data_3EC2 # _model_server_result.job_id 8kRlNZYDlPjYapSBZ7kLAQ _model_server_result.datetime_utc '2024-12-01 18:45:40' _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 3ec2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":222}' # _entry.id 3EC2 # _exptl.entry_id 3EC2 _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 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 3EC2 _cell.length_a 84.492 _cell.length_b 84.492 _cell.length_c 51.113 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EC2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 covale ? covale1 A C LEU 85 A LEU 126 1_555 A N MSE 86 A MSE 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C MSE 86 A MSE 127 1_555 A N ASP 87 A ASP 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale3 A C GLU 172 A GLU 213 1_555 A N MSE 173 A MSE 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale4 A C MSE 173 A MSE 214 1_555 A N ASN 174 A ASN 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? # _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 3EC2 _atom_sites.fract_transf_matrix[1][1] 0.011835 _atom_sites.fract_transf_matrix[1][2] 0.006833 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013666 _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] 0.019564 _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 B 2 ADP A 1 222 222 ADP ADP . C 3 MG A 1 300 300 MG MG . D 4 HOH A 1 2 2 HOH WAT . D 4 HOH A 2 3 3 HOH WAT . D 4 HOH A 3 4 4 HOH WAT . D 4 HOH A 4 5 5 HOH WAT . D 4 HOH A 5 6 6 HOH WAT . D 4 HOH A 6 7 7 HOH WAT . D 4 HOH A 7 8 8 HOH WAT . D 4 HOH A 8 9 9 HOH WAT . D 4 HOH A 9 10 10 HOH WAT . D 4 HOH A 10 11 11 HOH WAT . D 4 HOH A 11 12 12 HOH WAT . D 4 HOH A 12 13 13 HOH WAT . D 4 HOH A 13 14 14 HOH WAT . D 4 HOH A 14 15 15 HOH WAT . D 4 HOH A 15 16 16 HOH WAT . D 4 HOH A 16 17 17 HOH WAT . D 4 HOH A 17 18 18 HOH WAT . D 4 HOH A 18 19 19 HOH WAT . D 4 HOH A 19 20 20 HOH WAT . D 4 HOH A 20 21 21 HOH WAT . D 4 HOH A 21 22 22 HOH WAT . D 4 HOH A 22 23 23 HOH WAT . D 4 HOH A 23 24 24 HOH WAT . D 4 HOH A 24 25 25 HOH WAT . D 4 HOH A 25 26 26 HOH WAT . D 4 HOH A 26 27 27 HOH WAT . D 4 HOH A 27 28 28 HOH WAT . D 4 HOH A 28 29 29 HOH WAT . D 4 HOH A 29 30 30 HOH WAT . D 4 HOH A 30 31 31 HOH WAT . D 4 HOH A 31 32 32 HOH WAT . D 4 HOH A 32 33 33 HOH WAT . D 4 HOH A 33 34 34 HOH WAT . D 4 HOH A 34 35 35 HOH WAT . D 4 HOH A 35 36 36 HOH WAT . D 4 HOH A 36 37 37 HOH WAT . D 4 HOH A 37 38 38 HOH WAT . D 4 HOH A 38 39 39 HOH WAT . D 4 HOH A 39 40 40 HOH WAT . D 4 HOH A 40 41 41 HOH WAT . D 4 HOH A 41 223 42 HOH WAT . D 4 HOH A 42 224 43 HOH WAT . D 4 HOH A 43 225 44 HOH WAT . D 4 HOH A 44 226 45 HOH WAT . D 4 HOH A 45 227 46 HOH WAT . D 4 HOH A 46 228 47 HOH WAT . D 4 HOH A 47 229 48 HOH WAT . # 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 . . . B 2 26.023 16.096 23.807 1 54.64 ? PB ADP 222 A 1 HETATM 2 O O1B ADP . . . B 2 25.607 16.207 25.261 1 53.04 ? O1B ADP 222 A 1 HETATM 3 O O2B ADP . . . B 2 25.618 17.22 22.87 1 52.85 ? O2B ADP 222 A 1 HETATM 4 O O3B ADP . . . B 2 25.675 14.68 23.389 1 56.09 ? O3B ADP 222 A 1 HETATM 5 P PA ADP . . . B 2 28.484 15.76 25.072 1 52.25 ? PA ADP 222 A 1 HETATM 6 O O1A ADP . . . B 2 28.436 16.867 26.084 1 52.98 ? O1A ADP 222 A 1 HETATM 7 O O2A ADP . . . B 2 27.967 14.472 25.68 1 51.49 ? O2A ADP 222 A 1 HETATM 8 O O3A ADP . . . B 2 27.63 16.207 23.772 1 50.98 ? O3A ADP 222 A 1 HETATM 9 O O5' ADP . . . B 2 29.943 15.589 24.466 1 53.4 ? O5' ADP 222 A 1 HETATM 10 C C5' ADP . . . B 2 30.454 14.338 24.064 1 56.63 ? C5' ADP 222 A 1 HETATM 11 C C4' ADP . . . B 2 31.891 14.264 24.517 1 59.35 ? C4' ADP 222 A 1 HETATM 12 O O4' ADP . . . B 2 32.661 15.232 23.817 1 62.75 ? O4' ADP 222 A 1 HETATM 13 C C3' ADP . . . B 2 31.997 14.606 25.977 1 62.57 ? C3' ADP 222 A 1 HETATM 14 O O3' ADP . . . B 2 32.845 13.631 26.566 1 62.57 ? O3' ADP 222 A 1 HETATM 15 C C2' ADP . . . B 2 32.622 15.995 26.03 1 64.78 ? C2' ADP 222 A 1 HETATM 16 O O2' ADP . . . B 2 33.508 16.063 27.118 1 67.65 ? O2' ADP 222 A 1 HETATM 17 C C1' ADP . . . B 2 33.341 16.126 24.711 1 65.73 ? C1' ADP 222 A 1 HETATM 18 N N9 ADP . . . B 2 33.313 17.492 24.141 1 69.31 ? N9 ADP 222 A 1 HETATM 19 C C8 ADP . . . B 2 32.439 17.951 23.224 1 70.89 ? C8 ADP 222 A 1 HETATM 20 N N7 ADP . . . B 2 32.717 19.232 22.853 1 73.18 ? N7 ADP 222 A 1 HETATM 21 C C5 ADP . . . B 2 33.815 19.61 23.517 1 75.12 ? C5 ADP 222 A 1 HETATM 22 C C6 ADP . . . B 2 34.655 20.853 23.59 1 77.34 ? C6 ADP 222 A 1 HETATM 23 N N6 ADP . . . B 2 34.36 21.998 22.864 1 78.91 ? N6 ADP 222 A 1 HETATM 24 N N1 ADP . . . B 2 35.717 20.807 24.427 1 77.57 ? N1 ADP 222 A 1 HETATM 25 C C2 ADP . . . B 2 36.02 19.702 25.153 1 78.02 ? C2 ADP 222 A 1 HETATM 26 N N3 ADP . . . B 2 35.305 18.554 25.13 1 77.41 ? N3 ADP 222 A 1 HETATM 27 C C4 ADP . . . B 2 34.208 18.451 24.359 1 73.98 ? C4 ADP 222 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #