data_7D2Z # _model_server_result.job_id mG_yxdOJ-sVs-mNXsAC9dQ _model_server_result.datetime_utc '2024-10-12 05:25:41' _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 7d2z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":714}' # _entry.id 7D2Z # _exptl.entry_id 7D2Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 46.025 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FORMIC ACID' _entity.pdbx_number_of_molecules 13 _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 7D2Z _cell.length_a 92.393 _cell.length_b 92.393 _cell.length_c 101.145 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7D2Z _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,P,Q,R,S,T,U,V,W,X,Y _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 ? 4 D N N ? 4 E N N ? 4 H N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 R N N ? 4 S N N ? 4 U N N ? 4 V N N ? 4 W N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 3 6 1 FUC NAG C1 O1 . O3 HO3 . sing 6 ? 3 7 1 FUC NAG C1 O1 . O6 HO6 . 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 3 n C NAG 1 C 1 NAG B 3102 NAG 3 n C NAG 2 C 2 NAG B 3105 NAG 3 n C BMA 3 C 3 BMA B 3106 BMA 3 n C MAN 4 C 4 MAN B 3108 MAN 3 n C MAN 5 C 5 MAN B 3107 MAN 3 n C FUC 6 C 6 FUC B 3103 FUC 3 n C FUC 7 C 7 FUC B 3104 FUC # 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 26 A CYS 22 1_555 A SG CYS 100 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 B SG CYS 10 B CYS 336 1_555 B SG CYS 35 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf3 B SG CYS 53 B CYS 379 1_555 B SG CYS 106 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf4 B SG CYS 65 B CYS 391 1_555 B SG CYS 199 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf5 B SG CYS 154 B CYS 480 1_555 B SG CYS 162 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 B ND2 ASN 17 B ASN 343 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 C O3 NAG . C NAG 1 1_555 C C1 FUC . C FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _chem_comp.formula 'C H2 O2' _chem_comp.formula_weight 46.025 _chem_comp.id FMT _chem_comp.mon_nstd_flag . _chem_comp.name 'FORMIC ACID' _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 C O1 FMT doub 113 n n C O2 FMT sing 114 n n C H FMT sing 115 n n O2 HO2 FMT sing 116 n n # _atom_sites.entry_id 7D2Z _atom_sites.fract_transf_matrix[1][1] 0.010823 _atom_sites.fract_transf_matrix[1][2] 0.006249 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012498 _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] 0.009887 _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 FMT A 1 601 601 FMT FMT . E 4 FMT A 1 602 701 FMT FMT . F 5 GOL A 1 603 801 GOL GOL . G 6 ACT A 1 604 1001 ACT ACT . H 4 FMT A 1 605 2 FMT FMT . I 6 ACT B 1 701 701 ACT ACT . J 4 FMT B 1 702 1701 FMT FMT . K 4 FMT B 1 703 1801 FMT FMT . L 4 FMT B 1 704 1901 FMT FMT . M 4 FMT B 1 705 2301 FMT FMT . N 4 FMT B 1 706 2601 FMT FMT . O 5 GOL B 1 707 2801 GOL GOL . P 5 GOL B 1 708 3001 GOL GOL . Q 5 GOL B 1 709 3101 GOL GOL . R 4 FMT B 1 710 3201 FMT FMT . S 4 FMT B 1 711 3401 FMT FMT . T 5 GOL B 1 712 3501 GOL GOL . U 4 FMT B 1 713 3 FMT FMT . V 4 FMT B 1 714 4 FMT FMT . W 4 FMT B 1 715 5 FMT FMT . X 7 HOH A 1 701 88 HOH HOH . X 7 HOH A 2 702 82 HOH HOH . X 7 HOH A 3 703 48 HOH HOH . X 7 HOH A 4 704 30 HOH HOH . X 7 HOH A 5 705 78 HOH HOH . X 7 HOH A 6 706 133 HOH HOH . X 7 HOH A 7 707 47 HOH HOH . X 7 HOH A 8 708 102 HOH HOH . X 7 HOH A 9 709 42 HOH HOH . X 7 HOH A 10 710 79 HOH HOH . X 7 HOH A 11 711 35 HOH HOH . X 7 HOH A 12 712 65 HOH HOH . X 7 HOH A 13 713 121 HOH HOH . X 7 HOH A 14 714 157 HOH HOH . X 7 HOH A 15 715 77 HOH HOH . X 7 HOH A 16 716 72 HOH HOH . X 7 HOH A 17 717 153 HOH HOH . X 7 HOH A 18 718 85 HOH HOH . X 7 HOH A 19 719 164 HOH HOH . X 7 HOH A 20 720 91 HOH HOH . X 7 HOH A 21 721 127 HOH HOH . X 7 HOH A 22 722 110 HOH HOH . X 7 HOH A 23 723 59 HOH HOH . X 7 HOH A 24 724 96 HOH HOH . X 7 HOH A 25 725 60 HOH HOH . X 7 HOH A 26 726 83 HOH HOH . X 7 HOH A 27 727 143 HOH HOH . X 7 HOH A 28 728 130 HOH HOH . X 7 HOH A 29 729 147 HOH HOH . X 7 HOH A 30 730 54 HOH HOH . X 7 HOH A 31 731 162 HOH HOH . X 7 HOH A 32 732 75 HOH HOH . X 7 HOH A 33 733 138 HOH HOH . X 7 HOH A 34 734 124 HOH HOH . X 7 HOH A 35 735 183 HOH HOH . Y 7 HOH B 1 801 6 HOH HOH . Y 7 HOH B 2 802 107 HOH HOH . Y 7 HOH B 3 803 98 HOH HOH . Y 7 HOH B 4 804 14 HOH HOH . Y 7 HOH B 5 805 22 HOH HOH . Y 7 HOH B 6 806 94 HOH HOH . Y 7 HOH B 7 807 178 HOH HOH . Y 7 HOH B 8 808 92 HOH HOH . Y 7 HOH B 9 809 117 HOH HOH . Y 7 HOH B 10 810 8 HOH HOH . Y 7 HOH B 11 811 25 HOH HOH . Y 7 HOH B 12 812 37 HOH HOH . Y 7 HOH B 13 813 185 HOH HOH . Y 7 HOH B 14 814 10 HOH HOH . Y 7 HOH B 15 815 7 HOH HOH . Y 7 HOH B 16 816 5 HOH HOH . Y 7 HOH B 17 817 173 HOH HOH . Y 7 HOH B 18 818 84 HOH HOH . Y 7 HOH B 19 819 115 HOH HOH . Y 7 HOH B 20 820 97 HOH HOH . Y 7 HOH B 21 821 29 HOH HOH . Y 7 HOH B 22 822 114 HOH HOH . Y 7 HOH B 23 823 9 HOH HOH . Y 7 HOH B 24 824 15 HOH HOH . Y 7 HOH B 25 825 34 HOH HOH . Y 7 HOH B 26 826 18 HOH HOH . Y 7 HOH B 27 827 180 HOH HOH . Y 7 HOH B 28 828 26 HOH HOH . Y 7 HOH B 29 829 27 HOH HOH . Y 7 HOH B 30 830 19 HOH HOH . Y 7 HOH B 31 831 45 HOH HOH . Y 7 HOH B 32 832 20 HOH HOH . Y 7 HOH B 33 833 1 HOH HOH . Y 7 HOH B 34 834 13 HOH HOH . Y 7 HOH B 35 835 3 HOH HOH . Y 7 HOH B 36 836 171 HOH HOH . Y 7 HOH B 37 837 67 HOH HOH . Y 7 HOH B 38 838 58 HOH HOH . Y 7 HOH B 39 839 126 HOH HOH . Y 7 HOH B 40 840 16 HOH HOH . Y 7 HOH B 41 841 4 HOH HOH . Y 7 HOH B 42 842 90 HOH HOH . Y 7 HOH B 43 843 64 HOH HOH . Y 7 HOH B 44 844 156 HOH HOH . Y 7 HOH B 45 845 86 HOH HOH . Y 7 HOH B 46 846 132 HOH HOH . Y 7 HOH B 47 847 52 HOH HOH . Y 7 HOH B 48 848 56 HOH HOH . Y 7 HOH B 49 849 2 HOH HOH . Y 7 HOH B 50 850 136 HOH HOH . Y 7 HOH B 51 851 51 HOH HOH . Y 7 HOH B 52 852 89 HOH HOH . Y 7 HOH B 53 853 28 HOH HOH . Y 7 HOH B 54 854 70 HOH HOH . Y 7 HOH B 55 855 53 HOH HOH . Y 7 HOH B 56 856 12 HOH HOH . Y 7 HOH B 57 857 160 HOH HOH . Y 7 HOH B 58 858 123 HOH HOH . Y 7 HOH B 59 859 41 HOH HOH . Y 7 HOH B 60 860 99 HOH HOH . Y 7 HOH B 61 861 168 HOH HOH . Y 7 HOH B 62 862 55 HOH HOH . Y 7 HOH B 63 863 43 HOH HOH . Y 7 HOH B 64 864 176 HOH HOH . Y 7 HOH B 65 865 103 HOH HOH . Y 7 HOH B 66 866 21 HOH HOH . Y 7 HOH B 67 867 175 HOH HOH . Y 7 HOH B 68 868 39 HOH HOH . Y 7 HOH B 69 869 23 HOH HOH . Y 7 HOH B 70 870 112 HOH HOH . Y 7 HOH B 71 871 66 HOH HOH . Y 7 HOH B 72 872 68 HOH HOH . Y 7 HOH B 73 873 87 HOH HOH . Y 7 HOH B 74 874 76 HOH HOH . Y 7 HOH B 75 875 142 HOH HOH . Y 7 HOH B 76 876 179 HOH HOH . Y 7 HOH B 77 877 44 HOH HOH . Y 7 HOH B 78 878 49 HOH HOH . Y 7 HOH B 79 879 63 HOH HOH . Y 7 HOH B 80 880 165 HOH HOH . Y 7 HOH B 81 881 74 HOH HOH . Y 7 HOH B 82 882 50 HOH HOH . Y 7 HOH B 83 883 169 HOH HOH . Y 7 HOH B 84 884 46 HOH HOH . Y 7 HOH B 85 885 31 HOH HOH . Y 7 HOH B 86 886 158 HOH HOH . Y 7 HOH B 87 887 71 HOH HOH . Y 7 HOH B 88 888 149 HOH HOH . Y 7 HOH B 89 889 33 HOH HOH . Y 7 HOH B 90 890 81 HOH HOH . Y 7 HOH B 91 891 36 HOH HOH . Y 7 HOH B 92 892 62 HOH HOH . Y 7 HOH B 93 893 80 HOH HOH . Y 7 HOH B 94 894 106 HOH HOH . Y 7 HOH B 95 895 32 HOH HOH . Y 7 HOH B 96 896 100 HOH HOH . Y 7 HOH B 97 897 181 HOH HOH . Y 7 HOH B 98 898 120 HOH HOH . Y 7 HOH B 99 899 17 HOH HOH . Y 7 HOH B 100 900 167 HOH HOH . Y 7 HOH B 101 901 101 HOH HOH . Y 7 HOH B 102 902 24 HOH HOH . Y 7 HOH B 103 903 159 HOH HOH . Y 7 HOH B 104 904 93 HOH HOH . Y 7 HOH B 105 905 139 HOH HOH . Y 7 HOH B 106 906 108 HOH HOH . Y 7 HOH B 107 907 128 HOH HOH . Y 7 HOH B 108 908 105 HOH HOH . Y 7 HOH B 109 909 150 HOH HOH . Y 7 HOH B 110 910 61 HOH HOH . Y 7 HOH B 111 911 184 HOH HOH . Y 7 HOH B 112 912 57 HOH HOH . Y 7 HOH B 113 913 40 HOH HOH . Y 7 HOH B 114 914 141 HOH HOH . Y 7 HOH B 115 915 166 HOH HOH . Y 7 HOH B 116 916 119 HOH HOH . Y 7 HOH B 117 917 95 HOH HOH . Y 7 HOH B 118 918 177 HOH HOH . Y 7 HOH B 119 919 129 HOH HOH . Y 7 HOH B 120 920 182 HOH HOH . Y 7 HOH B 121 921 122 HOH HOH . Y 7 HOH B 122 922 146 HOH HOH . Y 7 HOH B 123 923 170 HOH HOH . Y 7 HOH B 124 924 69 HOH HOH . Y 7 HOH B 125 925 118 HOH HOH . Y 7 HOH B 126 926 151 HOH HOH . Y 7 HOH B 127 927 148 HOH HOH . Y 7 HOH B 128 928 111 HOH HOH . Y 7 HOH B 129 929 172 HOH HOH . Y 7 HOH B 130 930 38 HOH HOH . Y 7 HOH B 131 931 104 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 C FMT . . . V 4 21.733 -19.735 -17.325 1 61.24 ? C FMT 714 B 1 HETATM 2 O O1 FMT . . . V 4 22.81 -19.759 -17.942 1 61.25 ? O1 FMT 714 B 1 HETATM 3 O O2 FMT . . . V 4 21.513 -19.177 -16.238 1 56.18 ? O2 FMT 714 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 3 #