data_3KO4 # _model_server_result.job_id YXZ7Db5gfTA0qQ5_4s-qsw _model_server_result.datetime_utc '2024-11-24 04:58:02' _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 3ko4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":165}' # _entry.id 3KO4 # _exptl.entry_id 3KO4 _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 72.86 _cell.angle_beta 76.45 _cell.angle_gamma 88.32 _cell.entry_id 3KO4 _cell.length_a 51.174 _cell.length_b 53.005 _cell.length_c 90.432 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KO4 _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,J,K 1 1 C,D,H,I,L,M 2 1 E,F 3 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 ? 2 G N N ? 2 H N N ? 2 I N N # _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 3KO4 _atom_sites.fract_transf_matrix[1][1] 0.019541 _atom_sites.fract_transf_matrix[1][2] -0.000573 _atom_sites.fract_transf_matrix[1][3] -0.004752 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018874 _atom_sites.fract_transf_matrix[2][3] -0.005853 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011909 _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 G 2 ADP B 1 165 1 ADP ADP . H 2 ADP C 1 165 2 ADP ADP . I 2 ADP D 1 165 3 ADP ADP . J 3 HOH A 1 165 2 HOH HOH . K 3 HOH B 1 166 1 HOH HOH . K 3 HOH B 2 167 4 HOH HOH . K 3 HOH B 3 168 5 HOH HOH . K 3 HOH B 4 169 7 HOH HOH . K 3 HOH B 5 170 8 HOH HOH . K 3 HOH B 6 171 9 HOH HOH . L 3 HOH C 1 166 6 HOH HOH . M 3 HOH D 1 166 3 HOH HOH . M 3 HOH D 2 167 10 HOH HOH . # 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 2 2.343 -24.075 -0.618 0.6 65 ? PB ADP 165 B 1 HETATM 2 O O1B ADP . . . G 2 2.83 -22.864 0.153 0.6 64.48 ? O1B ADP 165 B 1 HETATM 3 O O2B ADP . . . G 2 1.326 -24.998 0.02 0.6 64.65 ? O2B ADP 165 B 1 HETATM 4 O O3B ADP . . . G 2 3.608 -24.984 -1.035 0.6 64.48 ? O3B ADP 165 B 1 HETATM 5 P PA ADP . . . G 2 2.634 -22.668 -3.056 0.6 63.72 ? PA ADP 165 B 1 HETATM 6 O O1A ADP . . . G 2 4.021 -23.264 -3.14 0.6 63.96 ? O1A ADP 165 B 1 HETATM 7 O O2A ADP . . . G 2 1.852 -22.489 -4.333 0.6 63.11 ? O2A ADP 165 B 1 HETATM 8 O O3A ADP . . . G 2 1.762 -23.575 -2.044 0.6 64.17 ? O3A ADP 165 B 1 HETATM 9 O O5' ADP . . . G 2 2.696 -21.228 -2.317 0.6 63.64 ? O5' ADP 165 B 1 HETATM 10 C C5' ADP . . . G 2 3.894 -20.461 -2.118 0.6 63.27 ? C5' ADP 165 B 1 HETATM 11 C C4' ADP . . . G 2 4.693 -20.25 -3.414 0.6 63.26 ? C4' ADP 165 B 1 HETATM 12 O O4' ADP . . . G 2 3.889 -20.425 -4.585 0.6 62.85 ? O4' ADP 165 B 1 HETATM 13 C C3' ADP . . . G 2 5.292 -18.861 -3.516 0.6 63.09 ? C3' ADP 165 B 1 HETATM 14 O O3' ADP . . . G 2 6.642 -18.988 -3.984 0.6 63.64 ? O3' ADP 165 B 1 HETATM 15 C C2' ADP . . . G 2 4.452 -18.117 -4.535 0.6 62.69 ? C2' ADP 165 B 1 HETATM 16 O O2' ADP . . . G 2 5.302 -17.44 -5.468 0.6 62.89 ? O2' ADP 165 B 1 HETATM 17 C C1' ADP . . . G 2 3.628 -19.183 -5.245 0.6 62.03 ? C1' ADP 165 B 1 HETATM 18 N N9 ADP . . . G 2 2.16 -18.913 -5.209 0.6 61.56 ? N9 ADP 165 B 1 HETATM 19 C C8 ADP . . . G 2 1.283 -19.453 -4.345 0.6 61.53 ? C8 ADP 165 B 1 HETATM 20 N N7 ADP . . . G 2 0.018 -19.028 -4.577 0.6 61.32 ? N7 ADP 165 B 1 HETATM 21 C C5 ADP . . . G 2 0.07 -18.191 -5.617 0.6 61.07 ? C5 ADP 165 B 1 HETATM 22 C C6 ADP . . . G 2 -0.91 -17.384 -6.373 0.6 61.58 ? C6 ADP 165 B 1 HETATM 23 N N6 ADP . . . G 2 -2.223 -17.402 -6.044 0.6 61.74 ? N6 ADP 165 B 1 HETATM 24 N N1 ADP . . . G 2 -0.45 -16.639 -7.405 0.6 61.68 ? N1 ADP 165 B 1 HETATM 25 C C2 ADP . . . G 2 0.855 -16.621 -7.742 0.6 61.54 ? C2 ADP 165 B 1 HETATM 26 N N3 ADP . . . G 2 1.798 -17.325 -7.088 0.6 61.48 ? N3 ADP 165 B 1 HETATM 27 C C4 ADP . . . G 2 1.477 -18.12 -6.037 0.6 61.22 ? C4 ADP 165 B 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #