data_7ZBH # _model_server_result.job_id Xvj1tacYMmkUedZQA_cClA _model_server_result.datetime_utc '2024-12-26 23:53:15' _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 7zbh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":701}' # _entry.id 7ZBH # _exptl.entry_id 7ZBH _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 124.31 _cell.angle_gamma 90 _cell.entry_id 7ZBH _cell.length_a 153.81 _cell.length_b 192.8 _cell.length_c 114.13 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZBH _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 ? 2 G N N ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q 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 349 A ASP 510 1_555 H ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc2 B NE2 HIS 273 B HIS 434 1_555 J ZN ZN . B ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc3 B NE2 HIS 277 B HIS 438 1_555 J ZN ZN . B ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.73 ? metalc ? metalc4 B OD2 ASP 349 B ASP 510 1_555 J ZN ZN . B ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 ? metalc ? metalc5 C NE2 HIS 273 D HIS 434 1_555 L ZN ZN . D ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc6 C NE2 HIS 277 D HIS 438 1_555 L ZN ZN . D ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? metalc ? metalc7 C OD2 ASP 349 D ASP 510 1_555 L ZN ZN . D ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc8 D NE2 HIS 273 F HIS 434 1_555 N ZN ZN . F ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc9 D OD2 ASP 349 F ASP 510 1_555 N ZN ZN . F ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc10 E NE2 HIS 273 I HIS 434 1_555 P ZN ZN . I ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? metalc ? metalc11 E NE2 HIS 277 I HIS 438 1_555 P ZN ZN . I ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc12 E OD2 ASP 349 I ASP 510 1_555 P ZN ZN . I ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc13 F NE2 HIS 273 K HIS 434 1_555 R ZN ZN . K ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc14 F OD2 ASP 349 K ASP 510 1_555 R ZN ZN . K ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? # _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 7ZBH _atom_sites.fract_transf_matrix[1][1] 0.006502 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004437 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005187 _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] 0.010608 _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 2 ADP A 1 701 610 ADP ADP . H 3 ZN A 1 702 171 ZN ZN . I 2 ADP B 1 701 610 ADP ADP . J 3 ZN B 1 702 171 ZN ZN . K 2 ADP D 1 701 610 ADP ADP . L 3 ZN D 1 702 171 ZN ZN . M 2 ADP F 1 701 610 ADP ADP . N 3 ZN F 1 702 171 ZN ZN . O 2 ADP I 1 701 610 ADP ADP . P 3 ZN I 1 702 171 ZN ZN . Q 2 ADP K 1 701 610 ADP ADP . R 3 ZN K 1 702 171 ZN ZN . # 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 2 -8.614 8.007 37.956 0 156.15 ? PB ADP 701 I 1 HETATM 2 O O1B ADP . . . O 2 -8.568 9.202 37.031 0 168.26 ? O1B ADP 701 I 1 HETATM 3 O O2B ADP . . . O 2 -7.673 8.094 39.111 0 171.12 ? O2B ADP 701 I 1 HETATM 4 O O3B ADP . . . O 2 -8.466 6.702 37.228 0 159.18 ? O3B ADP 701 I 1 HETATM 5 P PA ADP . . . O 2 -11.331 7.209 38.03 0 132.99 ? PA ADP 701 I 1 HETATM 6 O O1A ADP . . . O 2 -11.15 6.916 36.582 0 163.24 ? O1A ADP 701 I 1 HETATM 7 O O2A ADP . . . O 2 -12.639 7.836 38.335 0 118.12 ? O2A ADP 701 I 1 HETATM 8 O O3A ADP . . . O 2 -10.088 8.05 38.593 0 98.72 ? O3A ADP 701 I 1 HETATM 9 O O5' ADP . . . O 2 -11.208 5.869 38.886 0 133.09 ? O5' ADP 701 I 1 HETATM 10 C C5' ADP . . . O 2 -12.105 4.843 38.427 0 127.25 ? C5' ADP 701 I 1 HETATM 11 C C4' ADP . . . O 2 -12.169 3.736 39.444 0 133.63 ? C4' ADP 701 I 1 HETATM 12 O O4' ADP . . . O 2 -12.343 4.304 40.765 0 162.47 ? O4' ADP 701 I 1 HETATM 13 C C3' ADP . . . O 2 -13.319 2.737 39.246 0 134.69 ? C3' ADP 701 I 1 HETATM 14 O O3' ADP . . . O 2 -12.896 1.381 39.26 0 135.65 ? O3' ADP 701 I 1 HETATM 15 C C2' ADP . . . O 2 -14.298 3.052 40.378 0 128.7 ? C2' ADP 701 I 1 HETATM 16 O O2' ADP . . . O 2 -14.918 1.89 40.884 0 114.95 ? O2' ADP 701 I 1 HETATM 17 C C1' ADP . . . O 2 -13.377 3.627 41.439 0 144.22 ? C1' ADP 701 I 1 HETATM 18 N N9 ADP . . . O 2 -14.015 4.587 42.328 0 152.46 ? N9 ADP 701 I 1 HETATM 19 C C8 ADP . . . O 2 -14.299 5.89 42.073 0 161.88 ? C8 ADP 701 I 1 HETATM 20 N N7 ADP . . . O 2 -14.802 6.545 43.093 0 147.67 ? N7 ADP 701 I 1 HETATM 21 C C5 ADP . . . O 2 -14.934 5.583 44.057 0 131.97 ? C5 ADP 701 I 1 HETATM 22 C C6 ADP . . . O 2 -15.457 5.622 45.375 0 113.77 ? C6 ADP 701 I 1 HETATM 23 N N6 ADP . . . O 2 -15.941 6.719 45.954 0 105.34 ? N6 ADP 701 I 1 HETATM 24 N N1 ADP . . . O 2 -15.435 4.469 46.055 0 123.77 ? N1 ADP 701 I 1 HETATM 25 C C2 ADP . . . O 2 -14.94 3.375 45.472 0 138.87 ? C2 ADP 701 I 1 HETATM 26 N N3 ADP . . . O 2 -14.423 3.211 44.265 0 144.51 ? N3 ADP 701 I 1 HETATM 27 C C4 ADP . . . O 2 -14.45 4.358 43.614 0 140.97 ? C4 ADP 701 I 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #