data_5OCH # _model_server_result.job_id 2_dwnZHO6Tq3CpP825C2sg _model_server_result.datetime_utc '2025-03-06 09:25:22' _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 5och # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":1001}' # _entry.id 5OCH # _exptl.entry_id 5OCH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _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 90.5 _cell.angle_gamma 90 _cell.entry_id 5OCH _cell.length_a 181.08 _cell.length_b 98.5 _cell.length_c 214.87 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OCH _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,K,L,M,N 1 1 C,D,O,P,Q,R,S 2 1 E,F,T,U,V,W,X,Y 3 1 G,H,Z,AA,BA,CA,DA,EA 4 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 ? 6 I N N ? 6 L N N ? 6 O N N ? 6 Q N N ? 6 T N N ? 6 W N N ? 6 Z N N ? 6 CA 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 covale ? covale1 A C PRO 373 A PRO 482 1_555 A N YCM 374 A YCM 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale2 A C YCM 374 A YCM 483 1_555 A N ARG 375 A ARG 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? covale ? covale3 B C GLY 351 B GLY 460 1_555 B N YCM 352 B YCM 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? covale ? covale4 B C YCM 352 B YCM 461 1_555 B N CYS 353 B CYS 462 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale5 B C PRO 373 B PRO 482 1_555 B N YCM 374 B YCM 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale6 B C YCM 374 B YCM 483 1_555 B N ARG 375 B ARG 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale7 C C PRO 373 C PRO 482 1_555 C N YCM 374 C YCM 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? covale ? covale8 C C YCM 374 C YCM 483 1_555 C N ARG 375 C ARG 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale9 D C PRO 373 D PRO 482 1_555 D N YCM 374 D YCM 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale10 D C YCM 374 D YCM 483 1_555 D N ARG 375 D ARG 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale11 E C ARG 256 E ARG 365 1_555 E N YCM 257 E YCM 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale12 E C YCM 257 E YCM 366 1_555 E N ARG 258 E ARG 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? covale ? covale13 E C PRO 373 E PRO 482 1_555 E N YCM 374 E YCM 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale14 E C YCM 374 E YCM 483 1_555 E N ARG 375 E ARG 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? covale ? covale15 F C VAL 368 F VAL 477 1_555 F N YCM 369 F YCM 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale16 F C YCM 369 F YCM 478 1_555 F N PHE 370 F PHE 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 F C PRO 373 F PRO 482 1_555 F N YCM 374 F YCM 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale18 F C YCM 374 F YCM 483 1_555 F N ARG 375 F ARG 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale19 G C VAL 368 G VAL 477 1_555 G N YCM 369 G YCM 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale20 G C YCM 369 G YCM 478 1_555 G N PHE 370 G PHE 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale21 G C PRO 373 G PRO 482 1_555 G N YCM 374 G YCM 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale22 G C YCM 374 G YCM 483 1_555 G N ARG 375 G ARG 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? metalc ? metalc1 A OG1 THR 405 A THR 514 1_555 J MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc2 I O3B ADP . A ADP 1001 1_555 J MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc3 B OG1 THR 405 B THR 514 1_555 M MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc4 L O3B ADP . B ADP 1001 1_555 M MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc5 C OG1 THR 405 C THR 514 1_555 P MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc6 O O3B ADP . C ADP 1001 1_555 P MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc7 D OG1 THR 405 D THR 514 1_555 R MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc8 Q O3B ADP . D ADP 1001 1_555 R MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc9 E OG1 THR 405 E THR 514 1_555 U MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc10 T O1B ADP . E ADP 1001 1_555 U MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc11 F OG1 THR 405 F THR 514 1_555 X MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc12 W O1B ADP . F ADP 1001 1_555 X MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc13 G OG1 THR 405 G THR 514 1_555 AA MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc14 Z O3B ADP . G ADP 1001 1_555 AA MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc15 H OG1 THR 405 H THR 514 1_555 DA MG MG . H MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc16 CA O3B ADP . H ADP 1001 1_555 DA MG MG . H MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? # _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 5OCH _atom_sites.fract_transf_matrix[1][1] 0.005522 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000048 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010152 _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] 0.004654 _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 6 ADP A 1 1001 1001 ADP ADP . J 7 MG A 1 1002 1002 MG MG . K 8 Y01 A 1 1003 1003 Y01 Y01 . L 6 ADP B 1 1001 1001 ADP ADP . M 7 MG B 1 1002 1002 MG MG . N 8 Y01 B 1 1003 1003 Y01 Y01 . O 6 ADP C 1 1001 1001 ADP ADP . P 7 MG C 1 1002 1002 MG MG . Q 6 ADP D 1 1001 1001 ADP ADP . R 7 MG D 1 1002 1002 MG MG . S 8 Y01 D 1 1003 1003 Y01 Y01 . T 6 ADP E 1 1001 1001 ADP ADP . U 7 MG E 1 1002 1002 MG MG . V 8 Y01 E 1 1003 1003 Y01 Y01 . W 6 ADP F 1 1001 1001 ADP ADP . X 7 MG F 1 1002 1002 MG MG . Y 8 Y01 F 1 1003 1003 Y01 Y01 . Z 6 ADP G 1 1001 1001 ADP ADP . AA 7 MG G 1 1002 1002 MG MG . BA 8 Y01 G 1 1003 1003 Y01 Y01 . CA 6 ADP H 1 1001 1001 ADP ADP . DA 7 MG H 1 1002 1002 MG MG . EA 8 Y01 H 1 1003 1003 Y01 Y01 . # 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 . . . W 6 129.484 38.842 527.823 1 118.02 ? PB ADP 1001 F 1 HETATM 2 O O1B ADP . . . W 6 129.642 40.361 528.01 1 118.18 ? O1B ADP 1001 F 1 HETATM 3 O O2B ADP . . . W 6 130.776 38.18 528.317 1 119.39 ? O2B ADP 1001 F 1 HETATM 4 O O3B ADP . . . W 6 128.26 38.283 528.472 1 118.2 ? O3B ADP 1001 F 1 HETATM 5 P PA ADP . . . W 6 128.769 39.364 525.044 1 109.53 ? PA ADP 1001 F 1 HETATM 6 O O1A ADP . . . W 6 129.87 40.202 524.403 1 109.28 ? O1A ADP 1001 F 1 HETATM 7 O O2A ADP . . . W 6 127.602 40.142 525.495 1 108.41 ? O2A ADP 1001 F 1 HETATM 8 O O3A ADP . . . W 6 129.435 38.574 526.253 1 113.94 ? O3A ADP 1001 F 1 HETATM 9 O O5' ADP . . . W 6 128.375 38.242 523.976 1 108.91 ? O5' ADP 1001 F 1 HETATM 10 C C5' ADP . . . W 6 127.466 37.151 524.225 1 109.57 ? C5' ADP 1001 F 1 HETATM 11 C C4' ADP . . . W 6 127.456 36.213 523.041 1 111.03 ? C4' ADP 1001 F 1 HETATM 12 O O4' ADP . . . W 6 127.39 36.962 521.807 1 111.53 ? O4' ADP 1001 F 1 HETATM 13 C C3' ADP . . . W 6 128.643 35.257 522.912 1 111.83 ? C3' ADP 1001 F 1 HETATM 14 O O3' ADP . . . W 6 128.213 33.944 522.568 1 112.73 ? O3' ADP 1001 F 1 HETATM 15 C C2' ADP . . . W 6 129.506 35.915 521.83 1 111.27 ? C2' ADP 1001 F 1 HETATM 16 O O2' ADP . . . W 6 130.283 34.976 521.097 1 110.33 ? O2' ADP 1001 F 1 HETATM 17 C C1' ADP . . . W 6 128.45 36.587 520.948 1 112.45 ? C1' ADP 1001 F 1 HETATM 18 N N9 ADP . . . W 6 128.922 37.789 520.262 1 115.27 ? N9 ADP 1001 F 1 HETATM 19 C C8 ADP . . . W 6 129.304 38.969 520.845 1 116.89 ? C8 ADP 1001 F 1 HETATM 20 N N7 ADP . . . W 6 129.733 39.873 519.994 1 117.53 ? N7 ADP 1001 F 1 HETATM 21 C C5 ADP . . . W 6 129.625 39.24 518.764 1 116.85 ? C5 ADP 1001 F 1 HETATM 22 C C6 ADP . . . W 6 129.962 39.647 517.458 1 116.67 ? C6 ADP 1001 F 1 HETATM 23 N N6 ADP . . . W 6 130.526 40.823 517.173 1 117.14 ? N6 ADP 1001 F 1 HETATM 24 N N1 ADP . . . W 6 129.742 38.77 516.449 1 116.06 ? N1 ADP 1001 F 1 HETATM 25 C C2 ADP . . . W 6 129.229 37.568 516.74 1 115.76 ? C2 ADP 1001 F 1 HETATM 26 N N3 ADP . . . W 6 128.884 37.072 517.933 1 115.73 ? N3 ADP 1001 F 1 HETATM 27 C C4 ADP . . . W 6 129.114 37.959 518.913 1 116.06 ? C4 ADP 1001 F 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #