data_5IFW # _model_server_result.job_id Y2QPVrFKtMNcsvLM_UyFVg _model_server_result.datetime_utc '2024-12-01 11:56:29' _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 5ifw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":902}' # _entry.id 5IFW # _exptl.entry_id 5IFW _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5IFW _cell.length_a 143.344 _cell.length_b 208.361 _cell.length_c 99.129 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IFW _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 99.129 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D 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 5IFW _atom_sites.fract_transf_matrix[1][1] 0.006976 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004799 _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] 0.010088 _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 C 3 ADP B 1 901 1 ADP ADP . D 3 ADP B 1 902 1 ADP ADP . E 4 HOH A 1 601 6 HOH HOH . E 4 HOH A 2 602 15 HOH HOH . E 4 HOH A 3 603 7 HOH HOH . F 4 HOH B 1 1001 24 HOH HOH . F 4 HOH B 2 1002 13 HOH HOH . F 4 HOH B 3 1003 1 HOH HOH . F 4 HOH B 4 1004 3 HOH HOH . F 4 HOH B 5 1005 9 HOH HOH . F 4 HOH B 6 1006 17 HOH HOH . F 4 HOH B 7 1007 11 HOH HOH . F 4 HOH B 8 1008 8 HOH HOH . F 4 HOH B 9 1009 5 HOH HOH . F 4 HOH B 10 1010 14 HOH HOH . F 4 HOH B 11 1011 12 HOH HOH . F 4 HOH B 12 1012 10 HOH HOH . F 4 HOH B 13 1013 23 HOH HOH . F 4 HOH B 14 1014 4 HOH HOH . F 4 HOH B 15 1015 18 HOH HOH . F 4 HOH B 16 1016 22 HOH HOH . F 4 HOH B 17 1017 16 HOH HOH . F 4 HOH B 18 1018 21 HOH HOH . F 4 HOH B 19 1019 2 HOH HOH . F 4 HOH B 20 1020 19 HOH HOH . F 4 HOH B 21 1021 20 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 . . . D 3 35.287 82.1 66.282 1 73.71 ? PB ADP 902 B 1 HETATM 2 O O1B ADP . . . D 3 34.421 82.935 65.373 1 76.7 ? O1B ADP 902 B 1 HETATM 3 O O2B ADP . . . D 3 36.052 82.879 67.325 1 76.55 ? O2B ADP 902 B 1 HETATM 4 O O3B ADP . . . D 3 36.139 81.083 65.563 1 83.76 ? O3B ADP 902 B 1 HETATM 5 P PA ADP . . . D 3 33.316 81.82 68.304 1 88.3 ? PA ADP 902 B 1 HETATM 6 O O1A ADP . . . D 3 31.887 81.417 68.036 1 92.01 ? O1A ADP 902 B 1 HETATM 7 O O2A ADP . . . D 3 33.649 83.283 68.47 1 78.18 ? O2A ADP 902 B 1 HETATM 8 O O3A ADP . . . D 3 34.205 81.221 67.096 1 91.02 ? O3A ADP 902 B 1 HETATM 9 O O5' ADP . . . D 3 33.792 81.008 69.611 1 78.62 ? O5' ADP 902 B 1 HETATM 10 C C5' ADP . . . D 3 33.925 79.587 69.572 1 85.88 ? C5' ADP 902 B 1 HETATM 11 C C4' ADP . . . D 3 33.808 79.027 70.986 1 87.23 ? C4' ADP 902 B 1 HETATM 12 O O4' ADP . . . D 3 35.035 79.228 71.691 1 83.28 ? O4' ADP 902 B 1 HETATM 13 C C3' ADP . . . D 3 32.702 79.709 71.777 1 81.46 ? C3' ADP 902 B 1 HETATM 14 O O3' ADP . . . D 3 31.647 78.785 72.061 1 90.34 ? O3' ADP 902 B 1 HETATM 15 C C2' ADP . . . D 3 33.346 80.189 73.064 1 79.64 ? C2' ADP 902 B 1 HETATM 16 O O2' ADP . . . D 3 32.751 79.54 74.193 1 85.49 ? O2' ADP 902 B 1 HETATM 17 C C1' ADP . . . D 3 34.817 79.818 72.974 1 81.56 ? C1' ADP 902 B 1 HETATM 18 N N9 ADP . . . D 3 35.655 81.04 73.06 1 80.25 ? N9 ADP 902 B 1 HETATM 19 C C8 ADP . . . D 3 36.321 81.584 72.025 1 83.06 ? C8 ADP 902 B 1 HETATM 20 N N7 ADP . . . D 3 37.005 82.69 72.408 1 85.81 ? N7 ADP 902 B 1 HETATM 21 C C5 ADP . . . D 3 36.781 82.874 73.718 1 80.65 ? C5 ADP 902 B 1 HETATM 22 C C6 ADP . . . D 3 37.206 83.861 74.738 1 80.9 ? C6 ADP 902 B 1 HETATM 23 N N6 ADP . . . D 3 38.025 84.894 74.417 1 81.79 ? N6 ADP 902 B 1 HETATM 24 N N1 ADP . . . D 3 36.748 83.693 75.997 1 87.02 ? N1 ADP 902 B 1 HETATM 25 C C2 ADP . . . D 3 35.935 82.669 76.323 1 86.28 ? C2 ADP 902 B 1 HETATM 26 N N3 ADP . . . D 3 35.511 81.738 75.447 1 84.5 ? N3 ADP 902 B 1 HETATM 27 C C4 ADP . . . D 3 35.893 81.781 74.148 1 82.26 ? C4 ADP 902 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #