data_4CDG # _model_server_result.job_id 4v1qUaB-O0NxT53acKHqsQ _model_server_result.datetime_utc '2024-10-28 02:27:44' _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 4cdg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1634}' # _entry.id 4CDG # _exptl.entry_id 4CDG _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 69.39 _cell.angle_beta 89.84 _cell.angle_gamma 77.07 _cell.entry_id 4CDG _cell.length_a 59.666 _cell.length_b 88.425 _cell.length_c 95.12 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CDG _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS dimeric 2 author_and_software_defined_assembly 1 PQS dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F 1 1 B,D,G,H 2 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 E N N ? 3 G 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 C SG CYS 44 C CYS 44 1_555 C SG CYS 117 C CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 D SG CYS 44 D CYS 44 1_555 D SG CYS 117 D CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A SG CYS 403 A CYS 1036 1_555 F ZN ZN . A ZN 1643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc2 A SG CYS 422 A CYS 1055 1_555 F ZN ZN . A ZN 1643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc3 A SG CYS 430 A CYS 1063 1_555 F ZN ZN . A ZN 1643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc4 A SG CYS 433 A CYS 1066 1_555 F ZN ZN . A ZN 1643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc5 B SG CYS 403 B CYS 1036 1_555 H ZN ZN . B ZN 1643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc6 B SG CYS 422 B CYS 1055 1_555 H ZN ZN . B ZN 1643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc7 B SG CYS 430 B CYS 1063 1_555 H ZN ZN . B ZN 1643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc8 B SG CYS 433 B CYS 1066 1_555 H ZN ZN . B ZN 1643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? # _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 4CDG _atom_sites.fract_transf_matrix[1][1] 0.01676 _atom_sites.fract_transf_matrix[1][2] -0.003848 _atom_sites.fract_transf_matrix[1][3] 0.001437 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011603 _atom_sites.fract_transf_matrix[2][3] -0.004485 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011271 _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 E 3 ADP A 1 1634 1634 ADP ADP . F 4 ZN A 1 1643 1643 ZN ZN . G 3 ADP B 1 1634 1634 ADP ADP . H 4 ZN B 1 1643 1643 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 . . . E 3 9.765 128.595 -42.977 1 51.06 ? PB ADP 1634 A 1 HETATM 2 O O1B ADP . . . E 3 8.862 129.804 -42.93 1 44.63 ? O1B ADP 1634 A 1 HETATM 3 O O2B ADP . . . E 3 9.619 127.663 -41.799 1 52.72 ? O2B ADP 1634 A 1 HETATM 4 O O3B ADP . . . E 3 9.83 127.905 -44.317 1 45.93 ? O3B ADP 1634 A 1 HETATM 5 P PA ADP . . . E 3 12.047 129.766 -44.072 1 37.79 ? PA ADP 1634 A 1 HETATM 6 O O1A ADP . . . E 3 11.105 130.684 -44.815 1 60.75 ? O1A ADP 1634 A 1 HETATM 7 O O2A ADP . . . E 3 12.714 128.612 -44.778 1 49.35 ? O2A ADP 1634 A 1 HETATM 8 O O3A ADP . . . E 3 11.248 129.189 -42.802 1 39.52 ? O3A ADP 1634 A 1 HETATM 9 O O5' ADP . . . E 3 13.182 130.646 -43.343 1 34.59 ? O5' ADP 1634 A 1 HETATM 10 C C5' ADP . . . E 3 13.053 132.062 -43.26 1 48.71 ? C5' ADP 1634 A 1 HETATM 11 C C4' ADP . . . E 3 14.418 132.734 -43.135 1 45.18 ? C4' ADP 1634 A 1 HETATM 12 O O4' ADP . . . E 3 15.262 132.092 -42.175 1 53.89 ? O4' ADP 1634 A 1 HETATM 13 C C3' ADP . . . E 3 15.169 132.748 -44.458 1 52.8 ? C3' ADP 1634 A 1 HETATM 14 O O3' ADP . . . E 3 15.236 134.095 -44.938 1 64.62 ? O3' ADP 1634 A 1 HETATM 15 C C2' ADP . . . E 3 16.56 132.234 -44.145 1 57.68 ? C2' ADP 1634 A 1 HETATM 16 O O2' ADP . . . E 3 17.543 133.15 -44.632 1 84.19 ? O2' ADP 1634 A 1 HETATM 17 C C1' ADP . . . E 3 16.616 132.149 -42.629 1 60.59 ? C1' ADP 1634 A 1 HETATM 18 N N9 ADP . . . E 3 17.353 130.937 -42.202 1 52.12 ? N9 ADP 1634 A 1 HETATM 19 C C8 ADP . . . E 3 16.926 129.666 -42.318 1 44.15 ? C8 ADP 1634 A 1 HETATM 20 N N7 ADP . . . E 3 17.846 128.797 -41.827 1 47.04 ? N7 ADP 1634 A 1 HETATM 21 C C5 ADP . . . E 3 18.891 129.523 -41.385 1 51.05 ? C5 ADP 1634 A 1 HETATM 22 C C6 ADP . . . E 3 20.203 129.247 -40.751 1 62.32 ? C6 ADP 1634 A 1 HETATM 23 N N6 ADP . . . E 3 20.601 127.981 -40.479 1 61.09 ? N6 ADP 1634 A 1 HETATM 24 N N1 ADP . . . E 3 20.995 130.302 -40.45 1 64.91 ? N1 ADP 1634 A 1 HETATM 25 C C2 ADP . . . E 3 20.621 131.568 -40.71 1 61.69 ? C2 ADP 1634 A 1 HETATM 26 N N3 ADP . . . E 3 19.449 131.89 -41.283 1 58.87 ? N3 ADP 1634 A 1 HETATM 27 C C4 ADP . . . E 3 18.56 130.932 -41.637 1 52.28 ? C4 ADP 1634 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #