data_5EUL # _model_server_result.job_id 1RrwBHjj6-JF9VmVP5Qmhg _model_server_result.datetime_utc '2025-01-12 11:03:50' _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 5eul # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1003}' # _entry.id 5EUL # _exptl.entry_id 5EUL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 7 _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 5EUL _cell.length_a 127.798 _cell.length_b 127.798 _cell.length_c 554.772 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EUL _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,O,P,Q,R,S,T,U,V,W,X,Y _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 7 _struct_asym.id G _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 disulf ? disulf1 A SG CYS 775 A CYS 775 1_555 B SG CYS 60 Y CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf2 D SG CYS 22 V CYS 22 1_555 D SG CYS 95 V CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 E MG MG . A MG 1001 1_555 G O3B ADP . A ADP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc2 F BE BEF . A BEF 1002 1_555 G O1B ADP . A ADP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? # _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 5EUL _atom_sites.fract_transf_matrix[1][1] 0.007825 _atom_sites.fract_transf_matrix[1][2] 0.004518 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009035 _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] 0.001803 _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 5 MG A 1 1001 1001 MG MG . F 6 BEF A 1 1002 1002 BEF BEF . G 7 ADP A 1 1003 1003 ADP ADP . H 8 TBR A 1 1004 1 TBR TBR . I 8 TBR A 1 1005 2 TBR TBR . J 8 TBR A 1 1006 3 TBR TBR . K 8 TBR A 1 1007 4 TBR TBR . L 8 TBR A 1 1008 5 TBR TBR . M 8 TBR A 1 1009 6 TBR TBR . N 8 TBR A 1 1010 7 TBR TBR . O 8 TBR A 1 1011 8 TBR TBR . P 8 TBR A 1 1012 10 TBR TBR . Q 8 TBR A 1 1013 12 TBR TBR . R 8 TBR A 1 1014 13 TBR TBR . S 8 TBR A 1 1015 14 TBR TBR . T 8 TBR A 1 1016 16 TBR TBR . U 8 TBR A 1 1017 17 TBR TBR . V 8 TBR A 1 1018 18 TBR TBR . W 8 TBR Y 1 501 9 TBR TBR . X 8 TBR Y 1 502 11 TBR TBR . Y 8 TBR Y 1 503 15 TBR TBR . # 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 . . . G 7 5.254 20.546 -0.43 1 231.69 ? PB ADP 1003 A 1 HETATM 2 O O1B ADP . . . G 7 5.836 19.252 -0.95 1 258.23 ? O1B ADP 1003 A 1 HETATM 3 O O2B ADP . . . G 7 4.419 20.375 0.813 1 227.94 ? O2B ADP 1003 A 1 HETATM 4 O O3B ADP . . . G 7 6.234 21.695 -0.374 1 238.69 ? O3B ADP 1003 A 1 HETATM 5 P PA ADP . . . G 7 2.661 20.619 -1.657 1 237.85 ? PA ADP 1003 A 1 HETATM 6 O O1A ADP . . . G 7 2.121 21.343 -2.86 1 264.61 ? O1A ADP 1003 A 1 HETATM 7 O O2A ADP . . . G 7 1.986 20.829 -0.306 1 220.16 ? O2A ADP 1003 A 1 HETATM 8 O O3A ADP . . . G 7 4.221 21.023 -1.573 1 238 ? O3A ADP 1003 A 1 HETATM 9 O O5' ADP . . . G 7 2.64 19.059 -2.078 1 220.34 ? O5' ADP 1003 A 1 HETATM 10 C C5' ADP . . . G 7 2.567 18.731 -3.471 1 226.81 ? C5' ADP 1003 A 1 HETATM 11 C C4' ADP . . . G 7 2.2 17.269 -3.733 1 225.71 ? C4' ADP 1003 A 1 HETATM 12 O O4' ADP . . . G 7 1.139 16.851 -2.872 1 217.64 ? O4' ADP 1003 A 1 HETATM 13 C C3' ADP . . . G 7 1.728 17.055 -5.167 1 230.82 ? C3' ADP 1003 A 1 HETATM 14 O O3' ADP . . . G 7 2.516 16.039 -5.791 1 228.03 ? O3' ADP 1003 A 1 HETATM 15 C C2' ADP . . . G 7 0.292 16.578 -5.071 1 229.63 ? C2' ADP 1003 A 1 HETATM 16 O O2' ADP . . . G 7 0.065 15.461 -5.937 1 232.54 ? O2' ADP 1003 A 1 HETATM 17 C C1' ADP . . . G 7 0.116 16.184 -3.614 1 227.15 ? C1' ADP 1003 A 1 HETATM 18 N N9 ADP . . . G 7 -1.208 16.615 -3.106 1 229.54 ? N9 ADP 1003 A 1 HETATM 19 C C8 ADP . . . G 7 -1.735 17.847 -3.231 1 242.24 ? C8 ADP 1003 A 1 HETATM 20 N N7 ADP . . . G 7 -2.961 17.915 -2.653 1 241.52 ? N7 ADP 1003 A 1 HETATM 21 C C5 ADP . . . G 7 -3.235 16.7 -2.142 1 227.04 ? C5 ADP 1003 A 1 HETATM 22 C C6 ADP . . . G 7 -4.359 16.08 -1.401 1 225.52 ? C6 ADP 1003 A 1 HETATM 23 N N6 ADP . . . G 7 -5.467 16.791 -1.08 1 217.71 ? N6 ADP 1003 A 1 HETATM 24 N N1 ADP . . . G 7 -4.241 14.779 -1.054 1 232.89 ? N1 ADP 1003 A 1 HETATM 25 C C2 ADP . . . G 7 -3.147 14.059 -1.365 1 229.54 ? C2 ADP 1003 A 1 HETATM 26 N N3 ADP . . . G 7 -2.092 14.556 -2.035 1 222.27 ? N3 ADP 1003 A 1 HETATM 27 C C4 ADP . . . G 7 -2.077 15.846 -2.446 1 222.91 ? C4 ADP 1003 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #