data_1PF9 # _model_server_result.job_id EnSVUPSTLvENH-1bQIMAYg _model_server_result.datetime_utc '2024-12-26 03:20:35' _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 1pf9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":701}' # _entry.id 1PF9 # _exptl.entry_id 1PF9 _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 7 _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 1PF9 _cell.length_a 255.26 _cell.length_b 265.25 _cell.length_c 184.4 _cell.Z_PDB 56 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PF9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 21-meric _pdbx_struct_assembly.oligomeric_count 21 _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,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 W N N ? 4 Y N N ? 4 AA N N ? 4 CA N N ? 4 EA N N ? 4 GA N N ? 4 IA 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 A OD1 ASP 86 A ASP 87 1_555 V MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc2 V MG MG . A MG 601 1_555 W O1B ADP . A ADP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc3 V MG MG . A MG 601 1_555 W O2A ADP . A ADP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? metalc ? metalc4 B OD1 ASP 86 B ASP 87 1_555 X MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc5 X MG MG . B MG 602 1_555 Y O1B ADP . B ADP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc6 X MG MG . B MG 602 1_555 Y O2A ADP . B ADP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc7 C OD1 ASP 86 C ASP 87 1_555 Z MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc8 Z MG MG . C MG 603 1_555 AA O2A ADP . C ADP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc9 Z MG MG . C MG 603 1_555 AA O1B ADP . C ADP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc10 D OD1 ASP 86 D ASP 87 1_555 BA MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc11 BA MG MG . D MG 604 1_555 CA O1B ADP . D ADP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc12 BA MG MG . D MG 604 1_555 CA O2A ADP . D ADP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.801 ? metalc ? metalc13 E OD1 ASP 86 E ASP 87 1_555 DA MG MG . E MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc14 DA MG MG . E MG 605 1_555 EA O2A ADP . E ADP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc15 DA MG MG . E MG 605 1_555 EA O1B ADP . E ADP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc16 F OD1 ASP 86 F ASP 87 1_555 FA MG MG . F MG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc17 FA MG MG . F MG 606 1_555 GA O1B ADP . F ADP 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc18 FA MG MG . F MG 606 1_555 GA O2A ADP . F ADP 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.675 ? metalc ? metalc19 G OD1 ASP 86 G ASP 87 1_555 HA MG MG . G MG 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc20 HA MG MG . G MG 607 1_555 IA O2A ADP . G ADP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.841 ? metalc ? metalc21 HA MG MG . G MG 607 1_555 IA O1B ADP . G ADP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? # _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 1PF9 _atom_sites.fract_transf_matrix[1][1] 0.003918 _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] 0.00377 _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] 0.005423 _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 V 3 MG A 1 601 601 MG MG . W 4 ADP A 1 700 700 ADP ADP . X 3 MG B 1 602 602 MG MG . Y 4 ADP B 1 701 701 ADP ADP . Z 3 MG C 1 603 603 MG MG . AA 4 ADP C 1 702 702 ADP ADP . BA 3 MG D 1 604 604 MG MG . CA 4 ADP D 1 703 703 ADP ADP . DA 3 MG E 1 605 605 MG MG . EA 4 ADP E 1 704 704 ADP ADP . FA 3 MG F 1 606 606 MG MG . GA 4 ADP F 1 705 705 ADP ADP . HA 3 MG G 1 607 607 MG MG . IA 4 ADP G 1 706 706 ADP ADP . JA 5 HOH A 1 800 800 HOH HOH . KA 5 HOH B 1 801 801 HOH HOH . LA 5 HOH C 1 802 802 HOH HOH . MA 5 HOH D 1 803 803 HOH HOH . NA 5 HOH E 1 804 804 HOH HOH . OA 5 HOH F 1 805 805 HOH HOH . PA 5 HOH G 1 806 806 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 . . . Y 4 43.962 -83.649 -18.272 1 10.42 ? PB ADP 701 B 1 HETATM 2 O O1B ADP . . . Y 4 43.131 -84.06 -19.422 1 8 ? O1B ADP 701 B 1 HETATM 3 O O2B ADP . . . Y 4 44.928 -84.709 -17.715 1 7.64 ? O2B ADP 701 B 1 HETATM 4 O O3B ADP . . . Y 4 44.731 -82.362 -18.678 1 10.21 ? O3B ADP 701 B 1 HETATM 5 P PA ADP . . . Y 4 41.646 -82.705 -17.202 1 8.28 ? PA ADP 701 B 1 HETATM 6 O O1A ADP . . . Y 4 41.399 -81.844 -16.012 1 6.4 ? O1A ADP 701 B 1 HETATM 7 O O2A ADP . . . Y 4 41.644 -82.013 -18.579 1 7.7 ? O2A ADP 701 B 1 HETATM 8 O O3A ADP . . . Y 4 43.025 -83.443 -16.987 1 8.76 ? O3A ADP 701 B 1 HETATM 9 O O5' ADP . . . Y 4 40.684 -83.978 -17.228 1 8.01 ? O5' ADP 701 B 1 HETATM 10 C C5' ADP . . . Y 4 40.409 -84.426 -15.933 1 8.26 ? C5' ADP 701 B 1 HETATM 11 C C4' ADP . . . Y 4 39.885 -85.842 -15.728 1 8.16 ? C4' ADP 701 B 1 HETATM 12 O O4' ADP . . . Y 4 38.713 -85.687 -14.978 1 9.51 ? O4' ADP 701 B 1 HETATM 13 C C3' ADP . . . Y 4 39.495 -86.651 -16.923 1 9.1 ? C3' ADP 701 B 1 HETATM 14 O O3' ADP . . . Y 4 40.4 -87.7 -16.79 1 9.07 ? O3' ADP 701 B 1 HETATM 15 C C2' ADP . . . Y 4 38.107 -87.2 -16.648 1 9.07 ? C2' ADP 701 B 1 HETATM 16 O O2' ADP . . . Y 4 38.206 -88.586 -16.431 1 9.26 ? O2' ADP 701 B 1 HETATM 17 C C1' ADP . . . Y 4 37.767 -86.646 -15.3 1 8.52 ? C1' ADP 701 B 1 HETATM 18 N N9 ADP . . . Y 4 36.448 -86.064 -15.214 1 7.42 ? N9 ADP 701 B 1 HETATM 19 C C8 ADP . . . Y 4 35.816 -85.238 -16.082 1 7.41 ? C8 ADP 701 B 1 HETATM 20 N N7 ADP . . . Y 4 34.593 -84.991 -15.536 1 8.65 ? N7 ADP 701 B 1 HETATM 21 C C5 ADP . . . Y 4 34.444 -85.65 -14.342 1 8.36 ? C5 ADP 701 B 1 HETATM 22 C C6 ADP . . . Y 4 33.415 -85.764 -13.362 1 8.49 ? C6 ADP 701 B 1 HETATM 23 N N6 ADP . . . Y 4 32.164 -85.352 -13.571 1 8.11 ? N6 ADP 701 B 1 HETATM 24 N N1 ADP . . . Y 4 33.627 -86.548 -12.232 1 8.43 ? N1 ADP 701 B 1 HETATM 25 C C2 ADP . . . Y 4 34.842 -87.207 -12.06 1 7.58 ? C2 ADP 701 B 1 HETATM 26 N N3 ADP . . . Y 4 35.838 -87.088 -13.013 1 7.38 ? N3 ADP 701 B 1 HETATM 27 C C4 ADP . . . Y 4 35.644 -86.323 -14.131 1 7.91 ? C4 ADP 701 B 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 105 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #