n n C2 H22 EDO sing 90 n n O2 HO2 EDO sing 91 n n # _atom_sites.entry_id 4YDI _atom_sites.fract_transf_matrix[1][1] 0.007055 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005805 _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] 0.010895 _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 NAG G 1 501 734 NAG NAG . E 4 NAG G 1 502 741 NAG NAG . F 4 NAG G 1 503 762 NAG NAG . G 4 NAG G 1 504 776 NAG NAG . H 4 NAG G 1 505 832 NAG NAG . I 4 NAG G 1 506 863 NAG NAG . J 4 NAG G 1 507 886 NAG NAG . K 4 NAG G 1 508 892 NAG NAG . L 4 NAG G 1 509 948 NAG NAG . M 4 NAG G 1 510 855 NAG NAG . N 4 NAG G 1 511 898 NAG NAG . O 4 NAG G 1 512 965 NAG NAG . P 5 SO4 G 1 513 1 SO4 SO4 . Q 5 SO4 H 1 301 2 SO4 SO4 . R 5 SO4 H 1 302 3 SO4 SO4 . S 6 EDO H 1 303 4 EDO EDO . T 5 SO4 H 1 304 7 SO4 SO4 . U 4 NAG L 1 301 607 NAG NAG . V 7 HOH G 1 601 25 HOH HOH . V 7 HOH G 2 602 32 HOH HOH . V 7 HOH G 3 603 40 HOH HOH . V 7 HOH G 4 604 29 HOH HOH . V 7 HOH G 5 605 42 HOH HOH . V 7 HOH G 6 606 20 HOH HOH . V 7 HOH G 7 607 47 HOH HOH . V 7 HOH G 8 608 41 HOH HOH . V 7 HOH G 9 609 27 HOH HOH . W 7 HOH H 1 401 24 HOH HOH . W 7 HOH H 2 402 45 HOH HOH . W 7 HOH H 3 403 37 HOH HOH . W 7 HOH H 4 404 31 HOH HOH . W 7 HOH H 5 405 19 HOH HOH . W 7 HOH H 6 406 44 HOH HOH . W 7 HOH H 7 407 46 HOH HOH . W 7 HOH H 8 408 26 HOH HOH . X 7 HOH L 1 401 43 HOH HOH . X 7 HOH L 2 402 18 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 EDO . . . S 6 -35.168 -19.322 -0.847 1 75.61 ? C1 EDO 303 H 1 HETATM 2 O O1 EDO . . . S 6 -35.205 -18.939 0.533 1 73.23 ? O1 EDO 303 H 1 HETATM 3 C C2 EDO . . . S 6 -34.77 -20.789 -0.96 1 78.01 ? C2 EDO 303 H 1 HETATM 4 O O2 EDO . . . S 6 -34.591 -21.132 -2.339 1 78.06 ? O2 EDO 303 H 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 4 #