data_4HQJ # _model_server_result.job_id d8aNyWz1xWBXC0qqw5fXMQ _model_server_result.datetime_utc '2024-11-23 22:37:51' _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 4hqj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1101}' # _entry.id 4HQJ # _exptl.entry_id 4HQJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 4HQJ _cell.length_a 109.073 _cell.length_b 219.578 _cell.length_c 261.958 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HQJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H,I,J,K,L,M,N 1 1 D,E,F,O,P,Q,R,S,T,U,V,W 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 O 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 disulf ? disulf1 B SG CYS 126 B CYS 126 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 B SG CYS 213 B CYS 213 1_555 B SG CYS 276 B CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 E SG CYS 126 D CYS 126 1_555 E SG CYS 149 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 E SG CYS 213 D CYS 213 1_555 E SG CYS 276 D CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A O VAL 327 A VAL 322 1_555 J NA NA . A NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc2 A O ALA 328 A ALA 323 1_555 J NA NA . A NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc3 A O VAL 330 A VAL 325 1_555 J NA NA . A NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc4 A OE2 GLU 332 A GLU 327 1_555 J NA NA . A NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc5 A OD2 ASP 374 A ASP 369 1_555 I MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc6 A O THR 376 A THR 371 1_555 I MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc7 A OD2 ASP 715 A ASP 710 1_555 I MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc8 A OG1 THR 779 A THR 774 1_555 L NA NA . A NA 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc9 A OG SER 780 A SER 775 1_555 K NA NA . A NA 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc10 A OD1 ASN 781 A ASN 776 1_555 K NA NA . A NA 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc11 A OE2 GLU 784 A GLU 779 1_555 K NA NA . A NA 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc12 A OD2 ASP 809 A ASP 804 1_555 J NA NA . A NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc13 A OD1 ASP 809 A ASP 804 1_555 J NA NA . A NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? metalc ? metalc14 A OD1 ASP 809 A ASP 804 1_555 K NA NA . A NA 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc15 A OE1 GLN 859 A GLN 854 1_555 L NA NA . A NA 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc16 A OE1 GLN 928 A GLN 923 1_555 L NA NA . A NA 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc17 A OD2 ASP 931 A ASP 926 1_555 L NA NA . A NA 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc18 D O VAL 327 C VAL 322 1_555 R NA NA . C NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc19 D O ALA 328 C ALA 323 1_555 R NA NA . C NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc20 D O ALA 328 C ALA 323 1_555 S NA NA . C NA 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.169 ? metalc ? metalc21 D O VAL 330 C VAL 325 1_555 R NA NA . C NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc22 D OE2 GLU 332 C GLU 327 1_555 R NA NA . C NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc23 D OD2 ASP 374 C ASP 369 1_555 Q MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc24 D O THR 376 C THR 371 1_555 Q MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc25 D OD2 ASP 715 C ASP 710 1_555 Q MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc26 D OG1 THR 779 C THR 774 1_555 T NA NA . C NA 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc27 D OG SER 780 C SER 775 1_555 S NA NA . C NA 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc28 D OD1 ASN 781 C ASN 776 1_555 S NA NA . C NA 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc29 D OE2 GLU 784 C GLU 779 1_555 S NA NA . C NA 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc30 D OD2 ASP 809 C ASP 804 1_555 R NA NA . C NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc31 D OD1 ASP 809 C ASP 804 1_555 R NA NA . C NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? metalc ? metalc32 D OD1 ASP 809 C ASP 804 1_555 S NA NA . C NA 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc33 D OE1 GLN 859 C GLN 854 1_555 T NA NA . C NA 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc34 D OE1 GLN 928 C GLN 923 1_555 T NA NA . C NA 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc35 D OD2 ASP 931 C ASP 926 1_555 T NA NA . C NA 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? # _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 4HQJ _atom_sites.fract_transf_matrix[1][1] 0.009168 _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] 0.004554 _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] 0.003817 _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 G 4 ADP A 1 1101 1017 ADP ADP . H 5 ALF A 1 1102 1018 ALF ALF . I 6 MG A 1 1103 1019 MG MG . J 7 NA A 1 1104 1021 NA NA . K 7 NA A 1 1105 1022 NA NA . L 7 NA A 1 1106 1023 NA NA . M 8 CLR A 1 1107 401 CLR CLR . N 8 CLR A 1 1108 402 CLR CLR . O 4 ADP C 1 1101 1017 ADP ADP . P 5 ALF C 1 1102 1018 ALF ALF . Q 6 MG C 1 1103 1019 MG MG . R 7 NA C 1 1104 1021 NA NA . S 7 NA C 1 1105 1022 NA NA . T 7 NA C 1 1106 1023 NA NA . U 8 CLR C 1 1107 401 CLR CLR . V 8 CLR C 1 1108 402 CLR CLR . W 8 CLR D 1 400 400 CLR CLR . # 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 . . . O 4 24.671 101.797 11.373 1 233.76 ? PB ADP 1101 C 1 HETATM 2 O O1B ADP . . . O 4 25.4 102.357 10.172 1 232.65 ? O1B ADP 1101 C 1 HETATM 3 O O2B ADP . . . O 4 23.163 101.897 11.256 1 228.59 ? O2B ADP 1101 C 1 HETATM 4 O O3B ADP . . . O 4 25.224 102.269 12.72 1 237.86 ? O3B ADP 1101 C 1 HETATM 5 P PA ADP . . . O 4 26.317 99.429 11.722 1 235.28 ? PA ADP 1101 C 1 HETATM 6 O O1A ADP . . . O 4 25.965 97.963 11.786 1 233.17 ? O1A ADP 1101 C 1 HETATM 7 O O2A ADP . . . O 4 26.972 100.07 12.921 1 237.68 ? O2A ADP 1101 C 1 HETATM 8 O O3A ADP . . . O 4 24.943 100.199 11.337 1 232.67 ? O3A ADP 1101 C 1 HETATM 9 O O5' ADP . . . O 4 27.3 99.614 10.459 1 233.36 ? O5' ADP 1101 C 1 HETATM 10 C C5' ADP . . . O 4 28.056 100.808 10.278 1 233.38 ? C5' ADP 1101 C 1 HETATM 11 C C4' ADP . . . O 4 28.881 100.689 9.007 1 227.6 ? C4' ADP 1101 C 1 HETATM 12 O O4' ADP . . . O 4 28.289 99.719 8.147 1 222.65 ? O4' ADP 1101 C 1 HETATM 13 C C3' ADP . . . O 4 28.932 102.002 8.245 1 225.41 ? C3' ADP 1101 C 1 HETATM 14 O O3' ADP . . . O 4 30.272 102.491 8.248 1 222.91 ? O3' ADP 1101 C 1 HETATM 15 C C2' ADP . . . O 4 28.527 101.688 6.823 1 218.01 ? C2' ADP 1101 C 1 HETATM 16 O O2' ADP . . . O 4 29.584 102.013 5.917 1 208.2 ? O2' ADP 1101 C 1 HETATM 17 C C1' ADP . . . O 4 28.277 100.194 6.806 1 215.12 ? C1' ADP 1101 C 1 HETATM 18 N N9 ADP . . . O 4 26.942 99.97 6.231 1 214.73 ? N9 ADP 1101 C 1 HETATM 19 C C8 ADP . . . O 4 25.764 100.392 6.723 1 220.47 ? C8 ADP 1101 C 1 HETATM 20 N N7 ADP . . . O 4 24.741 100.003 5.918 1 215.27 ? N7 ADP 1101 C 1 HETATM 21 C C5 ADP . . . O 4 25.277 99.323 4.888 1 206.15 ? C5 ADP 1101 C 1 HETATM 22 C C6 ADP . . . O 4 24.782 98.632 3.674 1 193.23 ? C6 ADP 1101 C 1 HETATM 23 N N6 ADP . . . O 4 23.464 98.577 3.367 1 192.84 ? N6 ADP 1101 C 1 HETATM 24 N N1 ADP . . . O 4 25.701 98.053 2.873 1 175.89 ? N1 ADP 1101 C 1 HETATM 25 C C2 ADP . . . O 4 27.022 98.089 3.147 1 170.91 ? C2 ADP 1101 C 1 HETATM 26 N N3 ADP . . . O 4 27.543 98.694 4.226 1 184.19 ? N3 ADP 1101 C 1 HETATM 27 C C4 ADP . . . O 4 26.73 99.314 5.106 1 202.96 ? C4 ADP 1101 C 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #