data_8ZMX # _model_server_result.job_id '_anx9hkbhYOglkNpdPWIrQ' _model_server_result.datetime_utc '2024-12-01 00:34:55' _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 8zmx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 8ZMX # _exptl.entry_id 8ZMX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 8ZMX _cell.length_a 157.09 _cell.length_b 157.09 _cell.length_c 111.45 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ZMX _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,E,H 1 2 C,F,I 1 4 A,C,D,F,G,I 2 1,4 B,E,H 2 2,3 # 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_444 -y-1/2,x-1/2,z-1/4 0 -1 0 1 0 0 0 0 1 -78.545 -78.545 -27.8625 3 'crystal symmetry operation' 6_445 x-1/2,-y-1/2,-z+1/4 1 0 0 0 -1 0 0 0 -1 -78.545 -78.545 27.8625 4 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C21 H28 N7 O17 P3' _chem_comp.formula_weight 743.405 _chem_comp.id NAP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" # 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 PA O1A NAP doub 237 n n PA O2A NAP sing 238 n n PA O5B NAP sing 239 n n PA O3 NAP sing 240 n n O2A HOA2 NAP sing 241 n n O5B C5B NAP sing 242 n n C5B C4B NAP sing 243 n n C5B H51A NAP sing 244 n n C5B H52A NAP sing 245 n n C4B O4B NAP sing 246 n n C4B C3B NAP sing 247 n n C4B H4B NAP sing 248 n n O4B C1B NAP sing 249 n n C3B O3B NAP sing 250 n n C3B C2B NAP sing 251 n n C3B H3B NAP sing 252 n n O3B HO3A NAP sing 253 n n C2B O2B NAP sing 254 n n C2B C1B NAP sing 255 n n C2B H2B NAP sing 256 n n O2B P2B NAP sing 257 n n C1B N9A NAP sing 258 n n C1B H1B NAP sing 259 n n N9A C8A NAP sing 260 n y N9A C4A NAP sing 261 n y C8A N7A NAP doub 262 n y C8A H8A NAP sing 263 n n N7A C5A NAP sing 264 n y C5A C6A NAP sing 265 n y C5A C4A NAP doub 266 n y C6A N6A NAP sing 267 n n C6A N1A NAP doub 268 n y N6A H61A NAP sing 269 n n N6A H62A NAP sing 270 n n N1A C2A NAP sing 271 n y C2A N3A NAP doub 272 n y C2A H2A NAP sing 273 n n N3A C4A NAP sing 274 n y O3 PN NAP sing 275 n n PN O1N NAP doub 276 n n PN O2N NAP sing 277 n n PN O5D NAP sing 278 n n O5D C5D NAP sing 279 n n C5D C4D NAP sing 280 n n C5D H51N NAP sing 281 n n C5D H52N NAP sing 282 n n C4D O4D NAP sing 283 n n C4D C3D NAP sing 284 n n C4D H4D NAP sing 285 n n O4D C1D NAP sing 286 n n C3D O3D NAP sing 287 n n C3D C2D NAP sing 288 n n C3D H3D NAP sing 289 n n O3D HO3N NAP sing 290 n n C2D O2D NAP sing 291 n n C2D C1D NAP sing 292 n n C2D H2D NAP sing 293 n n O2D HO2N NAP sing 294 n n C1D N1N NAP sing 295 n n C1D H1D NAP sing 296 n n N1N C2N NAP sing 297 n y N1N C6N NAP doub 298 n y C2N C3N NAP doub 299 n y C2N H2N NAP sing 300 n n C3N C7N NAP sing 301 n n C3N C4N NAP sing 302 n y C7N O7N NAP doub 303 n n C7N N7N NAP sing 304 n n N7N H71N NAP sing 305 n n N7N H72N NAP sing 306 n n C4N C5N NAP doub 307 n y C4N H4N NAP sing 308 n n C5N C6N NAP sing 309 n y C5N H5N NAP sing 310 n n C6N H6N NAP sing 311 n n P2B O1X NAP doub 312 n n P2B O2X NAP sing 313 n n P2B O3X NAP sing 314 n n O2X HOP2 NAP sing 315 n n O3X HOP3 NAP sing 316 n n # _atom_sites.entry_id 8ZMX _atom_sites.fract_transf_matrix[1][1] 0.006366 _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] 0.006366 _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] 0.008973 _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 NAP A 1 401 401 NAP NAP . E 2 NAP B 1 401 401 NAP NAP . F 2 NAP C 1 401 401 NAP NAP . G 3 HOH A 1 501 21 HOH HOH . G 3 HOH A 2 502 15 HOH HOH . G 3 HOH A 3 503 11 HOH HOH . G 3 HOH A 4 504 31 HOH HOH . G 3 HOH A 5 505 13 HOH HOH . G 3 HOH A 6 506 30 HOH HOH . G 3 HOH A 7 507 17 HOH HOH . G 3 HOH A 8 508 24 HOH HOH . H 3 HOH B 1 501 2 HOH HOH . H 3 HOH B 2 502 29 HOH HOH . H 3 HOH B 3 503 10 HOH HOH . H 3 HOH B 4 504 16 HOH HOH . H 3 HOH B 5 505 12 HOH HOH . H 3 HOH B 6 506 28 HOH HOH . H 3 HOH B 7 507 22 HOH HOH . I 3 HOH C 1 501 5 HOH HOH . I 3 HOH C 2 502 9 HOH HOH . I 3 HOH C 3 503 7 HOH HOH . I 3 HOH C 4 504 26 HOH HOH . I 3 HOH C 5 505 23 HOH HOH . I 3 HOH C 6 506 1 HOH HOH . I 3 HOH C 7 507 6 HOH HOH . I 3 HOH C 8 508 20 HOH HOH . I 3 HOH C 9 509 18 HOH HOH . I 3 HOH C 10 510 4 HOH HOH . I 3 HOH C 11 511 3 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 PA NAP . . . E 2 20.092 -56.723 38.236 1 64.81 ? PA NAP 401 B 1 HETATM 2 O O1A NAP . . . E 2 21.151 -57.262 39.135 1 58.5 ? O1A NAP 401 B 1 HETATM 3 O O2A NAP . . . E 2 19.266 -57.629 37.384 1 62.65 ? O2A NAP 401 B 1 HETATM 4 O O5B NAP . . . E 2 19.133 -55.771 39.105 1 63.72 ? O5B NAP 401 B 1 HETATM 5 C C5B NAP . . . E 2 17.995 -55.058 38.556 1 64.5 ? C5B NAP 401 B 1 HETATM 6 C C4B NAP . . . E 2 17.062 -54.719 39.693 1 65.41 ? C4B NAP 401 B 1 HETATM 7 O O4B NAP . . . E 2 15.899 -54.006 39.199 1 67.17 ? O4B NAP 401 B 1 HETATM 8 C C3B NAP . . . E 2 16.5 -55.918 40.468 1 66.61 ? C3B NAP 401 B 1 HETATM 9 O O3B NAP . . . E 2 17.393 -56.345 41.493 1 60.21 ? O3B NAP 401 B 1 HETATM 10 C C2B NAP . . . E 2 15.151 -55.402 40.956 1 66.12 ? C2B NAP 401 B 1 HETATM 11 O O2B NAP . . . E 2 15.384 -54.589 42.098 1 65.97 ? O2B NAP 401 B 1 HETATM 12 C C1B NAP . . . E 2 14.723 -54.521 39.787 1 67.5 ? C1B NAP 401 B 1 HETATM 13 N N9A NAP . . . E 2 13.949 -55.188 38.747 1 69.18 ? N9A NAP 401 B 1 HETATM 14 C C8A NAP . . . E 2 14.23 -56.384 38.134 1 69.19 ? C8A NAP 401 B 1 HETATM 15 N N7A NAP . . . E 2 13.355 -56.714 37.215 1 71.94 ? N7A NAP 401 B 1 HETATM 16 C C5A NAP . . . E 2 12.451 -55.664 37.209 1 67.62 ? C5A NAP 401 B 1 HETATM 17 C C6A NAP . . . E 2 11.294 -55.419 36.449 1 75.27 ? C6A NAP 401 B 1 HETATM 18 N N6A NAP . . . E 2 10.846 -56.245 35.508 1 81.39 ? N6A NAP 401 B 1 HETATM 19 N N1A NAP . . . E 2 10.618 -54.268 36.687 1 80.88 ? N1A NAP 401 B 1 HETATM 20 C C2A NAP . . . E 2 11.081 -53.441 37.634 1 76.15 ? C2A NAP 401 B 1 HETATM 21 N N3A NAP . . . E 2 12.154 -53.572 38.411 1 74.81 ? N3A NAP 401 B 1 HETATM 22 C C4A NAP . . . E 2 12.806 -54.716 38.147 1 68.07 ? C4A NAP 401 B 1 HETATM 23 O O3 NAP . . . E 2 20.847 -55.74 37.23 1 67.63 ? O3 NAP 401 B 1 HETATM 24 P PN NAP . . . E 2 22.175 -54.896 37.475 1 67.18 ? PN NAP 401 B 1 HETATM 25 O O1N NAP . . . E 2 23.401 -55.694 37.172 1 64.73 ? O1N NAP 401 B 1 HETATM 26 O O2N NAP . . . E 2 22.041 -54.264 38.82 1 66.53 ? O2N NAP 401 B 1 HETATM 27 O O5D NAP . . . E 2 21.976 -53.768 36.37 1 73.8 ? O5D NAP 401 B 1 HETATM 28 C C5D NAP . . . E 2 21.306 -54.138 35.159 1 71.08 ? C5D NAP 401 B 1 HETATM 29 C C4D NAP . . . E 2 21.134 -52.898 34.323 1 70.13 ? C4D NAP 401 B 1 HETATM 30 O O4D NAP . . . E 2 22.332 -52.093 34.442 1 66.46 ? O4D NAP 401 B 1 HETATM 31 C C3D NAP . . . E 2 20.911 -53.184 32.832 1 72 ? C3D NAP 401 B 1 HETATM 32 O O3D NAP . . . E 2 19.614 -52.735 32.471 1 82.24 ? O3D NAP 401 B 1 HETATM 33 C C2D NAP . . . E 2 22.042 -52.412 32.144 1 74.98 ? C2D NAP 401 B 1 HETATM 34 O O2D NAP . . . E 2 21.576 -51.678 31.022 1 74.69 ? O2D NAP 401 B 1 HETATM 35 C C1D NAP . . . E 2 22.677 -51.509 33.2 1 63.9 ? C1D NAP 401 B 1 HETATM 36 N N1N NAP . . . E 2 24.167 -51.532 33.102 1 63.76 ? N1N NAP 401 B 1 HETATM 37 C C2N NAP . . . E 2 24.812 -50.796 32.136 1 65.74 ? C2N NAP 401 B 1 HETATM 38 C C3N NAP . . . E 2 26.205 -50.74 32.107 1 64.28 ? C3N NAP 401 B 1 HETATM 39 C C7N NAP . . . E 2 26.861 -49.705 31.222 1 67.87 ? C7N NAP 401 B 1 HETATM 40 O O7N NAP . . . E 2 26.166 -48.826 30.699 1 65.55 ? O7N NAP 401 B 1 HETATM 41 N N7N NAP . . . E 2 28.174 -49.796 31.04 1 61.77 ? N7N NAP 401 B 1 HETATM 42 C C4N NAP . . . E 2 26.932 -51.628 32.906 1 62.22 ? C4N NAP 401 B 1 HETATM 43 C C5N NAP . . . E 2 26.279 -52.355 33.879 1 57.71 ? C5N NAP 401 B 1 HETATM 44 C C6N NAP . . . E 2 24.903 -52.265 33.983 1 62.2 ? C6N NAP 401 B 1 HETATM 45 P P2B NAP . . . E 2 14.19 -54.788 43.167 1 67.61 ? P2B NAP 401 B 1 HETATM 46 O O1X NAP . . . E 2 12.915 -54.193 42.59 1 65.46 ? O1X NAP 401 B 1 HETATM 47 O O2X NAP . . . E 2 14.685 -54.051 44.396 1 65.81 ? O2X NAP 401 B 1 HETATM 48 O O3X NAP . . . E 2 14.074 -56.294 43.408 1 70.34 ? O3X NAP 401 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 48 #