data_5IYX # _model_server_result.job_id eOlVC-bpZ-AXre0HWmktug _model_server_result.datetime_utc '2024-10-20 19:56:01' _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 5iyx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":711}' # _entry.id 5IYX # _exptl.entry_id 5IYX _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 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 90 _cell.entry_id 5IYX _cell.length_a 74.507 _cell.length_b 100.456 _cell.length_c 142.759 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IYX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,P _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 ? 6 J N N ? 6 K N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 4 n D NAG 1 D 1 NAG A 701 NAG 4 n D NAG 2 D 2 NAG A 702 NAG 4 n E NAG 1 E 1 NAG A 704 NAG 4 n E NAG 2 E 2 NAG A 705 NAG 4 n F NAG 1 F 1 NAG A 706 NAG 4 n F NAG 2 F 2 NAG A 707 NAG 4 n G NAG 1 G 1 NAG A 709 NAG 4 n G NAG 2 G 2 NAG A 710 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 40 A CYS 54 1_555 A SG CYS 47 A CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 72 A CYS 86 1_555 A SG CYS 99 A CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf3 A SG CYS 362 A CYS 376 1_555 A SG CYS 388 A CYS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 592 A CYS 606 1_555 A SG CYS 599 A CYS 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf5 C SG CYS 39 C CYS 58 1_555 C SG CYS 46 C CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? disulf ? disulf6 C SG CYS 183 C CYS 202 1_555 C SG CYS 191 C CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? covale ? covale1 A ND2 ASN 84 A ASN 98 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A ND2 ASN 88 A ASN 102 1_555 H C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale3 A ND2 ASN 136 A ASN 150 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 A ND2 ASN 255 A ASN 269 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 268 A ASN 282 1_555 I C1 NAG . A NAG 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale6 A ND2 ASN 562 A ASN 576 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 B C ALA 8 B ALA 63 1_555 B N HYP 9 B HYP 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale8 B C HYP 9 B HYP 64 1_555 B N SER 10 B SER 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 C ND2 ASN 131 C ASN 150 1_555 L C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? covale ? covale10 C ND2 ASN 165 C ASN 184 1_555 M C1 NAG . C NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale13 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 5IYX _atom_sites.fract_transf_matrix[1][1] 0.013422 _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] 0.009955 _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] 0.007005 _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 H 5 NAG A 1 703 703 NAG NAG . I 5 NAG A 1 708 708 NAG NAG . J 6 EDO A 1 711 711 EDO EDO . K 6 EDO A 1 712 712 EDO EDO . L 5 NAG C 1 301 301 NAG NAG . M 5 NAG C 1 302 302 NAG NAG . N 7 HOH A 1 801 801 HOH HOH . N 7 HOH A 2 802 802 HOH HOH . N 7 HOH A 3 803 803 HOH HOH . N 7 HOH A 4 804 804 HOH HOH . N 7 HOH A 5 805 805 HOH HOH . N 7 HOH A 6 806 806 HOH HOH . N 7 HOH A 7 807 807 HOH HOH . N 7 HOH A 8 808 808 HOH HOH . N 7 HOH A 9 809 809 HOH HOH . N 7 HOH A 10 810 812 HOH HOH . N 7 HOH A 11 811 810 HOH HOH . N 7 HOH A 12 812 811 HOH HOH . N 7 HOH A 13 813 813 HOH HOH . N 7 HOH A 14 814 815 HOH HOH . N 7 HOH A 15 815 817 HOH HOH . N 7 HOH A 16 816 816 HOH HOH . N 7 HOH A 17 817 814 HOH HOH . N 7 HOH A 18 818 818 HOH HOH . N 7 HOH A 19 819 819 HOH HOH . N 7 HOH A 20 820 820 HOH HOH . N 7 HOH A 21 821 821 HOH HOH . N 7 HOH A 22 822 822 HOH HOH . N 7 HOH A 23 823 823 HOH HOH . N 7 HOH A 24 824 824 HOH HOH . N 7 HOH A 25 825 825 HOH HOH . N 7 HOH A 26 826 826 HOH HOH . N 7 HOH A 27 827 827 HOH HOH . N 7 HOH A 28 828 828 HOH HOH . N 7 HOH A 29 829 829 HOH HOH . N 7 HOH A 30 830 831 HOH HOH . N 7 HOH A 31 831 830 HOH HOH . N 7 HOH A 32 832 832 HOH HOH . N 7 HOH A 33 833 833 HOH HOH . N 7 HOH A 34 834 834 HOH HOH . N 7 HOH A 35 835 835 HOH HOH . N 7 HOH A 36 836 837 HOH HOH . N 7 HOH A 37 837 423 HOH HOH . N 7 HOH A 38 838 836 HOH HOH . N 7 HOH A 39 839 839 HOH HOH . N 7 HOH A 40 840 838 HOH HOH . N 7 HOH A 41 841 841 HOH HOH . N 7 HOH A 42 842 840 HOH HOH . N 7 HOH A 43 843 842 HOH HOH . N 7 HOH A 44 844 843 HOH HOH . N 7 HOH A 45 845 844 HOH HOH . N 7 HOH A 46 846 846 HOH HOH . N 7 HOH A 47 847 845 HOH HOH . N 7 HOH A 48 848 847 HOH HOH . N 7 HOH A 49 849 848 HOH HOH . N 7 HOH A 50 850 851 HOH HOH . N 7 HOH A 51 851 853 HOH HOH . N 7 HOH A 52 852 849 HOH HOH . N 7 HOH A 53 853 852 HOH HOH . N 7 HOH A 54 854 850 HOH HOH . N 7 HOH A 55 855 855 HOH HOH . N 7 HOH A 56 856 854 HOH HOH . N 7 HOH A 57 857 857 HOH HOH . N 7 HOH A 58 858 856 HOH HOH . N 7 HOH A 59 859 858 HOH HOH . N 7 HOH A 60 860 859 HOH HOH . N 7 HOH A 61 861 860 HOH HOH . N 7 HOH A 62 862 861 HOH HOH . N 7 HOH A 63 863 862 HOH HOH . N 7 HOH A 64 864 863 HOH HOH . N 7 HOH A 65 865 864 HOH HOH . N 7 HOH A 66 866 865 HOH HOH . N 7 HOH A 67 867 866 HOH HOH . N 7 HOH A 68 868 868 HOH HOH . N 7 HOH A 69 869 867 HOH HOH . N 7 HOH A 70 870 870 HOH HOH . N 7 HOH A 71 871 869 HOH HOH . N 7 HOH A 72 872 871 HOH HOH . N 7 HOH A 73 873 873 HOH HOH . N 7 HOH A 74 874 872 HOH HOH . N 7 HOH A 75 875 874 HOH HOH . N 7 HOH A 76 876 875 HOH HOH . N 7 HOH A 77 877 876 HOH HOH . N 7 HOH A 78 878 877 HOH HOH . N 7 HOH A 79 879 878 HOH HOH . N 7 HOH A 80 880 879 HOH HOH . N 7 HOH A 81 881 880 HOH HOH . N 7 HOH A 82 882 881 HOH HOH . N 7 HOH A 83 883 882 HOH HOH . N 7 HOH A 84 884 883 HOH HOH . N 7 HOH A 85 885 884 HOH HOH . N 7 HOH A 86 886 885 HOH HOH . N 7 HOH A 87 887 886 HOH HOH . N 7 HOH A 88 888 887 HOH HOH . N 7 HOH A 89 889 889 HOH HOH . O 7 HOH B 1 101 101 HOH HOH . O 7 HOH B 2 102 102 HOH HOH . O 7 HOH B 3 103 103 HOH HOH . O 7 HOH B 4 104 104 HOH HOH . O 7 HOH B 5 105 105 HOH HOH . O 7 HOH B 6 106 106 HOH HOH . P 7 HOH C 1 401 401 HOH HOH . P 7 HOH C 2 402 403 HOH HOH . P 7 HOH C 3 403 402 HOH HOH . P 7 HOH C 4 404 404 HOH HOH . P 7 HOH C 5 405 405 HOH HOH . P 7 HOH C 6 406 406 HOH HOH . P 7 HOH C 7 407 407 HOH HOH . P 7 HOH C 8 408 408 HOH HOH . P 7 HOH C 9 409 409 HOH HOH . P 7 HOH C 10 410 410 HOH HOH . P 7 HOH C 11 411 411 HOH HOH . P 7 HOH C 12 412 412 HOH HOH . P 7 HOH C 13 413 413 HOH HOH . P 7 HOH C 14 414 414 HOH HOH . P 7 HOH C 15 415 416 HOH HOH . P 7 HOH C 16 416 418 HOH HOH . P 7 HOH C 17 417 419 HOH HOH . P 7 HOH C 18 418 420 HOH HOH . P 7 HOH C 19 419 422 HOH HOH . P 7 HOH C 20 420 421 HOH HOH . P 7 HOH C 21 421 424 HOH HOH . P 7 HOH C 22 422 425 HOH HOH . P 7 HOH C 23 423 417 HOH HOH . P 7 HOH C 24 424 426 HOH HOH . P 7 HOH C 25 425 427 HOH HOH . P 7 HOH C 26 426 428 HOH HOH . P 7 HOH C 27 427 429 HOH HOH . P 7 HOH C 28 428 430 HOH HOH . P 7 HOH C 29 429 431 HOH HOH . P 7 HOH C 30 430 433 HOH HOH . P 7 HOH C 31 431 432 HOH HOH . P 7 HOH C 32 432 434 HOH HOH . P 7 HOH C 33 433 435 HOH HOH . P 7 HOH C 34 434 436 HOH HOH . P 7 HOH C 35 435 437 HOH HOH . P 7 HOH C 36 436 438 HOH HOH . P 7 HOH C 37 437 439 HOH HOH . P 7 HOH C 38 438 440 HOH HOH . P 7 HOH C 39 439 441 HOH HOH . P 7 HOH C 40 440 888 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 . . . J 6 23.978 -2.435 -5.854 1 70.05 ? C1 EDO 711 A 1 HETATM 2 O O1 EDO . . . J 6 22.749 -2.943 -5.327 1 69.87 ? O1 EDO 711 A 1 HETATM 3 C C2 EDO . . . J 6 24.528 -3.385 -6.916 1 72.2 ? C2 EDO 711 A 1 HETATM 4 O O2 EDO . . . J 6 25.63 -2.767 -7.595 1 72.13 ? O2 EDO 711 A 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 4 #