data_4CGZ # _model_server_result.job_id US4B1WAICewFyAqT76Y4QA _model_server_result.datetime_utc '2025-01-19 08:35:57' _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 4cgz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2292}' # _entry.id 4CGZ # _exptl.entry_id 4CGZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 90 _cell.entry_id 4CGZ _cell.length_a 149.53 _cell.length_b 149.53 _cell.length_c 64.06 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CGZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 77 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 42' # _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 _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 5 _struct_asym.id E _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 403 A CYS 1036 1_555 D ZN ZN . A ZN 2291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc2 A SG CYS 422 A CYS 1055 1_555 D ZN ZN . A ZN 2291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc3 A SG CYS 430 A CYS 1063 1_555 D ZN ZN . A ZN 2291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc4 A SG CYS 433 A CYS 1066 1_555 D ZN ZN . A ZN 2291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? hydrog WATSON-CRICK hydrog1 B N1 DA 1 B DA 1 1_555 C N3 DT 12 C DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 1 B DA 1 1_555 C O4 DT 12 C DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 2 B DG 2 1_555 C N3 DC 11 C DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 2 B DG 2 1_555 C O2 DC 11 C DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 2 B DG 2 1_555 C N4 DC 11 C DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 3 B DC 3 1_555 C N1 DG 10 C DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 3 B DC 3 1_555 C O6 DG 10 C DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 3 B DC 3 1_555 C N2 DG 10 C DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DG 4 B DG 4 1_555 C N3 DC 9 C DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N2 DG 4 B DG 4 1_555 C O2 DC 9 C DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O6 DG 4 B DG 4 1_555 C N4 DC 9 C DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DT 5 B DT 5 1_555 C N1 DA 8 C DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O4 DT 5 B DT 5 1_555 C N6 DA 8 C DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DC 6 B DC 6 1_555 C N1 DG 7 C DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 DC 6 B DC 6 1_555 C O6 DG 7 C DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 DC 6 B DC 6 1_555 C N2 DG 7 C DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 DG 7 B DG 7 1_555 C N3 DC 6 C DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N2 DG 7 B DG 7 1_555 C O2 DC 6 C DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O6 DG 7 B DG 7 1_555 C N4 DC 6 C DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 DA 8 B DA 8 1_555 C N3 DT 5 C DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N6 DA 8 B DA 8 1_555 C O4 DT 5 C DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 DG 9 B DG 9 1_555 C N3 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 DG 9 B DG 9 1_555 C O2 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 DG 9 B DG 9 1_555 C N4 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N1 DA 10 B DA 10 1_555 C N3 DT 3 C DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N6 DA 10 B DA 10 1_555 C O4 DT 3 C DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N3 DT 11 B DT 11 1_555 C N1 DA 2 C DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O4 DT 11 B DT 11 1_555 C N6 DA 2 C DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N3 DC 12 B DC 12 1_555 C N1 DG 1 C DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N4 DC 12 B DC 12 1_555 C O6 DG 1 C DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B O2 DC 12 B DC 12 1_555 C N2 DG 1 C DG 1 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 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 4CGZ _atom_sites.fract_transf_matrix[1][1] 0.006688 _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] 0.006688 _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] 0.01561 _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 4 ZN A 1 2291 2291 ZN ZN . E 5 ADP A 1 2292 2292 ADP ADP . # 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 . . . E 5 -15.892 44.77 -15.425 1 154.48 ? PB ADP 2292 A 1 HETATM 2 O O1B ADP . . . E 5 -15.708 44.376 -13.98 1 150.56 ? O1B ADP 2292 A 1 HETATM 3 O O2B ADP . . . E 5 -14.667 45.413 -16.03 1 146.31 ? O2B ADP 2292 A 1 HETATM 4 O O3B ADP . . . E 5 -16.538 43.714 -16.286 1 158.64 ? O3B ADP 2292 A 1 HETATM 5 P PA ADP . . . E 5 -18.547 45.664 -15.673 1 152.44 ? PA ADP 2292 A 1 HETATM 6 O O1A ADP . . . E 5 -18.995 44.547 -14.762 1 136.98 ? O1A ADP 2292 A 1 HETATM 7 O O2A ADP . . . E 5 -18.771 45.57 -17.164 1 163.73 ? O2A ADP 2292 A 1 HETATM 8 O O3A ADP . . . E 5 -16.982 45.956 -15.437 1 150.41 ? O3A ADP 2292 A 1 HETATM 9 O O5' ADP . . . E 5 -19.197 47.035 -15.146 1 150.38 ? O5' ADP 2292 A 1 HETATM 10 C C5' ADP . . . E 5 -19.791 47.046 -13.856 1 163.12 ? C5' ADP 2292 A 1 HETATM 11 C C4' ADP . . . E 5 -21.005 47.95 -13.873 1 162.63 ? C4' ADP 2292 A 1 HETATM 12 O O4' ADP . . . E 5 -20.743 49.06 -14.723 1 158.97 ? O4' ADP 2292 A 1 HETATM 13 C C3' ADP . . . E 5 -22.206 47.207 -14.429 1 162.44 ? C3' ADP 2292 A 1 HETATM 14 O O3' ADP . . . E 5 -23.198 47.07 -13.41 1 170.83 ? O3' ADP 2292 A 1 HETATM 15 C C2' ADP . . . E 5 -22.76 48.075 -15.533 1 170.39 ? C2' ADP 2292 A 1 HETATM 16 O O2' ADP . . . E 5 -24.114 48.42 -15.216 1 173.96 ? O2' ADP 2292 A 1 HETATM 17 C C1' ADP . . . E 5 -21.885 49.319 -15.543 1 170.56 ? C1' ADP 2292 A 1 HETATM 18 N N9 ADP . . . E 5 -21.43 49.669 -16.914 1 170.69 ? N9 ADP 2292 A 1 HETATM 19 C C8 ADP . . . E 5 -20.422 49.075 -17.581 1 171.95 ? C8 ADP 2292 A 1 HETATM 20 N N7 ADP . . . E 5 -20.248 49.631 -18.807 1 166.21 ? N7 ADP 2292 A 1 HETATM 21 C C5 ADP . . . E 5 -21.157 50.609 -18.928 1 162.62 ? C5 ADP 2292 A 1 HETATM 22 C C6 ADP . . . E 5 -21.516 51.589 -19.965 1 167.38 ? C6 ADP 2292 A 1 HETATM 23 N N6 ADP . . . E 5 -20.839 51.615 -21.134 1 167.66 ? N6 ADP 2292 A 1 HETATM 24 N N1 ADP . . . E 5 -22.531 52.441 -19.711 1 170.24 ? N1 ADP 2292 A 1 HETATM 25 C C2 ADP . . . E 5 -23.202 52.408 -18.55 1 167.37 ? C2 ADP 2292 A 1 HETATM 26 N N3 ADP . . . E 5 -22.928 51.542 -17.565 1 166.26 ? N3 ADP 2292 A 1 HETATM 27 C C4 ADP . . . E 5 -21.935 50.633 -17.688 1 164.13 ? C4 ADP 2292 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #