data_6BML # _model_server_result.job_id gDOUkSjtOWLIRlga1eqiLw _model_server_result.datetime_utc '2024-10-20 00:41:50' _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 6bml # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":404}' # _entry.id 6BML # _exptl.entry_id 6BML _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 6BML _cell.length_a 99.794 _cell.length_b 99.794 _cell.length_c 159.947 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BML _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 5 _struct_asym.id J _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 SG CYS 124 A CYS 128 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc2 A SG CYS 127 A CYS 131 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc3 A ND1 HIS 137 A HIS 141 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc4 A SG CYS 138 A CYS 142 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc5 A SG CYS 141 A CYS 145 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc6 A SG CYS 144 A CYS 148 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc7 A ND1 HIS 151 A HIS 155 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? covale ? covale1 A SG CYS 152 A CYS 156 1_555 E C2 PLM . A PLM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.778 ? metalc ? metalc8 A SG CYS 158 A CYS 162 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc9 B SG CYS 124 B CYS 128 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc10 B SG CYS 127 B CYS 131 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc11 B ND1 HIS 137 B HIS 141 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc12 B SG CYS 138 B CYS 142 1_555 H ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc13 B SG CYS 141 B CYS 145 1_555 H ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc14 B SG CYS 144 B CYS 148 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc15 B ND1 HIS 151 B HIS 155 1_555 H ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale2 B SG CYS 152 B CYS 156 1_555 I C2 PLM . B PLM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc16 B SG CYS 158 B CYS 162 1_555 H ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id PAP _chem_comp.mon_nstd_flag . _chem_comp.name "3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6BML _atom_sites.fract_transf_matrix[1][1] 0.010021 _atom_sites.fract_transf_matrix[1][2] 0.005785 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011571 _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] 0.006252 _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 C 2 ZN A 1 401 401 ZN ZN . D 2 ZN A 1 402 402 ZN ZN . E 3 PLM A 1 403 501 PLM B2P . F 4 PO4 A 1 404 701 PO4 PO4 . G 2 ZN B 1 401 401 ZN ZN . H 2 ZN B 1 402 402 ZN ZN . I 3 PLM B 1 403 501 PLM B2P . J 5 PAP B 1 404 601 PAP ACO . K 4 PO4 B 1 405 701 PO4 PO4 . L 6 HOH A 1 501 2 HOH HOH . L 6 HOH A 2 502 1 HOH HOH . M 6 HOH B 1 501 3 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 P PB PAP . . . J 5 -5.167 -14.259 -0.265 1 122.46 1 PB PAP 404 B 1 HETATM 2 O O1B PAP . . . J 5 -5.632 -15.015 -1.467 1 110.33 ? O1B PAP 404 B 1 HETATM 3 O O2B PAP . . . J 5 -3.819 -13.648 -0.509 1 102.83 -1 O2B PAP 404 B 1 HETATM 4 O O3B PAP . . . J 5 -5.039 -15.308 1.013 0.52 100.38 -1 O3B PAP 404 B 1 HETATM 5 P PA PAP . . . J 5 -5.876 -11.48 0.2 0 138.48 1 PA PAP 404 B 1 HETATM 6 O O1A PAP . . . J 5 -7.104 -10.591 -0.043 1 108.49 -1 O1A PAP 404 B 1 HETATM 7 O O2A PAP . . . J 5 -5.371 -11.273 1.557 1 136.8 ? O2A PAP 404 B 1 HETATM 8 O O3A PAP . . . J 5 -6.268 -13.067 0.043 1 125.37 ? O3A PAP 404 B 1 HETATM 9 O O5' PAP . . . J 5 -4.687 -11.105 -0.968 1 124.38 ? O5' PAP 404 B 1 HETATM 10 C C5' PAP . . . J 5 -4.996 -11.554 -2.287 1 125.78 ? C5' PAP 404 B 1 HETATM 11 C C4' PAP . . . J 5 -3.932 -11.249 -3.331 1 121.17 ? C4' PAP 404 B 1 HETATM 12 O O4' PAP . . . J 5 -4.068 -12.102 -4.322 1 115.01 ? O4' PAP 404 B 1 HETATM 13 C C3' PAP . . . J 5 -4.228 -9.823 -3.974 1 129.94 ? C3' PAP 404 B 1 HETATM 14 O O3' PAP . . . J 5 -3.114 -9.246 -4.359 0 134.68 ? O3' PAP 404 B 1 HETATM 15 P P PAP . . . J 5 -3.013 -7.546 -4.193 1 161 1 P PAP 404 B 1 HETATM 16 O O1 PAP . . . J 5 -2.329 -6.941 -5.444 0.61 144.19 -1 O1 PAP 404 B 1 HETATM 17 O O2 PAP . . . J 5 -4.414 -6.964 -4.058 0 138.2 -1 O2 PAP 404 B 1 HETATM 18 O O3 PAP . . . J 5 -2.205 -7.215 -2.965 1 112.29 ? O3 PAP 404 B 1 HETATM 19 C C2' PAP . . . J 5 -5.137 -10.104 -5.204 1 132.27 ? C2' PAP 404 B 1 HETATM 20 O O2' PAP . . . J 5 -4.612 -9.428 -6.381 0.57 132.15 ? O2' PAP 404 B 1 HETATM 21 C C1' PAP . . . J 5 -5.136 -11.434 -5.404 0 129.35 ? C1' PAP 404 B 1 HETATM 22 N N9 PAP . . . J 5 -6.452 -11.965 -5.221 0 124.62 ? N9 PAP 404 B 1 HETATM 23 C C8 PAP . . . J 5 -7.385 -11.633 -4.332 1 115.35 ? C8 PAP 404 B 1 HETATM 24 N N7 PAP . . . J 5 -8.447 -12.398 -4.536 1 107.56 ? N7 PAP 404 B 1 HETATM 25 C C5 PAP . . . J 5 -8.185 -13.2 -5.561 0 117.07 ? C5 PAP 404 B 1 HETATM 26 C C6 PAP . . . J 5 -8.944 -14.186 -6.192 0 117.47 ? C6 PAP 404 B 1 HETATM 27 N N6 PAP . . . J 5 -10.297 -14.522 -5.774 1 109.31 ? N6 PAP 404 B 1 HETATM 28 N N1 PAP . . . J 5 -8.45 -14.857 -7.207 1 109.28 ? N1 PAP 404 B 1 HETATM 29 C C2 PAP . . . J 5 -7.181 -14.586 -7.647 1 98.37 ? C2 PAP 404 B 1 HETATM 30 N N3 PAP . . . J 5 -6.441 -13.633 -7.04 0.94 112.65 ? N3 PAP 404 B 1 HETATM 31 C C4 PAP . . . J 5 -6.953 -12.937 -5.988 1 119.89 ? C4 PAP 404 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 43 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #