data_6S2U # _model_server_result.job_id PXiaINZdwtZ6ifR8T5ESAQ _model_server_result.datetime_utc '2024-10-20 08:18:45' _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 6s2u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 6S2U # _exptl.entry_id 6S2U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 602.176 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid' _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 111 _cell.angle_gamma 90 _cell.entry_id 6S2U _cell.length_a 120.739 _cell.length_b 50.346 _cell.length_c 86.057 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S2U _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id D _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 metalc ? metalc1 A NE2 HIS 52 A HIS 52 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc2 A NE2 HIS 76 A HIS 76 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc3 A OD2 ASP 146 A ASP 146 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc4 D O10 GN3 . A GN3 403 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc5 D O9 GN3 . A GN3 403 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc6 D O7 GN3 . A GN3 403 1_555 G MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc7 D O5 GN3 . A GN3 403 1_555 G MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? # _chem_comp.formula 'C10 H18 N6 O16 P4' _chem_comp.formula_weight 602.176 _chem_comp.id GN3 _chem_comp.mon_nstd_flag . _chem_comp.name '[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic 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 O15 C9 GN3 doub 168 n n N5 C9 GN3 sing 169 n n N5 C GN3 sing 170 n n C9 C2 GN3 sing 171 n n N C GN3 sing 172 n n C N1 GN3 doub 173 n n C2 N2 GN3 sing 174 n y C2 C1 GN3 doub 175 n y N2 C3 GN3 doub 176 n y N1 C1 GN3 sing 177 n n C1 N3 GN3 sing 178 n y O10 P2 GN3 doub 179 n n C3 N3 GN3 sing 180 n y N3 C4 GN3 sing 181 n n O13 P3 GN3 doub 182 n n P2 O9 GN3 sing 183 n n P2 O8 GN3 sing 184 n n P2 N4 GN3 sing 185 n n O12 P3 GN3 sing 186 n n C7 C8 GN3 sing 187 n n C7 O8 GN3 sing 188 n n C7 C5 GN3 sing 189 n n C8 C4 GN3 sing 190 n n C8 O14 GN3 sing 191 n n C4 O GN3 sing 192 n n P3 N4 GN3 sing 193 n n P3 O11 GN3 sing 194 n n C6 C5 GN3 sing 195 n n C6 O1 GN3 sing 196 n n O C5 GN3 sing 197 n n O1 P GN3 sing 198 n n P O4 GN3 sing 199 n n P O2 GN3 doub 200 n n P O3 GN3 sing 201 n n O4 P1 GN3 sing 202 n n O7 P1 GN3 doub 203 n n P1 O6 GN3 sing 204 n n P1 O5 GN3 sing 205 n n N5 H1 GN3 sing 206 n n N H2 GN3 sing 207 n n N H3 GN3 sing 208 n n C3 H4 GN3 sing 209 n n C4 H5 GN3 sing 210 n n C8 H6 GN3 sing 211 n n O14 H7 GN3 sing 212 n n C7 H8 GN3 sing 213 n n N4 H9 GN3 sing 214 n n O12 H10 GN3 sing 215 n n O11 H11 GN3 sing 216 n n O9 H12 GN3 sing 217 n n C5 H13 GN3 sing 218 n n C6 H14 GN3 sing 219 n n C6 H15 GN3 sing 220 n n O3 H16 GN3 sing 221 n n O6 H17 GN3 sing 222 n n O5 H18 GN3 sing 223 n n # _atom_sites.entry_id 6S2U _atom_sites.fract_transf_matrix[1][1] 0.008282 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003179 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019863 _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] 0.012447 _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 B 2 MN A 1 401 1 MN MN . C 3 AMP A 1 402 1 AMP AMP . D 4 GN3 A 1 403 501 GN3 GN3 . E 5 TMO A 1 404 601 TMO TMO . F 6 MG A 1 405 1 MG MG . G 6 MG A 1 406 2 MG MG . H 7 HOH A 1 501 21 HOH HOH . H 7 HOH A 2 502 7 HOH HOH . H 7 HOH A 3 503 12 HOH HOH . H 7 HOH A 4 504 8 HOH HOH . H 7 HOH A 5 505 11 HOH HOH . H 7 HOH A 6 506 16 HOH HOH . H 7 HOH A 7 507 3 HOH HOH . H 7 HOH A 8 508 13 HOH HOH . H 7 HOH A 9 509 1 HOH HOH . H 7 HOH A 10 510 15 HOH HOH . H 7 HOH A 11 511 2 HOH HOH . H 7 HOH A 12 512 10 HOH HOH . H 7 HOH A 13 513 4 HOH HOH . H 7 HOH A 14 514 18 HOH HOH . H 7 HOH A 15 515 9 HOH HOH . H 7 HOH A 16 516 5 HOH HOH . H 7 HOH A 17 517 20 HOH HOH . H 7 HOH A 18 518 6 HOH HOH . H 7 HOH A 19 519 19 HOH HOH . H 7 HOH A 20 520 14 HOH HOH . H 7 HOH A 21 521 17 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 O O15 GN3 . . . D 4 79.349 -61.41 101.022 1 162.6 ? O15 GN3 403 A 1 HETATM 2 C C9 GN3 . . . D 4 80.107 -61.435 101.99 1 161.84 ? C9 GN3 403 A 1 HETATM 3 N N5 GN3 . . . D 4 81.325 -62.086 101.913 1 161.96 ? N5 GN3 403 A 1 HETATM 4 C C GN3 . . . D 4 82.236 -62.171 102.935 1 161.08 ? C GN3 403 A 1 HETATM 5 N N GN3 . . . D 4 83.363 -62.841 102.684 1 160.6 ? N GN3 403 A 1 HETATM 6 C C2 GN3 . . . D 4 79.89 -60.839 103.287 1 159.63 ? C2 GN3 403 A 1 HETATM 7 N N2 GN3 . . . D 4 78.826 -60.108 103.788 1 157.44 ? N2 GN3 403 A 1 HETATM 8 C C3 GN3 . . . D 4 79.177 -59.827 105.023 1 155.58 ? C3 GN3 403 A 1 HETATM 9 N N3 GN3 . . . D 4 80.407 -60.329 105.364 1 153.89 ? N3 GN3 403 A 1 HETATM 10 C C1 GN3 . . . D 4 80.871 -60.983 104.247 1 158.48 ? C1 GN3 403 A 1 HETATM 11 N N1 GN3 . . . D 4 82.05 -61.627 104.138 1 160.35 ? N1 GN3 403 A 1 HETATM 12 C C4 GN3 . . . D 4 81.093 -60.2 106.658 1 146.33 ? C4 GN3 403 A 1 HETATM 13 C C8 GN3 . . . D 4 82.564 -59.799 106.529 1 142.62 ? C8 GN3 403 A 1 HETATM 14 O O14 GN3 . . . D 4 83.297 -60.208 107.678 1 141.84 ? O14 GN3 403 A 1 HETATM 15 C C7 GN3 . . . D 4 82.43 -58.281 106.483 1 139.08 ? C7 GN3 403 A 1 HETATM 16 O O8 GN3 . . . D 4 83.576 -57.582 107.016 1 136.43 ? O8 GN3 403 A 1 HETATM 17 P P2 GN3 . . . D 4 84.774 -56.778 106.405 1 131.16 ? P2 GN3 403 A 1 HETATM 18 O O10 GN3 . . . D 4 84.686 -56.52 104.976 1 130.03 ? O10 GN3 403 A 1 HETATM 19 N N4 GN3 . . . D 4 84.842 -55.397 107.268 1 128.7 ? N4 GN3 403 A 1 HETATM 20 P P3 GN3 . . . D 4 84.536 -53.818 107.005 1 128.27 ? P3 GN3 403 A 1 HETATM 21 O O13 GN3 . . . D 4 83.459 -53.443 106.102 1 126.88 ? O13 GN3 403 A 1 HETATM 22 O O12 GN3 . . . D 4 85.888 -53.191 106.451 1 129.84 ? O12 GN3 403 A 1 HETATM 23 O O11 GN3 . . . D 4 84.335 -53.039 108.363 1 128.61 ? O11 GN3 403 A 1 HETATM 24 O O9 GN3 . . . D 4 86.075 -57.637 106.666 1 130.5 ? O9 GN3 403 A 1 HETATM 25 C C5 GN3 . . . D 4 81.306 -58.012 107.481 1 136.33 ? C5 GN3 403 A 1 HETATM 26 O O GN3 . . . D 4 80.455 -59.178 107.403 1 141.25 ? O GN3 403 A 1 HETATM 27 C C6 GN3 . . . D 4 80.492 -56.774 107.204 1 128.58 ? C6 GN3 403 A 1 HETATM 28 O O1 GN3 . . . D 4 79.367 -56.74 108.108 1 120.09 ? O1 GN3 403 A 1 HETATM 29 P P GN3 . . . D 4 79.346 -56.753 109.689 1 108.5 ? P GN3 403 A 1 HETATM 30 O O3 GN3 . . . D 4 78.1 -57.359 110.204 1 105.96 ? O3 GN3 403 A 1 HETATM 31 O O2 GN3 . . . D 4 80.63 -57.443 110.14 1 107.38 ? O2 GN3 403 A 1 HETATM 32 O O4 GN3 . . . D 4 79.466 -55.224 110.115 1 102.99 ? O4 GN3 403 A 1 HETATM 33 P P1 GN3 . . . D 4 80.382 -54.462 111.174 1 99.23 ? P1 GN3 403 A 1 HETATM 34 O O7 GN3 . . . D 4 80.544 -53.03 110.791 1 99.96 ? O7 GN3 403 A 1 HETATM 35 O O6 GN3 . . . D 4 81.709 -55.226 111.209 1 96.36 ? O6 GN3 403 A 1 HETATM 36 O O5 GN3 . . . D 4 79.698 -54.643 112.532 1 99.36 ? O5 GN3 403 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #