data_6JDB # _model_server_result.job_id Cm8QC0NcW_CrK_kVx0peGQ _model_server_result.datetime_utc '2024-10-19 09:37:54' _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 6jdb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6JDB # _exptl.entry_id 6JDB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "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 90 _cell.entry_id 6JDB _cell.length_a 92.591 _cell.length_b 92.591 _cell.length_c 183.321 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JDB _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_666 -y+1,-x+1,-z+1 0 -1 0 -1 0 0 0 0 -1 92.591 92.591 183.321 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 ND1 HIS 155 A HIS 156 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc2 A SG CYS 165 A CYS 166 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc3 A SG CYS 167 A CYS 168 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc4 A SG CYS 172 A CYS 173 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6JDB _atom_sites.fract_transf_matrix[1][1] 0.0108 _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] 0.0108 _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] 0.005455 _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 ADP A 1 301 1 ADP ADP . C 3 BMX A 1 302 1 BMX BMX . D 4 ZN A 1 303 1 ZN ZN . E 5 HOH A 1 401 10 HOH HOH . E 5 HOH A 2 402 2 HOH HOH . E 5 HOH A 3 403 1 HOH HOH . E 5 HOH A 4 404 5 HOH HOH . E 5 HOH A 5 405 4 HOH HOH . E 5 HOH A 6 406 9 HOH HOH . E 5 HOH A 7 407 8 HOH HOH . E 5 HOH A 8 408 6 HOH HOH . E 5 HOH A 9 409 12 HOH HOH . E 5 HOH A 10 410 11 HOH HOH . E 5 HOH A 11 411 7 HOH HOH . E 5 HOH A 12 412 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 ADP . . . B 2 11.346 51.561 82.753 1 83.01 ? PB ADP 301 A 1 HETATM 2 O O1B ADP . . . B 2 10.719 51.541 81.38 1 84.86 ? O1B ADP 301 A 1 HETATM 3 O O2B ADP . . . B 2 10.557 52.53 83.609 1 84.31 ? O2B ADP 301 A 1 HETATM 4 O O3B ADP . . . B 2 12.787 52.002 82.631 1 76.1 ? O3B ADP 301 A 1 HETATM 5 P PA ADP . . . B 2 11.269 49.553 84.956 1 85.55 ? PA ADP 301 A 1 HETATM 6 O O1A ADP . . . B 2 10.225 48.46 85.045 1 86.93 ? O1A ADP 301 A 1 HETATM 7 O O2A ADP . . . B 2 10.907 50.679 85.915 1 76.72 ? O2A ADP 301 A 1 HETATM 8 O O3A ADP . . . B 2 11.348 50.031 83.375 1 80.2 ? O3A ADP 301 A 1 HETATM 9 O O5' ADP . . . B 2 12.758 48.918 85.306 1 81.02 ? O5' ADP 301 A 1 HETATM 10 C C5' ADP . . . B 2 13.279 47.941 84.434 1 78.06 ? C5' ADP 301 A 1 HETATM 11 C C4' ADP . . . B 2 14.577 47.334 85.03 1 73.55 ? C4' ADP 301 A 1 HETATM 12 O O4' ADP . . . B 2 14.357 46.94 86.258 1 77.9 ? O4' ADP 301 A 1 HETATM 13 C C3' ADP . . . B 2 15.018 46.077 84.27 1 68.57 ? C3' ADP 301 A 1 HETATM 14 O O3' ADP . . . B 2 16.362 45.957 84.348 1 67.69 ? O3' ADP 301 A 1 HETATM 15 C C2' ADP . . . B 2 14.422 44.915 85.071 1 77.72 ? C2' ADP 301 A 1 HETATM 16 O O2' ADP . . . B 2 15.336 43.742 84.944 1 78.44 ? O2' ADP 301 A 1 HETATM 17 C C1' ADP . . . B 2 14.426 45.321 86.312 1 79.18 ? C1' ADP 301 A 1 HETATM 18 N N9 ADP . . . B 2 13.259 44.84 87.003 1 80.95 ? N9 ADP 301 A 1 HETATM 19 C C8 ADP . . . B 2 12.009 44.84 86.523 1 83.73 ? C8 ADP 301 A 1 HETATM 20 N N7 ADP . . . B 2 11.196 44.338 87.456 1 82.92 ? N7 ADP 301 A 1 HETATM 21 C C5 ADP . . . B 2 11.948 44.032 88.524 1 84.56 ? C5 ADP 301 A 1 HETATM 22 C C6 ADP . . . B 2 11.601 43.491 89.742 1 83.13 ? C6 ADP 301 A 1 HETATM 23 N N6 ADP . . . B 2 10.254 43.115 90.15 1 81.24 ? N6 ADP 301 A 1 HETATM 24 N N1 ADP . . . B 2 12.541 43.268 90.654 1 81.6 ? N1 ADP 301 A 1 HETATM 25 C C2 ADP . . . B 2 13.839 43.583 90.387 1 76.95 ? C2 ADP 301 A 1 HETATM 26 N N3 ADP . . . B 2 14.179 44.119 89.186 1 80.95 ? N3 ADP 301 A 1 HETATM 27 C C4 ADP . . . B 2 13.227 44.34 88.253 1 82.67 ? C4 ADP 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #