data_6RK9 # _model_server_result.job_id kpkse3fztViGd3nJptePHQ _model_server_result.datetime_utc '2024-11-09 01:29:45' _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 6rk9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":802}' # _entry.id 6RK9 # _exptl.entry_id 6RK9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.086 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-OXALYLGLYCINE _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 103.97 _cell.angle_beta 91.49 _cell.angle_gamma 92.7 _cell.entry_id 6RK9 _cell.length_a 49.472 _cell.length_b 59.243 _cell.length_c 95.665 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RK9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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,H,J 1 1 B,F,G,I 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 G 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 A SG CYS 312 A CYS 641 1_555 A SG CYS 319 A CYS 648 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 B SG CYS 312 B CYS 641 1_555 B SG CYS 319 B CYS 648 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 C C DAL 1 C DAL 253 1_555 C N LYS 2 C LYS 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A NE2 HIS 350 A HIS 679 1_555 D MN MN . A MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc2 A NE2 HIS 396 A HIS 725 1_555 D MN MN . A MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc3 D MN MN . A MN 801 1_555 E O1 OGA . A OGA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc4 D MN MN . A MN 801 1_555 E O2' OGA . A OGA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc5 D MN MN . A MN 801 1_555 C OD2 ASP 3 C ASP 255 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.552 ? metalc ? metalc6 D MN MN . A MN 801 1_555 J O HOH . C HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc7 B NE2 HIS 350 B HIS 679 1_555 F MN MN . B MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc8 B NE2 HIS 396 B HIS 725 1_555 F MN MN . B MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc9 F MN MN . B MN 801 1_555 G O2' OGA . B OGA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc10 F MN MN . B MN 801 1_555 G O2 OGA . B OGA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc11 F MN MN . B MN 801 1_555 I O HOH . B HOH 925 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc12 F MN MN . B MN 801 1_555 I O HOH . B HOH 957 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? # _chem_comp.formula 'C4 H5 N O5' _chem_comp.formula_weight 147.086 _chem_comp.id OGA _chem_comp.mon_nstd_flag . _chem_comp.name N-OXALYLGLYCINE _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 C2 OGA sing 249 n n C1 O1 OGA doub 250 n n C1 O2 OGA sing 251 n n C2 O2' OGA doub 252 n n C2 N1 OGA sing 253 n n C4 C5 OGA sing 254 n n C4 N1 OGA sing 255 n n C4 H4C1 OGA sing 256 n n C4 H4C2 OGA sing 257 n n C5 O3 OGA sing 258 n n C5 O4 OGA doub 259 n n O2 H2 OGA sing 260 n n O3 H3 OGA sing 261 n n N1 H1 OGA sing 262 n n # _atom_sites.entry_id 6RK9 _atom_sites.fract_transf_matrix[1][1] 0.020213 _atom_sites.fract_transf_matrix[1][2] 0.000953 _atom_sites.fract_transf_matrix[1][3] 0.000781 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016898 _atom_sites.fract_transf_matrix[2][3] 0.004233 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.01078 _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 3 MN A 1 801 801 MN MN . E 4 OGA A 1 802 802 OGA OGA . F 3 MN B 1 801 801 MN MN . G 4 OGA B 1 802 802 OGA OGA . H 5 HOH A 1 901 123 HOH HOH . H 5 HOH A 2 902 1 HOH HOH . H 5 HOH A 3 903 56 HOH HOH . H 5 HOH A 4 904 17 HOH HOH . H 5 HOH A 5 905 134 HOH HOH . H 5 HOH A 6 906 135 HOH HOH . H 5 HOH A 7 907 108 HOH HOH . H 5 HOH A 8 908 242 HOH HOH . H 5 HOH A 9 909 219 HOH HOH . H 5 HOH A 10 910 91 HOH HOH . H 5 HOH A 11 911 59 HOH HOH . H 5 HOH A 12 912 122 HOH HOH . H 5 HOH A 13 913 8 HOH HOH . H 5 HOH A 14 914 110 HOH HOH . H 5 HOH A 15 915 79 HOH HOH . H 5 HOH A 16 916 170 HOH HOH . H 5 HOH A 17 917 167 HOH HOH . H 5 HOH A 18 918 18 HOH HOH . H 5 HOH A 19 919 243 HOH HOH . H 5 HOH A 20 920 223 HOH HOH . H 5 HOH A 21 921 85 HOH HOH . H 5 HOH A 22 922 194 HOH HOH . H 5 HOH A 23 923 136 HOH HOH . H 5 HOH A 24 924 63 HOH HOH . H 5 HOH A 25 925 46 HOH HOH . H 5 HOH A 26 926 36 HOH HOH . H 5 HOH A 27 927 65 HOH HOH . H 5 HOH A 28 928 169 HOH HOH . H 5 HOH A 29 929 109 HOH HOH . H 5 HOH A 30 930 118 HOH HOH . H 5 HOH A 31 931 3 HOH HOH . H 5 HOH A 32 932 16 HOH HOH . H 5 HOH A 33 933 87 HOH HOH . H 5 HOH A 34 934 26 HOH HOH . H 5 HOH A 35 935 25 HOH HOH . H 5 HOH A 36 936 184 HOH HOH . H 5 HOH A 37 937 13 HOH HOH . H 5 HOH A 38 938 28 HOH HOH . H 5 HOH A 39 939 90 HOH HOH . H 5 HOH A 40 940 205 HOH HOH . H 5 HOH A 41 941 88 HOH HOH . H 5 HOH A 42 942 234 HOH HOH . H 5 HOH A 43 943 203 HOH HOH . H 5 HOH A 44 944 213 HOH HOH . H 5 HOH A 45 945 57 HOH HOH . H 5 HOH A 46 946 24 HOH HOH . H 5 HOH A 47 947 78 HOH HOH . H 5 HOH A 48 948 80 HOH HOH . H 5 HOH A 49 949 66 HOH HOH . H 5 HOH A 50 950 30 HOH HOH . H 5 HOH A 51 951 38 HOH HOH . H 5 HOH A 52 952 187 HOH HOH . H 5 HOH A 53 953 12 HOH HOH . H 5 HOH A 54 954 139 HOH HOH . H 5 HOH A 55 955 84 HOH HOH . H 5 HOH A 56 956 62 HOH HOH . H 5 HOH A 57 957 125 HOH HOH . H 5 HOH A 58 958 195 HOH HOH . H 5 HOH A 59 959 86 HOH HOH . H 5 HOH A 60 960 117 HOH HOH . H 5 HOH A 61 961 131 HOH HOH . H 5 HOH A 62 962 240 HOH HOH . H 5 HOH A 63 963 120 HOH HOH . H 5 HOH A 64 964 174 HOH HOH . H 5 HOH A 65 965 82 HOH HOH . H 5 HOH A 66 966 77 HOH HOH . H 5 HOH A 67 967 31 HOH HOH . H 5 HOH A 68 968 189 HOH HOH . H 5 HOH A 69 969 157 HOH HOH . H 5 HOH A 70 970 209 HOH HOH . H 5 HOH A 71 971 20 HOH HOH . H 5 HOH A 72 972 15 HOH HOH . H 5 HOH A 73 973 5 HOH HOH . H 5 HOH A 74 974 47 HOH HOH . H 5 HOH A 75 975 119 HOH HOH . H 5 HOH A 76 976 94 HOH HOH . H 5 HOH A 77 977 45 HOH HOH . H 5 HOH A 78 978 181 HOH HOH . H 5 HOH A 79 979 33 HOH HOH . H 5 HOH A 80 980 124 HOH HOH . H 5 HOH A 81 981 10 HOH HOH . H 5 HOH A 82 982 246 HOH HOH . H 5 HOH A 83 983 95 HOH HOH . H 5 HOH A 84 984 241 HOH HOH . H 5 HOH A 85 985 107 HOH HOH . H 5 HOH A 86 986 212 HOH HOH . H 5 HOH A 87 987 121 HOH HOH . H 5 HOH A 88 988 204 HOH HOH . H 5 HOH A 89 989 133 HOH HOH . H 5 HOH A 90 990 14 HOH HOH . H 5 HOH A 91 991 58 HOH HOH . H 5 HOH A 92 992 93 HOH HOH . H 5 HOH A 93 993 67 HOH HOH . H 5 HOH A 94 994 171 HOH HOH . H 5 HOH A 95 995 159 HOH HOH . H 5 HOH A 96 996 50 HOH HOH . H 5 HOH A 97 997 185 HOH HOH . H 5 HOH A 98 998 44 HOH HOH . H 5 HOH A 99 999 207 HOH HOH . H 5 HOH A 100 1000 160 HOH HOH . H 5 HOH A 101 1001 32 HOH HOH . H 5 HOH A 102 1002 226 HOH HOH . H 5 HOH A 103 1003 198 HOH HOH . H 5 HOH A 104 1004 126 HOH HOH . H 5 HOH A 105 1005 211 HOH HOH . H 5 HOH A 106 1006 106 HOH HOH . H 5 HOH A 107 1007 218 HOH HOH . H 5 HOH A 108 1008 216 HOH HOH . H 5 HOH A 109 1009 248 HOH HOH . H 5 HOH A 110 1010 115 HOH HOH . H 5 HOH A 111 1011 127 HOH HOH . H 5 HOH A 112 1012 200 HOH HOH . H 5 HOH A 113 1013 81 HOH HOH . H 5 HOH A 114 1014 128 HOH HOH . H 5 HOH A 115 1015 140 HOH HOH . H 5 HOH A 116 1016 217 HOH HOH . H 5 HOH A 117 1017 116 HOH HOH . H 5 HOH A 118 1018 137 HOH HOH . H 5 HOH A 119 1019 162 HOH HOH . I 5 HOH B 1 901 55 HOH HOH . I 5 HOH B 2 902 23 HOH HOH . I 5 HOH B 3 903 196 HOH HOH . I 5 HOH B 4 904 193 HOH HOH . I 5 HOH B 5 905 177 HOH HOH . I 5 HOH B 6 906 64 HOH HOH . I 5 HOH B 7 907 225 HOH HOH . I 5 HOH B 8 908 7 HOH HOH . I 5 HOH B 9 909 2 HOH HOH . I 5 HOH B 10 910 48 HOH HOH . I 5 HOH B 11 911 233 HOH HOH . I 5 HOH B 12 912 176 HOH HOH . I 5 HOH B 13 913 9 HOH HOH . I 5 HOH B 14 914 210 HOH HOH . I 5 HOH B 15 915 153 HOH HOH . I 5 HOH B 16 916 40 HOH HOH . I 5 HOH B 17 917 156 HOH HOH . I 5 HOH B 18 918 72 HOH HOH . I 5 HOH B 19 919 220 HOH HOH . I 5 HOH B 20 920 150 HOH HOH . I 5 HOH B 21 921 114 HOH HOH . I 5 HOH B 22 922 22 HOH HOH . I 5 HOH B 23 923 221 HOH HOH . I 5 HOH B 24 924 147 HOH HOH . I 5 HOH B 25 925 112 HOH HOH . I 5 HOH B 26 926 39 HOH HOH . I 5 HOH B 27 927 143 HOH HOH . I 5 HOH B 28 928 69 HOH HOH . I 5 HOH B 29 929 53 HOH HOH . I 5 HOH B 30 930 229 HOH HOH . I 5 HOH B 31 931 182 HOH HOH . I 5 HOH B 32 932 41 HOH HOH . I 5 HOH B 33 933 141 HOH HOH . I 5 HOH B 34 934 232 HOH HOH . I 5 HOH B 35 935 4 HOH HOH . I 5 HOH B 36 936 11 HOH HOH . I 5 HOH B 37 937 68 HOH HOH . I 5 HOH B 38 938 75 HOH HOH . I 5 HOH B 39 939 105 HOH HOH . I 5 HOH B 40 940 99 HOH HOH . I 5 HOH B 41 941 129 HOH HOH . I 5 HOH B 42 942 230 HOH HOH . I 5 HOH B 43 943 149 HOH HOH . I 5 HOH B 44 944 146 HOH HOH . I 5 HOH B 45 945 103 HOH HOH . I 5 HOH B 46 946 250 HOH HOH . I 5 HOH B 47 947 97 HOH HOH . I 5 HOH B 48 948 27 HOH HOH . I 5 HOH B 49 949 6 HOH HOH . I 5 HOH B 50 950 34 HOH HOH . I 5 HOH B 51 951 98 HOH HOH . I 5 HOH B 52 952 83 HOH HOH . I 5 HOH B 53 953 35 HOH HOH . I 5 HOH B 54 954 145 HOH HOH . I 5 HOH B 55 955 42 HOH HOH . I 5 HOH B 56 956 70 HOH HOH . I 5 HOH B 57 957 111 HOH HOH . I 5 HOH B 58 958 183 HOH HOH . I 5 HOH B 59 959 60 HOH HOH . I 5 HOH B 60 960 51 HOH HOH . I 5 HOH B 61 961 102 HOH HOH . I 5 HOH B 62 962 144 HOH HOH . I 5 HOH B 63 963 173 HOH HOH . I 5 HOH B 64 964 130 HOH HOH . I 5 HOH B 65 965 92 HOH HOH . I 5 HOH B 66 966 100 HOH HOH . I 5 HOH B 67 967 52 HOH HOH . I 5 HOH B 68 968 101 HOH HOH . I 5 HOH B 69 969 202 HOH HOH . I 5 HOH B 70 970 89 HOH HOH . I 5 HOH B 71 971 192 HOH HOH . I 5 HOH B 72 972 49 HOH HOH . I 5 HOH B 73 973 178 HOH HOH . I 5 HOH B 74 974 76 HOH HOH . I 5 HOH B 75 975 158 HOH HOH . I 5 HOH B 76 976 148 HOH HOH . I 5 HOH B 77 977 19 HOH HOH . I 5 HOH B 78 978 190 HOH HOH . I 5 HOH B 79 979 197 HOH HOH . I 5 HOH B 80 980 163 HOH HOH . I 5 HOH B 81 981 206 HOH HOH . I 5 HOH B 82 982 132 HOH HOH . I 5 HOH B 83 983 54 HOH HOH . I 5 HOH B 84 984 152 HOH HOH . I 5 HOH B 85 985 21 HOH HOH . I 5 HOH B 86 986 151 HOH HOH . I 5 HOH B 87 987 73 HOH HOH . I 5 HOH B 88 988 37 HOH HOH . I 5 HOH B 89 989 208 HOH HOH . I 5 HOH B 90 990 201 HOH HOH . I 5 HOH B 91 991 71 HOH HOH . I 5 HOH B 92 992 239 HOH HOH . I 5 HOH B 93 993 188 HOH HOH . I 5 HOH B 94 994 161 HOH HOH . I 5 HOH B 95 995 155 HOH HOH . I 5 HOH B 96 996 96 HOH HOH . I 5 HOH B 97 997 236 HOH HOH . I 5 HOH B 98 998 231 HOH HOH . I 5 HOH B 99 999 238 HOH HOH . I 5 HOH B 100 1000 199 HOH HOH . I 5 HOH B 101 1001 175 HOH HOH . I 5 HOH B 102 1002 104 HOH HOH . I 5 HOH B 103 1003 29 HOH HOH . I 5 HOH B 104 1004 166 HOH HOH . I 5 HOH B 105 1005 191 HOH HOH . I 5 HOH B 106 1006 224 HOH HOH . I 5 HOH B 107 1007 228 HOH HOH . J 5 HOH C 1 301 113 HOH HOH . J 5 HOH C 2 302 138 HOH HOH . J 5 HOH C 3 303 154 HOH HOH . J 5 HOH C 4 304 244 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 OGA . . . E 4 54.897 4.271 -25.435 1 46.2 ? C1 OGA 802 A 1 HETATM 2 C C2 OGA . . . E 4 56.157 4.264 -24.592 1 46.62 ? C2 OGA 802 A 1 HETATM 3 C C4 OGA . . . E 4 57.274 3.165 -22.617 1 45.09 ? C4 OGA 802 A 1 HETATM 4 C C5 OGA . . . E 4 57.216 1.751 -22.066 1 44.26 ? C5 OGA 802 A 1 HETATM 5 O O1 OGA . . . E 4 54.728 5.081 -26.385 1 46.72 ? O1 OGA 802 A 1 HETATM 6 O O2 OGA . . . E 4 54.025 3.419 -25.135 1 45.69 ? O2 OGA 802 A 1 HETATM 7 O O2' OGA . . . E 4 57.075 4.988 -24.799 1 46.56 ? O2' OGA 802 A 1 HETATM 8 O O3 OGA . . . E 4 57.718 1.501 -20.952 1 44.25 ? O3 OGA 802 A 1 HETATM 9 N N1 OGA . . . E 4 56.154 3.3 -23.514 1 46.42 ? N1 OGA 802 A 1 HETATM 10 O O4 OGA . . . E 4 56.681 0.825 -22.725 1 43.79 ? O4 OGA 802 A 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 10 #