data_5W74 # _model_server_result.job_id dx-Uh0yHgPy0ceI_Qo_iBA _model_server_result.datetime_utc '2024-10-18 20:32:22' _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":"S","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 . . . S 2 87.672 -0.268 -25.105 1 114.47 ? PB ADP 600 F 1 HETATM 2 O O1B ADP . . . S 2 87.262 -0.917 -26.405 1 129.87 ? O1B ADP 600 F 1 HETATM 3 O O2B ADP . . . S 2 87.193 -0.998 -23.876 1 98.24 -1 O2B ADP 600 F 1 HETATM 4 O O3B ADP . . . S 2 87.441 1.223 -25.041 1 107.88 ? O3B ADP 600 F 1 HETATM 5 P PA ADP . . . S 2 90.147 -0.987 -23.863 1 133.16 ? PA ADP 600 F 1 HETATM 6 O O1A ADP . . . S 2 91.498 -1.382 -24.411 1 131.07 -1 O1A ADP 600 F 1 HETATM 7 O O2A ADP . . . S 2 89.327 -2.041 -23.162 1 157.68 ? O2A ADP 600 F 1 HETATM 8 O O3A ADP . . . S 2 89.282 -0.409 -25.1 1 127.58 ? O3A ADP 600 F 1 HETATM 9 O O5' ADP . . . S 2 90.387 0.244 -22.844 1 114.6 ? O5' ADP 600 F 1 HETATM 10 C C5' ADP . . . S 2 89.442 1.292 -22.628 1 112.27 ? C5' ADP 600 F 1 HETATM 11 C C4' ADP . . . S 2 89.63 1.869 -21.23 1 102.05 ? C4' ADP 600 F 1 HETATM 12 O O4' ADP . . . S 2 91.017 1.914 -20.886 1 101.21 ? O4' ADP 600 F 1 HETATM 13 C C3' ADP . . . S 2 89.097 3.29 -21.109 1 95.35 ? C3' ADP 600 F 1 HETATM 14 O O3' ADP . . . S 2 87.909 3.305 -20.308 1 91.25 ? O3' ADP 600 F 1 HETATM 15 C C2' ADP . . . S 2 90.199 4.089 -20.439 1 94.64 ? C2' ADP 600 F 1 HETATM 16 O O2' ADP . . . S 2 89.719 4.715 -19.246 1 99.47 ? O2' ADP 600 F 1 HETATM 17 C C1' ADP . . . S 2 91.269 3.071 -20.086 1 104.23 ? C1' ADP 600 F 1 HETATM 18 N N9 ADP . . . S 2 92.621 3.625 -20.348 1 114.32 ? N9 ADP 600 F 1 HETATM 19 C C8 ADP . . . S 2 93.213 3.743 -21.551 1 122.51 ? C8 ADP 600 F 1 HETATM 20 N N7 ADP . . . S 2 94.449 4.294 -21.432 1 126.2 ? N7 ADP 600 F 1 HETATM 21 C C5 ADP . . . S 2 94.658 4.541 -20.126 1 124.01 ? C5 ADP 600 F 1 HETATM 22 C C6 ADP . . . S 2 95.752 5.115 -19.307 1 142.35 ? C6 ADP 600 F 1 HETATM 23 N N6 ADP . . . S 2 96.901 5.546 -19.883 1 154 ? N6 ADP 600 F 1 HETATM 24 N N1 ADP . . . S 2 95.567 5.194 -17.97 1 153.65 ? N1 ADP 600 F 1 HETATM 25 C C2 ADP . . . S 2 94.431 4.768 -17.389 1 162.85 ? C2 ADP 600 F 1 HETATM 26 N N3 ADP . . . S 2 93.4 4.238 -18.069 1 150.9 ? N3 ADP 600 F 1 HETATM 27 C C4 ADP . . . S 2 93.449 4.102 -19.416 1 130.19 ? C4 ADP 600 F 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #