data_5E3H # _model_server_result.job_id 5EpVN7HcOyg-UorNnMQUfA _model_server_result.datetime_utc '2025-07-18 00:56:13' _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 5e3h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1006}' # _entry.id 5E3H # _exptl.entry_id 5E3H _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 1 _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 5E3H _cell.length_a 176.03 _cell.length_b 176.03 _cell.length_c 108.071 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5E3H _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 SG CYS 580 A CYS 810 1_555 D ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc2 A SG CYS 583 A CYS 813 1_555 D ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc3 A SG CYS 634 A CYS 864 1_555 D ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc4 A SG CYS 639 A CYS 869 1_555 D ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc5 F MG MG . A MG 1003 1_555 I O3B ADP . A ADP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? hydrog WATSON-CRICK hydrog1 B N3 C 1 B C 1 1_555 C N1 G 14 C G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 C 1 B C 1 1_555 C O6 G 14 C G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 C 1 B C 1 1_555 C N2 G 14 C G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 G 2 B G 2 1_555 C N3 C 13 C C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 G 2 B G 2 1_555 C O2 C 13 C C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 G 2 B G 2 1_555 C N4 C 13 C C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 A 3 B A 3 1_555 C N3 U 12 C U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N6 A 3 B A 3 1_555 C O4 U 12 C U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 C 4 B C 4 1_555 C N1 G 11 C G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 C 4 B C 4 1_555 C O6 G 11 C G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 C 4 B C 4 1_555 C N2 G 11 C G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 G 5 B G 5 1_555 C N3 C 10 C C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 G 5 B G 5 1_555 C O2 C 10 C C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 G 5 B G 5 1_555 C N4 C 10 C C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 C 6 B C 6 1_555 C N1 G 9 C G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N4 C 6 B C 6 1_555 C O6 G 9 C G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O2 C 6 B C 6 1_555 C N2 G 9 C G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 U 7 B U 7 1_555 C N1 A 8 C A 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O4 U 7 B U 7 1_555 C N6 A 8 C A 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 A 8 B A 8 1_555 C N3 U 7 C U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N6 A 8 B A 8 1_555 C O4 U 7 C U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 G 9 B G 9 1_555 C N3 C 6 C C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 G 9 B G 9 1_555 C O2 C 6 C C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 G 9 B G 9 1_555 C N4 C 6 C C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N3 C 10 B C 10 1_555 C N1 G 5 C G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N4 C 10 B C 10 1_555 C O6 G 5 C G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B O2 C 10 B C 10 1_555 C N2 G 5 C G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N1 G 11 B G 11 1_555 C N3 C 4 C C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N2 G 11 B G 11 1_555 C O2 C 4 C C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B O6 G 11 B G 11 1_555 C N4 C 4 C C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 40 n n PB O2B ADP sing 41 n n PB O3B ADP sing 42 n n PB O3A ADP sing 43 n n O2B HOB2 ADP sing 44 n n O3B HOB3 ADP sing 45 n n PA O1A ADP doub 46 n n PA O2A ADP sing 47 n n PA O3A ADP sing 48 n n PA O5' ADP sing 49 n n O2A HOA2 ADP sing 50 n n O5' C5' ADP sing 51 n n C5' C4' ADP sing 52 n n C5' "H5'1" ADP sing 53 n n C5' "H5'2" ADP sing 54 n n C4' O4' ADP sing 55 n n C4' C3' ADP sing 56 n n C4' H4' ADP sing 57 n n O4' C1' ADP sing 58 n n C3' O3' ADP sing 59 n n C3' C2' ADP sing 60 n n C3' H3' ADP sing 61 n n O3' HO3' ADP sing 62 n n C2' O2' ADP sing 63 n n C2' C1' ADP sing 64 n n C2' H2' ADP sing 65 n n O2' HO2' ADP sing 66 n n C1' N9 ADP sing 67 n n C1' H1' ADP sing 68 n n N9 C8 ADP sing 69 n y N9 C4 ADP sing 70 n y C8 N7 ADP doub 71 n y C8 H8 ADP sing 72 n n N7 C5 ADP sing 73 n y C5 C6 ADP sing 74 n y C5 C4 ADP doub 75 n y C6 N6 ADP sing 76 n n C6 N1 ADP doub 77 n y N6 HN61 ADP sing 78 n n N6 HN62 ADP sing 79 n n N1 C2 ADP sing 80 n y C2 N3 ADP doub 81 n y C2 H2 ADP sing 82 n n N3 C4 ADP sing 83 n y # _atom_sites.entry_id 5E3H _atom_sites.fract_transf_matrix[1][1] 0.005681 _atom_sites.fract_transf_matrix[1][2] 0.00328 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00656 _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] 0.009253 _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 D 3 ZN A 1 1001 1 ZN ZN . E 4 MG A 1 1002 3 MG MG . F 4 MG A 1 1003 7 MG MG . G 4 MG A 1 1004 8 MG MG . H 5 GOL A 1 1005 1 GOL GOL . I 6 ADP A 1 1006 1 ADP ADP . J 7 BEF A 1 1007 1 BEF BEF . # 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 . . . I 6 27.829 -77.34 6.562 1 98.46 ? PB ADP 1006 A 1 HETATM 2 O O1B ADP . . . I 6 28.041 -76.025 5.915 1 86.27 ? O1B ADP 1006 A 1 HETATM 3 O O2B ADP . . . I 6 27.883 -77.169 8.059 1 84.97 ? O2B ADP 1006 A 1 HETATM 4 O O3B ADP . . . I 6 26.524 -77.869 6.171 1 103.78 ? O3B ADP 1006 A 1 HETATM 5 P PA ADP . . . I 6 29.275 -78.773 4.591 1 81.78 ? PA ADP 1006 A 1 HETATM 6 O O1A ADP . . . I 6 28.428 -77.878 3.644 1 70.67 ? O1A ADP 1006 A 1 HETATM 7 O O2A ADP . . . I 6 28.925 -80.178 4.384 1 73.88 ? O2A ADP 1006 A 1 HETATM 8 O O3A ADP . . . I 6 28.989 -78.366 6.105 1 79.99 ? O3A ADP 1006 A 1 HETATM 9 O O5' ADP . . . I 6 30.744 -78.574 4.296 1 78.19 ? O5' ADP 1006 A 1 HETATM 10 C C5' ADP . . . I 6 31.147 -78.187 2.994 1 94.61 ? C5' ADP 1006 A 1 HETATM 11 C C4' ADP . . . I 6 32.497 -78.924 2.655 1 74.43 ? C4' ADP 1006 A 1 HETATM 12 O O4' ADP . . . I 6 32.946 -79.53 3.708 1 65.78 ? O4' ADP 1006 A 1 HETATM 13 C C3' ADP . . . I 6 32.27 -80.053 1.634 1 79.2 ? C3' ADP 1006 A 1 HETATM 14 O O3' ADP . . . I 6 32.582 -79.625 0.382 1 86.41 ? O3' ADP 1006 A 1 HETATM 15 C C2' ADP . . . I 6 33.226 -81.194 2.071 1 83.76 ? C2' ADP 1006 A 1 HETATM 16 O O2' ADP . . . I 6 34.229 -81.438 0.983 1 92.37 ? O2' ADP 1006 A 1 HETATM 17 C C1' ADP . . . I 6 33.826 -80.774 3.138 1 74.92 ? C1' ADP 1006 A 1 HETATM 18 N N9 ADP . . . I 6 33.892 -81.774 4.129 1 67.51 ? N9 ADP 1006 A 1 HETATM 19 C C8 ADP . . . I 6 32.912 -82.256 4.912 1 76.14 ? C8 ADP 1006 A 1 HETATM 20 N N7 ADP . . . I 6 33.451 -83.201 5.72 1 70.37 ? N7 ADP 1006 A 1 HETATM 21 C C5 ADP . . . I 6 34.778 -83.292 5.43 1 74.55 ? C5 ADP 1006 A 1 HETATM 22 C C6 ADP . . . I 6 35.811 -84.099 5.956 1 78.45 ? C6 ADP 1006 A 1 HETATM 23 N N6 ADP . . . I 6 35.784 -85.085 6.971 1 65.78 ? N6 ADP 1006 A 1 HETATM 24 N N1 ADP . . . I 6 37.067 -83.982 5.472 1 77.6 ? N1 ADP 1006 A 1 HETATM 25 C C2 ADP . . . I 6 37.334 -83.091 4.483 1 83.83 ? C2 ADP 1006 A 1 HETATM 26 N N3 ADP . . . I 6 36.326 -82.305 3.972 1 89.77 ? N3 ADP 1006 A 1 HETATM 27 C C4 ADP . . . I 6 35.054 -82.42 4.459 1 74.66 ? C4 ADP 1006 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #