data_4R7Y # _model_server_result.job_id kbPZLEqydrwirFBCbP0DZQ _model_server_result.datetime_utc '2024-12-26 17:59:44' _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 4r7y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2001}' # _entry.id 4R7Y # _exptl.entry_id 4R7Y _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 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 120 _cell.entry_id 4R7Y _cell.length_a 118.902 _cell.length_b 118.902 _cell.length_c 199.317 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4R7Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -59.451 102.972153 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -118.902 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 C N N ? 2 I 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 ND1 HIS 145 A HIS 144 1_555 E ZN ZN . A ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc2 A SG CYS 150 A CYS 149 1_555 E ZN ZN . A ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc3 A SG CYS 172 A CYS 171 1_555 E ZN ZN . A ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc4 A SG CYS 175 A CYS 174 1_555 E ZN ZN . A ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc5 A OG SER 349 A SER 1335 1_555 D MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc6 C O3B ADP . A ADP 2001 1_555 D MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc7 B ND1 HIS 145 B HIS 144 1_555 K ZN ZN . B ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc8 B SG CYS 150 B CYS 149 1_555 K ZN ZN . B ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc9 B SG CYS 172 B CYS 171 1_555 K ZN ZN . B ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc10 B SG CYS 175 B CYS 174 1_555 K ZN ZN . B ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc11 B OG SER 349 B SER 1335 1_555 J MG MG . B MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc12 I O3B ADP . B ADP 2001 1_555 J MG MG . B MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? # _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 4R7Y _atom_sites.fract_transf_matrix[1][1] 0.00841 _atom_sites.fract_transf_matrix[1][2] 0.004856 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009711 _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] 0.005017 _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 C 2 ADP A 1 2001 1 ADP ADP . D 3 MG A 1 2002 1 MG MG . E 4 ZN A 1 2003 1 ZN ZN2 . F 5 CL A 1 2004 1 CL CL . G 5 CL A 1 2005 2 CL CL . H 5 CL A 1 2006 3 CL CL . I 2 ADP B 1 2001 2 ADP ADP . J 3 MG B 1 2002 2 MG MG . K 4 ZN B 1 2003 2 ZN ZN2 . L 5 CL B 1 2004 4 CL CL . M 5 CL B 1 2005 5 CL CL . N 5 CL B 1 2006 6 CL CL . # 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 . . . C 2 -43.508 6.126 -56.967 1 113.33 ? PB ADP 2001 A 1 HETATM 2 O O1B ADP . . . C 2 -44.093 7.226 -57.974 1 113.6 ? O1B ADP 2001 A 1 HETATM 3 O O2B ADP . . . C 2 -42.091 6.44 -56.701 1 113.28 ? O2B ADP 2001 A 1 HETATM 4 O O3B ADP . . . C 2 -44.346 6.151 -55.596 1 113.73 ? O3B ADP 2001 A 1 HETATM 5 P PA ADP . . . C 2 -43.053 3.526 -56.688 1 115.03 ? PA ADP 2001 A 1 HETATM 6 O O1A ADP . . . C 2 -41.647 3.808 -56.331 1 114.94 ? O1A ADP 2001 A 1 HETATM 7 O O2A ADP . . . C 2 -43.947 3.465 -55.34 1 114.1 ? O2A ADP 2001 A 1 HETATM 8 O O3A ADP . . . C 2 -43.633 4.674 -57.67 1 114.27 ? O3A ADP 2001 A 1 HETATM 9 O O5' ADP . . . C 2 -43.173 2.104 -57.455 1 115.22 ? O5' ADP 2001 A 1 HETATM 10 C C5' ADP . . . C 2 -42.607 1.094 -56.616 1 115.7 ? C5' ADP 2001 A 1 HETATM 11 C C4' ADP . . . C 2 -42.689 -0.261 -57.314 1 115.33 ? C4' ADP 2001 A 1 HETATM 12 O O4' ADP . . . C 2 -41.978 -0.203 -58.571 1 115.56 ? O4' ADP 2001 A 1 HETATM 13 C C3' ADP . . . C 2 -42.027 -1.348 -56.458 1 115.15 ? C3' ADP 2001 A 1 HETATM 14 O O3' ADP . . . C 2 -42.994 -2.141 -55.762 1 114.92 ? O3' ADP 2001 A 1 HETATM 15 C C2' ADP . . . C 2 -41.175 -2.168 -57.452 1 114.82 ? C2' ADP 2001 A 1 HETATM 16 O O2' ADP . . . C 2 -41.544 -3.546 -57.439 1 114.64 ? O2' ADP 2001 A 1 HETATM 17 C C1' ADP . . . C 2 -41.425 -1.517 -58.839 1 115.16 ? C1' ADP 2001 A 1 HETATM 18 N N9 ADP . . . C 2 -40.191 -1.335 -59.663 1 114.54 ? N9 ADP 2001 A 1 HETATM 19 C C8 ADP . . . C 2 -40.107 -0.543 -60.773 1 114.32 ? C8 ADP 2001 A 1 HETATM 20 N N7 ADP . . . C 2 -38.911 -0.588 -61.292 1 114.14 ? N7 ADP 2001 A 1 HETATM 21 C C5 ADP . . . C 2 -38.137 -1.403 -60.551 1 114.01 ? C5 ADP 2001 A 1 HETATM 22 C C6 ADP . . . C 2 -36.779 -1.851 -60.641 1 113.9 ? C6 ADP 2001 A 1 HETATM 23 N N6 ADP . . . C 2 -35.941 -1.397 -61.639 1 113.55 ? N6 ADP 2001 A 1 HETATM 24 N N1 ADP . . . C 2 -36.326 -2.706 -59.702 1 113.24 ? N1 ADP 2001 A 1 HETATM 25 C C2 ADP . . . C 2 -37.11 -3.166 -58.723 1 113.24 ? C2 ADP 2001 A 1 HETATM 26 N N3 ADP . . . C 2 -38.386 -2.777 -58.608 1 113.85 ? N3 ADP 2001 A 1 HETATM 27 C C4 ADP . . . C 2 -38.937 -1.932 -59.509 1 114.06 ? C4 ADP 2001 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #