data_3KFE # _model_server_result.job_id yoj8YIGYxUiAa5bjNwi64w _model_server_result.datetime_utc '2024-10-18 14:34:42' _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 3kfe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":545}' # _entry.id 3KFE # _exptl.entry_id 3KFE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 124.12 _cell.angle_gamma 90 _cell.entry_id 3KFE _cell.length_a 261.45 _cell.length_b 161.92 _cell.length_c 147.37 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KFE _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_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 _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 ? 3 J N N ? 3 M N N ? 3 P N N ? 3 S N N ? 3 V N N ? 3 Y N N ? 3 BA N N ? 3 EA 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 A SG CYS 448 A CYS 470 1_555 A SG CYS 462 A CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 B SG CYS 448 B CYS 470 1_555 B SG CYS 462 B CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf3 C SG CYS 448 C CYS 470 1_555 C SG CYS 462 C CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf4 D SG CYS 448 D CYS 470 1_555 D SG CYS 462 D CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 E SG CYS 448 E CYS 470 1_555 E SG CYS 462 E CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf6 F SG CYS 448 F CYS 470 1_555 F SG CYS 462 F CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf7 G SG CYS 448 G CYS 470 1_555 G SG CYS 462 G CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf8 H SG CYS 448 H CYS 470 1_555 H SG CYS 462 H CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc1 A OD1 ASP 91 A ASP 91 1_555 I MG MG . A MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc2 I MG MG . A MG 544 1_555 J O2A ADP . A ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc3 I MG MG . A MG 544 1_555 K O2 SO4 . A SO4 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc4 B OD1 ASP 91 B ASP 91 1_555 L MG MG . B MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc5 L MG MG . B MG 544 1_555 M O2A ADP . B ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc6 L MG MG . B MG 544 1_555 N O2 SO4 . B SO4 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc7 C OD1 ASP 91 C ASP 91 1_555 O MG MG . C MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc8 O MG MG . C MG 544 1_555 P O2A ADP . C ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? metalc ? metalc9 O MG MG . C MG 544 1_555 Q O2 SO4 . C SO4 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc10 D OD1 ASP 91 D ASP 91 1_555 R MG MG . D MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc11 R MG MG . D MG 544 1_555 S O2A ADP . D ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc12 R MG MG . D MG 544 1_555 T O2 SO4 . D SO4 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc13 E OD1 ASP 91 E ASP 91 1_555 U MG MG . E MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc14 U MG MG . E MG 544 1_555 V O2A ADP . E ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc15 U MG MG . E MG 544 1_555 W O2 SO4 . E SO4 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc16 F OD1 ASP 91 F ASP 91 1_555 X MG MG . F MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc17 X MG MG . F MG 544 1_555 Y O2A ADP . F ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc18 X MG MG . F MG 544 1_555 Z O2 SO4 . F SO4 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc19 G OD1 ASP 91 G ASP 91 1_555 AA MG MG . G MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc20 AA MG MG . G MG 544 1_555 BA O2A ADP . G ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc21 AA MG MG . G MG 544 1_555 CA O2 SO4 . G SO4 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc22 H OD1 ASP 91 H ASP 91 1_555 DA MG MG . H MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc23 DA MG MG . H MG 544 1_555 EA O2A ADP . H ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc24 DA MG MG . H MG 544 1_555 FA O2 SO4 . H SO4 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? # _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 ? # _atom_sites.entry_id 3KFE _atom_sites.fract_transf_matrix[1][1] 0.003825 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002592 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006176 _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] 0.008197 _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 MG A 1 544 544 MG MG . J 3 ADP A 1 545 545 ADP ADP . K 4 SO4 A 1 546 546 SO4 SO4 . L 2 MG B 1 544 544 MG MG . M 3 ADP B 1 545 545 ADP ADP . N 4 SO4 B 1 546 546 SO4 SO4 . O 2 MG C 1 544 544 MG MG . P 3 ADP C 1 545 545 ADP ADP . Q 4 SO4 C 1 546 546 SO4 SO4 . R 2 MG D 1 544 544 MG MG . S 3 ADP D 1 545 545 ADP ADP . T 4 SO4 D 1 546 546 SO4 SO4 . U 2 MG E 1 544 544 MG MG . V 3 ADP E 1 545 545 ADP ADP . W 4 SO4 E 1 546 546 SO4 SO4 . X 2 MG F 1 544 544 MG MG . Y 3 ADP F 1 545 545 ADP ADP . Z 4 SO4 F 1 546 546 SO4 SO4 . AA 2 MG G 1 544 544 MG MG . BA 3 ADP G 1 545 545 ADP ADP . CA 4 SO4 G 1 546 546 SO4 SO4 . DA 2 MG H 1 544 544 MG MG . EA 3 ADP H 1 545 545 ADP ADP . FA 4 SO4 H 1 546 546 SO4 SO4 . # 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 . . . M 3 9.311 51.138 82.111 1 57.71 ? PB ADP 545 B 1 HETATM 2 O O1B ADP . . . M 3 10.39 50.246 81.561 1 49.48 ? O1B ADP 545 B 1 HETATM 3 O O2B ADP . . . M 3 9.554 51.768 83.461 1 71.19 ? O2B ADP 545 B 1 HETATM 4 O O3B ADP . . . M 3 8.847 52.172 81.13 1 47.67 ? O3B ADP 545 B 1 HETATM 5 P PA ADP . . . M 3 8.443 48.587 82.765 1 65.02 ? PA ADP 545 B 1 HETATM 6 O O1A ADP . . . M 3 7.229 47.695 82.783 1 63.11 ? O1A ADP 545 B 1 HETATM 7 O O2A ADP . . . M 3 9.673 48.194 81.984 1 54.09 ? O2A ADP 545 B 1 HETATM 8 O O3A ADP . . . M 3 8.108 50.111 82.354 1 76.23 ? O3A ADP 545 B 1 HETATM 9 O O5' ADP . . . M 3 8.926 48.784 84.284 1 52.46 ? O5' ADP 545 B 1 HETATM 10 C C5' ADP . . . M 3 10.332 48.625 84.48 1 87.02 ? C5' ADP 545 B 1 HETATM 11 C C4' ADP . . . M 3 10.76 48.736 85.931 1 68.84 ? C4' ADP 545 B 1 HETATM 12 O O4' ADP . . . M 3 10.929 47.426 86.462 1 75.83 ? O4' ADP 545 B 1 HETATM 13 C C3' ADP . . . M 3 12.103 49.451 86.118 1 73.07 ? C3' ADP 545 B 1 HETATM 14 O O3' ADP . . . M 3 11.968 50.448 87.145 1 50.58 ? O3' ADP 545 B 1 HETATM 15 C C2' ADP . . . M 3 13.024 48.455 86.757 1 76.31 ? C2' ADP 545 B 1 HETATM 16 O O2' ADP . . . M 3 13.59 49.208 87.838 1 90.21 ? O2' ADP 545 B 1 HETATM 17 C C1' ADP . . . M 3 12.08 47.397 87.311 1 75.57 ? C1' ADP 545 B 1 HETATM 18 N N9 ADP . . . M 3 12.645 46.039 87.352 1 53.66 ? N9 ADP 545 B 1 HETATM 19 C C8 ADP . . . M 3 13.236 45.416 86.32 1 61.54 ? C8 ADP 545 B 1 HETATM 20 N N7 ADP . . . M 3 13.636 44.182 86.71 1 68.26 ? N7 ADP 545 B 1 HETATM 21 C C5 ADP . . . M 3 13.301 44.019 87.993 1 62.59 ? C5 ADP 545 B 1 HETATM 22 C C6 ADP . . . M 3 13.44 42.939 89 1 79.35 ? C6 ADP 545 B 1 HETATM 23 N N6 ADP . . . M 3 14.032 41.771 88.669 1 83.76 ? N6 ADP 545 B 1 HETATM 24 N N1 ADP . . . M 3 12.959 43.162 90.249 1 75.39 ? N1 ADP 545 B 1 HETATM 25 C C2 ADP . . . M 3 12.374 44.338 90.567 1 69.5 ? C2 ADP 545 B 1 HETATM 26 N N3 ADP . . . M 3 12.218 45.355 89.68 1 61.23 ? N3 ADP 545 B 1 HETATM 27 C C4 ADP . . . M 3 12.649 45.258 88.411 1 55.52 ? C4 ADP 545 B 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #