data_5W74 # _model_server_result.job_id gxfig3kXHXrlSr0EZ_OT4g _model_server_result.datetime_utc '2024-10-18 20:26:05' _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 5w74 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":600}' # _entry.id 5W74 # _exptl.entry_id 5W74 _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 8 _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 5W74 _cell.length_a 152.72 _cell.length_b 221.93 _cell.length_c 262.15 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W74 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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 _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' 2_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 152.72 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q N N ? 2 S N N ? 2 U N N ? 2 W 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 metalc ? metalc1 I O1B ADP . A ADP 600 1_555 J MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc2 I O2B ADP . A ADP 600 1_555 J MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc3 I O2A ADP . A ADP 600 1_555 J MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc4 I O3A ADP . A ADP 600 1_555 J MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc5 B OD1 ASP 91 B ASP 91 1_555 L MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc6 K O1B ADP . B ADP 600 1_555 L MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc7 K O3A ADP . B ADP 600 1_555 L MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc8 C OD1 ASP 91 C ASP 91 1_555 N MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc9 M O3A ADP . C ADP 600 1_555 N MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc10 D OD1 ASP 91 D ASP 91 1_555 P MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc11 D OD2 ASP 91 D ASP 91 1_555 P MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? metalc ? metalc12 O O3A ADP . D ADP 600 1_555 P MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc13 E OD1 ASP 91 E ASP 91 1_555 R MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc14 Q O1B ADP . E ADP 600 1_555 R MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc15 Q O3A ADP . E ADP 600 1_555 R MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc16 F OD1 ASP 91 F ASP 91 1_555 T MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc17 S O3A ADP . F ADP 600 1_555 T MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc18 G OD1 ASP 91 G ASP 91 1_555 V MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc19 U O1B ADP . G ADP 600 1_555 V MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc20 U O3A ADP . G ADP 600 1_555 V MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc21 H OD1 ASP 91 H ASP 91 1_555 X MG MG . H MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc22 H OD2 ASP 91 H ASP 91 1_555 X MG MG . H MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? metalc ? metalc23 W O3A ADP . H ADP 600 1_555 X MG MG . H MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? # _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 5W74 _atom_sites.fract_transf_matrix[1][1] 0.006548 _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] 0.004506 _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] 0.003815 _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 I 2 ADP A 1 600 600 ADP ADP . J 3 MG A 1 601 601 MG MG . K 2 ADP B 1 600 600 ADP ADP . L 3 MG B 1 601 601 MG MG . M 2 ADP C 1 600 600 ADP ADP . N 3 MG C 1 601 601 MG MG . O 2 ADP D 1 600 600 ADP ADP . P 3 MG D 1 601 601 MG MG . Q 2 ADP E 1 600 600 ADP ADP . R 3 MG E 1 601 601 MG MG . S 2 ADP F 1 600 600 ADP ADP . T 3 MG F 1 601 601 MG MG . U 2 ADP G 1 600 600 ADP ADP . V 3 MG G 1 601 601 MG MG . W 2 ADP H 1 600 600 ADP ADP . X 3 MG H 1 601 601 MG MG . # 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 . . . U 2 123.864 -25.407 -26.099 1 92.63 ? PB ADP 600 G 1 HETATM 2 O O1B ADP . . . U 2 123.179 -25.639 -27.423 1 108.03 ? O1B ADP 600 G 1 HETATM 3 O O2B ADP . . . U 2 122.962 -25.619 -24.912 1 76.4 -1 O2B ADP 600 G 1 HETATM 4 O O3B ADP . . . U 2 124.679 -24.136 -26.031 1 86.04 ? O3B ADP 600 G 1 HETATM 5 P PA ADP . . . U 2 125.173 -27.56 -24.746 1 111.32 ? PA ADP 600 G 1 HETATM 6 O O1A ADP . . . U 2 125.891 -28.786 -25.256 1 109.23 -1 O1A ADP 600 G 1 HETATM 7 O O2A ADP . . . U 2 123.839 -27.757 -24.075 1 135.84 ? O2A ADP 600 G 1 HETATM 8 O O3A ADP . . . U 2 124.963 -26.591 -26.022 1 105.74 ? O3A ADP 600 G 1 HETATM 9 O O5' ADP . . . U 2 126.185 -26.795 -23.739 1 92.76 ? O5' ADP 600 G 1 HETATM 10 C C5' ADP . . . U 2 126.238 -25.378 -23.567 1 90.43 ? C5' ADP 600 G 1 HETATM 11 C C4' ADP . . . U 2 126.762 -25.04 -22.174 1 80.21 ? C4' ADP 600 G 1 HETATM 12 O O4' ADP . . . U 2 127.776 -25.965 -21.767 1 79.37 ? O4' ADP 600 G 1 HETATM 13 C C3' ADP . . . U 2 127.38 -23.649 -22.108 1 73.51 ? C3' ADP 600 G 1 HETATM 14 O O3' ADP . . . U 2 126.542 -22.769 -21.351 1 69.41 ? O3' ADP 600 G 1 HETATM 15 C C2' ADP . . . U 2 128.715 -23.821 -21.408 1 72.8 ? C2' ADP 600 G 1 HETATM 16 O O2' ADP . . . U 2 128.788 -22.966 -20.263 1 77.63 ? O2' ADP 600 G 1 HETATM 17 C C1' ADP . . . U 2 128.755 -25.28 -20.981 1 82.39 ? C1' ADP 600 G 1 HETATM 18 N N9 ADP . . . U 2 130.106 -25.871 -21.166 1 92.48 ? N9 ADP 600 G 1 HETATM 19 C C8 ADP . . . U 2 130.657 -26.272 -22.327 1 100.67 ? C8 ADP 600 G 1 HETATM 20 N N7 ADP . . . U 2 131.91 -26.76 -22.128 1 104.36 ? N7 ADP 600 G 1 HETATM 21 C C5 ADP . . . U 2 132.179 -26.671 -20.812 1 102.17 ? C5 ADP 600 G 1 HETATM 22 C C6 ADP . . . U 2 133.317 -27.007 -19.923 1 120.51 ? C6 ADP 600 G 1 HETATM 23 N N6 ADP . . . U 2 134.453 -27.552 -20.419 1 132.16 ? N6 ADP 600 G 1 HETATM 24 N N1 ADP . . . U 2 133.187 -26.753 -18.602 1 131.81 ? N1 ADP 600 G 1 HETATM 25 C C2 ADP . . . U 2 132.063 -26.212 -18.097 1 141.01 ? C2 ADP 600 G 1 HETATM 26 N N3 ADP . . . U 2 130.994 -25.884 -18.844 1 129.06 ? N3 ADP 600 G 1 HETATM 27 C C4 ADP . . . U 2 130.989 -26.08 -20.184 1 108.35 ? C4 ADP 600 G 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #