data_4NAT # _model_server_result.job_id 7IHXuzrmjyUSKwf1zB34TA _model_server_result.datetime_utc '2025-04-18 15:20:52' _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 4nat # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":202}' # _entry.id 4NAT # _exptl.entry_id 4NAT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 4NAT _cell.length_a 76.157 _cell.length_b 127.283 _cell.length_c 126.95 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NAT _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 76.157 0 -63.475 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 I N N ? 4 K 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 54 n n PB O2B ADP sing 55 n n PB O3B ADP sing 56 n n PB O3A ADP sing 57 n n O2B HOB2 ADP sing 58 n n O3B HOB3 ADP sing 59 n n PA O1A ADP doub 60 n n PA O2A ADP sing 61 n n PA O3A ADP sing 62 n n PA O5' ADP sing 63 n n O2A HOA2 ADP sing 64 n n O5' C5' ADP sing 65 n n C5' C4' ADP sing 66 n n C5' "H5'1" ADP sing 67 n n C5' "H5'2" ADP sing 68 n n C4' O4' ADP sing 69 n n C4' C3' ADP sing 70 n n C4' H4' ADP sing 71 n n O4' C1' ADP sing 72 n n C3' O3' ADP sing 73 n n C3' C2' ADP sing 74 n n C3' H3' ADP sing 75 n n O3' HO3' ADP sing 76 n n C2' O2' ADP sing 77 n n C2' C1' ADP sing 78 n n C2' H2' ADP sing 79 n n O2' HO2' ADP sing 80 n n C1' N9 ADP sing 81 n n C1' H1' ADP sing 82 n n N9 C8 ADP sing 83 n y N9 C4 ADP sing 84 n y C8 N7 ADP doub 85 n y C8 H8 ADP sing 86 n n N7 C5 ADP sing 87 n y C5 C6 ADP sing 88 n y C5 C4 ADP doub 89 n y C6 N6 ADP sing 90 n n C6 N1 ADP doub 91 n y N6 HN61 ADP sing 92 n n N6 HN62 ADP sing 93 n n N1 C2 ADP sing 94 n y C2 N3 ADP doub 95 n y C2 H2 ADP sing 96 n n N3 C4 ADP sing 97 n y # _atom_sites.entry_id 4NAT _atom_sites.fract_transf_matrix[1][1] 0.013131 _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] 0.007857 _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] 0.007877 _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 D 2 2W5 A 1 201 1 2W5 INH . E 3 EPE A 1 202 201 EPE EPE . F 4 ADP A 1 203 214 ADP ADP . G 2 2W5 B 1 201 1 2W5 INH . H 3 EPE B 1 202 201 EPE EPE . I 4 ADP B 1 203 214 ADP ADP . J 2 2W5 C 1 201 1 2W5 INH . K 4 ADP C 1 202 214 ADP ADP . L 5 HOH A 1 301 10 HOH HOH . L 5 HOH A 2 302 13 HOH HOH . L 5 HOH A 3 303 22 HOH HOH . L 5 HOH A 4 304 23 HOH HOH . L 5 HOH A 5 305 36 HOH HOH . L 5 HOH A 6 306 37 HOH HOH . L 5 HOH A 7 307 41 HOH HOH . L 5 HOH A 8 308 43 HOH HOH . L 5 HOH A 9 309 44 HOH HOH . L 5 HOH A 10 310 47 HOH HOH . L 5 HOH A 11 311 52 HOH HOH . L 5 HOH A 12 312 64 HOH HOH . L 5 HOH A 13 313 68 HOH HOH . L 5 HOH A 14 314 73 HOH HOH . L 5 HOH A 15 315 79 HOH HOH . L 5 HOH A 16 316 82 HOH HOH . L 5 HOH A 17 317 86 HOH HOH . L 5 HOH A 18 318 96 HOH HOH . L 5 HOH A 19 319 99 HOH HOH . L 5 HOH A 20 320 100 HOH HOH . L 5 HOH A 21 321 102 HOH HOH . L 5 HOH A 22 322 111 HOH HOH . L 5 HOH A 23 323 114 HOH HOH . L 5 HOH A 24 324 115 HOH HOH . L 5 HOH A 25 325 118 HOH HOH . L 5 HOH A 26 326 124 HOH HOH . L 5 HOH A 27 327 125 HOH HOH . L 5 HOH A 28 328 126 HOH HOH . L 5 HOH A 29 329 132 HOH HOH . L 5 HOH A 30 330 136 HOH HOH . L 5 HOH A 31 331 138 HOH HOH . L 5 HOH A 32 332 139 HOH HOH . L 5 HOH A 33 333 141 HOH HOH . L 5 HOH A 34 334 143 HOH HOH . L 5 HOH A 35 335 150 HOH HOH . M 5 HOH B 1 301 3 HOH HOH . M 5 HOH B 2 302 6 HOH HOH . M 5 HOH B 3 303 11 HOH HOH . M 5 HOH B 4 304 14 HOH HOH . M 5 HOH B 5 305 15 HOH HOH . M 5 HOH B 6 306 17 HOH HOH . M 5 HOH B 7 307 21 HOH HOH . M 5 HOH B 8 308 24 HOH HOH . M 5 HOH B 9 309 25 HOH HOH . M 5 HOH B 10 310 28 HOH HOH . M 5 HOH B 11 311 33 HOH HOH . M 5 HOH B 12 312 35 HOH HOH . M 5 HOH B 13 313 38 HOH HOH . M 5 HOH B 14 314 45 HOH HOH . M 5 HOH B 15 315 48 HOH HOH . M 5 HOH B 16 316 55 HOH HOH . M 5 HOH B 17 317 57 HOH HOH . M 5 HOH B 18 318 59 HOH HOH . M 5 HOH B 19 319 65 HOH HOH . M 5 HOH B 20 320 67 HOH HOH . M 5 HOH B 21 321 69 HOH HOH . M 5 HOH B 22 322 71 HOH HOH . M 5 HOH B 23 323 75 HOH HOH . M 5 HOH B 24 324 76 HOH HOH . M 5 HOH B 25 325 78 HOH HOH . M 5 HOH B 26 326 81 HOH HOH . M 5 HOH B 27 327 87 HOH HOH . M 5 HOH B 28 328 88 HOH HOH . M 5 HOH B 29 329 89 HOH HOH . M 5 HOH B 30 330 90 HOH HOH . M 5 HOH B 31 331 95 HOH HOH . M 5 HOH B 32 332 119 HOH HOH . M 5 HOH B 33 333 122 HOH HOH . M 5 HOH B 34 334 123 HOH HOH . M 5 HOH B 35 335 128 HOH HOH . M 5 HOH B 36 336 129 HOH HOH . M 5 HOH B 37 337 133 HOH HOH . M 5 HOH B 38 338 137 HOH HOH . M 5 HOH B 39 339 140 HOH HOH . M 5 HOH B 40 340 144 HOH HOH . N 5 HOH C 1 301 5 HOH HOH . N 5 HOH C 2 302 7 HOH HOH . N 5 HOH C 3 303 8 HOH HOH . N 5 HOH C 4 304 26 HOH HOH . N 5 HOH C 5 305 30 HOH HOH . N 5 HOH C 6 306 34 HOH HOH . N 5 HOH C 7 307 40 HOH HOH . N 5 HOH C 8 308 42 HOH HOH . N 5 HOH C 9 309 46 HOH HOH . N 5 HOH C 10 310 49 HOH HOH . N 5 HOH C 11 311 50 HOH HOH . N 5 HOH C 12 312 51 HOH HOH . N 5 HOH C 13 313 53 HOH HOH . N 5 HOH C 14 314 58 HOH HOH . N 5 HOH C 15 315 60 HOH HOH . N 5 HOH C 16 316 61 HOH HOH . N 5 HOH C 17 317 62 HOH HOH . N 5 HOH C 18 318 83 HOH HOH . N 5 HOH C 19 319 84 HOH HOH . N 5 HOH C 20 320 85 HOH HOH . N 5 HOH C 21 321 91 HOH HOH . N 5 HOH C 22 322 97 HOH HOH . N 5 HOH C 23 323 98 HOH HOH . N 5 HOH C 24 324 101 HOH HOH . N 5 HOH C 25 325 103 HOH HOH . N 5 HOH C 26 326 105 HOH HOH . N 5 HOH C 27 327 107 HOH HOH . N 5 HOH C 28 328 108 HOH HOH . N 5 HOH C 29 329 109 HOH HOH . N 5 HOH C 30 330 110 HOH HOH . N 5 HOH C 31 331 113 HOH HOH . N 5 HOH C 32 332 116 HOH HOH . N 5 HOH C 33 333 117 HOH HOH . N 5 HOH C 34 334 120 HOH HOH . N 5 HOH C 35 335 121 HOH HOH . N 5 HOH C 36 336 130 HOH HOH . N 5 HOH C 37 337 131 HOH HOH . N 5 HOH C 38 338 134 HOH HOH . N 5 HOH C 39 339 142 HOH HOH . N 5 HOH C 40 340 145 HOH HOH . N 5 HOH C 41 341 146 HOH HOH . N 5 HOH C 42 342 147 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 . . . K 4 26.556 15.52 -17.194 1 50 ? PB ADP 202 C 1 HETATM 2 O O1B ADP . . . K 4 26.768 15.412 -18.743 1 50 ? O1B ADP 202 C 1 HETATM 3 O O2B ADP . . . K 4 25.075 15.538 -16.773 1 50 ? O2B ADP 202 C 1 HETATM 4 O O3B ADP . . . K 4 27.211 14.445 -16.313 1 50 ? O3B ADP 202 C 1 HETATM 5 P PA ADP . . . K 4 27.17 18.509 -16.352 1 50 ? PA ADP 202 C 1 HETATM 6 O O1A ADP . . . K 4 28.61 18.986 -16.298 1 46.69 ? O1A ADP 202 C 1 HETATM 7 O O2A ADP . . . K 4 26.355 18.91 -15.103 1 50 ? O2A ADP 202 C 1 HETATM 8 O O3A ADP . . . K 4 27.358 16.874 -16.619 1 50 ? O3A ADP 202 C 1 HETATM 9 O O5' ADP . . . K 4 26.278 19.034 -17.625 1 50 ? O5' ADP 202 C 1 HETATM 10 C C5' ADP . . . K 4 25.807 18.277 -18.769 1 50 ? C5' ADP 202 C 1 HETATM 11 C C4' ADP . . . K 4 26.754 18.339 -19.982 1 50 ? C4' ADP 202 C 1 HETATM 12 O O4' ADP . . . K 4 26.399 19.494 -20.775 1 50 ? O4' ADP 202 C 1 HETATM 13 C C3' ADP . . . K 4 28.261 18.45 -19.636 1 50 ? C3' ADP 202 C 1 HETATM 14 O O3' ADP . . . K 4 29.043 17.411 -20.313 1 50 ? O3' ADP 202 C 1 HETATM 15 C C2' ADP . . . K 4 28.648 19.894 -19.992 1 50 ? C2' ADP 202 C 1 HETATM 16 O O2' ADP . . . K 4 30.028 19.984 -20.428 1 50 ? O2' ADP 202 C 1 HETATM 17 C C1' ADP . . . K 4 27.583 20.303 -21.047 1 50 ? C1' ADP 202 C 1 HETATM 18 N N9 ADP . . . K 4 27.195 21.766 -21.123 1 50 ? N9 ADP 202 C 1 HETATM 19 C C8 ADP . . . K 4 26.149 22.399 -20.482 1 50 ? C8 ADP 202 C 1 HETATM 20 N N7 ADP . . . K 4 26.088 23.712 -20.84 1 50 ? N7 ADP 202 C 1 HETATM 21 C C5 ADP . . . K 4 27.082 23.918 -21.755 1 50 ? C5 ADP 202 C 1 HETATM 22 C C6 ADP . . . K 4 27.6 25.066 -22.555 1 50 ? C6 ADP 202 C 1 HETATM 23 N N6 ADP . . . K 4 27.001 26.263 -22.426 1 50 ? N6 ADP 202 C 1 HETATM 24 N N1 ADP . . . K 4 28.669 24.897 -23.4 1 50 ? N1 ADP 202 C 1 HETATM 25 C C2 ADP . . . K 4 29.278 23.693 -23.515 1 50 ? C2 ADP 202 C 1 HETATM 26 N N3 ADP . . . K 4 28.86 22.595 -22.818 1 50 ? N3 ADP 202 C 1 HETATM 27 C C4 ADP . . . K 4 27.801 22.649 -21.935 1 50 ? C4 ADP 202 C 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #