data_4D81 # _model_server_result.job_id QALKw3vCjUnKKrtJuNtK6A _model_server_result.datetime_utc '2024-11-15 09:25:11' _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 4d81 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1364}' # _entry.id 4D81 # _exptl.entry_id 4D81 _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 4D81 _cell.length_a 65.269 _cell.length_b 65.269 _cell.length_c 112.521 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D81 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65' # _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 _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 # _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 4D81 _atom_sites.fract_transf_matrix[1][1] 0.015321 _atom_sites.fract_transf_matrix[1][2] 0.008846 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017691 _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] 0.008887 _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 1364 1364 ADP ADP . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 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 . . . B 2 -19.467 -19.675 1.402 1 41.92 ? PB ADP 1364 A 1 HETATM 2 O O1B ADP . . . B 2 -20.146 -18.749 0.434 1 43.61 ? O1B ADP 1364 A 1 HETATM 3 O O2B ADP . . . B 2 -17.96 -19.597 1.387 1 34.19 ? O2B ADP 1364 A 1 HETATM 4 O O3B ADP . . . B 2 -20.01 -19.683 2.817 1 38.88 ? O3B ADP 1364 A 1 HETATM 5 P PA ADP . . . B 2 -20.739 -21.412 -0.44 1 40.48 ? PA ADP 1364 A 1 HETATM 6 O O1A ADP . . . B 2 -19.911 -20.94 -1.591 1 40.21 ? O1A ADP 1364 A 1 HETATM 7 O O2A ADP . . . B 2 -22.187 -20.933 -0.393 1 41.33 ? O2A ADP 1364 A 1 HETATM 8 O O3A ADP . . . B 2 -19.882 -21.152 0.887 1 39.23 ? O3A ADP 1364 A 1 HETATM 9 O O5' ADP . . . B 2 -20.732 -23.02 -0.374 1 43.32 ? O5' ADP 1364 A 1 HETATM 10 C C5' ADP . . . B 2 -19.652 -23.765 -0.919 1 40.98 ? C5' ADP 1364 A 1 HETATM 11 C C4' ADP . . . B 2 -20.243 -25.071 -1.374 1 46.09 ? C4' ADP 1364 A 1 HETATM 12 O O4' ADP . . . B 2 -20.459 -25.84 -0.187 1 46.33 ? O4' ADP 1364 A 1 HETATM 13 C C3' ADP . . . B 2 -21.563 -25.044 -2.168 1 47.18 ? C3' ADP 1364 A 1 HETATM 14 O O3' ADP . . . B 2 -21.387 -25.284 -3.585 1 48.2 ? O3' ADP 1364 A 1 HETATM 15 C C2' ADP . . . B 2 -22.264 -26.249 -1.631 1 47.65 ? C2' ADP 1364 A 1 HETATM 16 O O2' ADP . . . B 2 -21.851 -27.365 -2.455 1 54.38 ? O2' ADP 1364 A 1 HETATM 17 C C1' ADP . . . B 2 -21.695 -26.523 -0.256 1 46.17 ? C1' ADP 1364 A 1 HETATM 18 N N9 ADP . . . B 2 -22.56 -26.117 0.874 1 42.97 ? N9 ADP 1364 A 1 HETATM 19 C C8 ADP . . . B 2 -22.254 -25.199 1.8 1 41.93 ? C8 ADP 1364 A 1 HETATM 20 N N7 ADP . . . B 2 -23.245 -25.112 2.715 1 39.41 ? N7 ADP 1364 A 1 HETATM 21 C C5 ADP . . . B 2 -24.166 -25.995 2.411 1 39.24 ? C5 ADP 1364 A 1 HETATM 22 C C6 ADP . . . B 2 -25.452 -26.39 2.982 1 42.5 ? C6 ADP 1364 A 1 HETATM 23 N N6 ADP . . . B 2 -25.91 -25.777 4.086 1 43.72 ? N6 ADP 1364 A 1 HETATM 24 N N1 ADP . . . B 2 -26.158 -27.333 2.338 1 42.22 ? N1 ADP 1364 A 1 HETATM 25 C C2 ADP . . . B 2 -25.695 -27.94 1.215 1 45.54 ? C2 ADP 1364 A 1 HETATM 26 N N3 ADP . . . B 2 -24.502 -27.656 0.666 1 43.04 ? N3 ADP 1364 A 1 HETATM 27 C C4 ADP . . . B 2 -23.712 -26.692 1.204 1 43.75 ? C4 ADP 1364 A 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 979 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #