data_5YSS # _model_server_result.job_id ZqOFjzHzOSzmJupn2nNmNw _model_server_result.datetime_utc '2025-02-05 07:48:33' _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 5yss # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 5YSS # _exptl.entry_id 5YSS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 101.47 _cell.angle_gamma 90 _cell.entry_id 5YSS _cell.length_a 62.47 _cell.length_b 148.259 _cell.length_c 62.382 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YSS _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,G,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N # _chem_comp.formula 'C21 H27 N7 O14 P2' _chem_comp.formula_weight 663.425 _chem_comp.id NAD _chem_comp.mon_nstd_flag . _chem_comp.name NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 PA O1A NAD doub 237 n n PA O2A NAD sing 238 n n PA O5B NAD sing 239 n n PA O3 NAD sing 240 n n O2A HOA2 NAD sing 241 n n O5B C5B NAD sing 242 n n C5B C4B NAD sing 243 n n C5B H51A NAD sing 244 n n C5B H52A NAD sing 245 n n C4B O4B NAD sing 246 n n C4B C3B NAD sing 247 n n C4B H4B NAD sing 248 n n O4B C1B NAD sing 249 n n C3B O3B NAD sing 250 n n C3B C2B NAD sing 251 n n C3B H3B NAD sing 252 n n O3B HO3A NAD sing 253 n n C2B O2B NAD sing 254 n n C2B C1B NAD sing 255 n n C2B H2B NAD sing 256 n n O2B HO2A NAD sing 257 n n C1B N9A NAD sing 258 n n C1B H1B NAD sing 259 n n N9A C8A NAD sing 260 n y N9A C4A NAD sing 261 n y C8A N7A NAD doub 262 n y C8A H8A NAD sing 263 n n N7A C5A NAD sing 264 n y C5A C6A NAD sing 265 n y C5A C4A NAD doub 266 n y C6A N6A NAD sing 267 n n C6A N1A NAD doub 268 n y N6A H61A NAD sing 269 n n N6A H62A NAD sing 270 n n N1A C2A NAD sing 271 n y C2A N3A NAD doub 272 n y C2A H2A NAD sing 273 n n N3A C4A NAD sing 274 n y O3 PN NAD sing 275 n n PN O1N NAD doub 276 n n PN O2N NAD sing 277 n n PN O5D NAD sing 278 n n O5D C5D NAD sing 279 n n C5D C4D NAD sing 280 n n C5D H51N NAD sing 281 n n C5D H52N NAD sing 282 n n C4D O4D NAD sing 283 n n C4D C3D NAD sing 284 n n C4D H4D NAD sing 285 n n O4D C1D NAD sing 286 n n C3D O3D NAD sing 287 n n C3D C2D NAD sing 288 n n C3D H3D NAD sing 289 n n O3D HO3N NAD sing 290 n n C2D O2D NAD sing 291 n n C2D C1D NAD sing 292 n n C2D H2D NAD sing 293 n n O2D HO2N NAD sing 294 n n C1D N1N NAD sing 295 n n C1D H1D NAD sing 296 n n N1N C2N NAD sing 297 n y N1N C6N NAD doub 298 n y C2N C3N NAD doub 299 n y C2N H2N NAD sing 300 n n C3N C7N NAD sing 301 n n C3N C4N NAD sing 302 n y C7N O7N NAD doub 303 n n C7N N7N NAD sing 304 n n N7N H71N NAD sing 305 n n N7N H72N NAD sing 306 n n C4N C5N NAD doub 307 n y C4N H4N NAD sing 308 n n C5N C6N NAD sing 309 n y C5N H5N NAD sing 310 n n C6N H6N NAD sing 311 n n # _atom_sites.entry_id 5YSS _atom_sites.fract_transf_matrix[1][1] 0.016008 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003247 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006745 _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] 0.016357 _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 E 2 NAD B 1 301 4 NAD NAD . F 2 NAD D 1 301 5 NAD NAD . G 3 HOH A 1 301 58 HOH HOH . G 3 HOH A 2 302 51 HOH HOH . G 3 HOH A 3 303 3 HOH HOH . G 3 HOH A 4 304 45 HOH HOH . G 3 HOH A 5 305 66 HOH HOH . G 3 HOH A 6 306 43 HOH HOH . G 3 HOH A 7 307 101 HOH HOH . G 3 HOH A 8 308 16 HOH HOH . G 3 HOH A 9 309 46 HOH HOH . G 3 HOH A 10 310 55 HOH HOH . G 3 HOH A 11 311 44 HOH HOH . G 3 HOH A 12 312 4 HOH HOH . G 3 HOH A 13 313 49 HOH HOH . G 3 HOH A 14 314 117 HOH HOH . G 3 HOH A 15 315 90 HOH HOH . G 3 HOH A 16 316 47 HOH HOH . G 3 HOH A 17 317 57 HOH HOH . G 3 HOH A 18 318 116 HOH HOH . G 3 HOH A 19 319 118 HOH HOH . G 3 HOH A 20 320 9 HOH HOH . H 3 HOH B 1 401 25 HOH HOH . H 3 HOH B 2 402 104 HOH HOH . H 3 HOH B 3 403 28 HOH HOH . H 3 HOH B 4 404 36 HOH HOH . H 3 HOH B 5 405 31 HOH HOH . H 3 HOH B 6 406 27 HOH HOH . H 3 HOH B 7 407 1 HOH HOH . H 3 HOH B 8 408 93 HOH HOH . H 3 HOH B 9 409 110 HOH HOH . H 3 HOH B 10 410 26 HOH HOH . H 3 HOH B 11 411 60 HOH HOH . H 3 HOH B 12 412 40 HOH HOH . H 3 HOH B 13 413 112 HOH HOH . H 3 HOH B 14 414 29 HOH HOH . H 3 HOH B 15 415 24 HOH HOH . H 3 HOH B 16 416 30 HOH HOH . I 3 HOH C 1 301 5 HOH HOH . I 3 HOH C 2 302 80 HOH HOH . I 3 HOH C 3 303 103 HOH HOH . I 3 HOH C 4 304 113 HOH HOH . I 3 HOH C 5 305 74 HOH HOH . I 3 HOH C 6 306 114 HOH HOH . I 3 HOH C 7 307 75 HOH HOH . I 3 HOH C 8 308 62 HOH HOH . I 3 HOH C 9 309 6 HOH HOH . I 3 HOH C 10 310 83 HOH HOH . I 3 HOH C 11 311 78 HOH HOH . I 3 HOH C 12 312 69 HOH HOH . I 3 HOH C 13 313 81 HOH HOH . I 3 HOH C 14 314 79 HOH HOH . I 3 HOH C 15 315 70 HOH HOH . I 3 HOH C 16 316 68 HOH HOH . I 3 HOH C 17 317 65 HOH HOH . J 3 HOH D 1 401 7 HOH HOH . J 3 HOH D 2 402 97 HOH HOH . J 3 HOH D 3 403 96 HOH HOH . J 3 HOH D 4 404 119 HOH HOH . J 3 HOH D 5 405 17 HOH HOH . J 3 HOH D 6 406 108 HOH HOH . J 3 HOH D 7 407 95 HOH HOH . J 3 HOH D 8 408 85 HOH HOH . J 3 HOH D 9 409 8 HOH HOH . J 3 HOH D 10 410 59 HOH HOH . J 3 HOH D 11 411 105 HOH HOH . J 3 HOH D 12 412 106 HOH HOH . J 3 HOH D 13 413 115 HOH HOH . J 3 HOH D 14 414 73 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 NAD . . . F 2 -11.922 -1.237 88.289 1 73.1 ? PA NAD 301 D 1 HETATM 2 O O1A NAD . . . F 2 -13.201 -1.825 87.771 1 79.08 ? O1A NAD 301 D 1 HETATM 3 O O2A NAD . . . F 2 -12.211 -0.155 89.289 1 69.73 ? O2A NAD 301 D 1 HETATM 4 O O5B NAD . . . F 2 -11.116 -0.627 87.019 1 71.69 ? O5B NAD 301 D 1 HETATM 5 C C5B NAD . . . F 2 -10.784 -1.583 85.988 1 72.28 ? C5B NAD 301 D 1 HETATM 6 C C4B NAD . . . F 2 -10.659 -0.846 84.592 1 71.9 ? C4B NAD 301 D 1 HETATM 7 O O4B NAD . . . F 2 -10.615 -1.745 83.639 1 70.45 ? O4B NAD 301 D 1 HETATM 8 C C3B NAD . . . F 2 -11.864 0.032 84.339 1 67.17 ? C3B NAD 301 D 1 HETATM 9 O O3B NAD . . . F 2 -11.461 1.289 83.982 1 68.55 ? O3B NAD 301 D 1 HETATM 10 C C2B NAD . . . F 2 -12.615 -0.695 83.168 1 70.12 ? C2B NAD 301 D 1 HETATM 11 O O2B NAD . . . F 2 -13.373 0.308 82.314 1 67.5 ? O2B NAD 301 D 1 HETATM 12 C C1B NAD . . . F 2 -11.664 -1.24 82.517 1 72.4 ? C1B NAD 301 D 1 HETATM 13 N N9A NAD . . . F 2 -12.061 -2.378 81.69 1 68.43 ? N9A NAD 301 D 1 HETATM 14 C C8A NAD . . . F 2 -12.695 -3.535 82.011 1 70.79 ? C8A NAD 301 D 1 HETATM 15 N N7A NAD . . . F 2 -12.828 -4.276 80.882 1 68.33 ? N7A NAD 301 D 1 HETATM 16 C C5A NAD . . . F 2 -12.266 -3.581 79.865 1 68.49 ? C5A NAD 301 D 1 HETATM 17 C C6A NAD . . . F 2 -12.127 -3.864 78.525 1 67.06 ? C6A NAD 301 D 1 HETATM 18 N N6A NAD . . . F 2 -12.566 -5.021 77.856 1 65.17 ? N6A NAD 301 D 1 HETATM 19 N N1A NAD . . . F 2 -11.518 -2.976 77.707 1 66.32 ? N1A NAD 301 D 1 HETATM 20 C C2A NAD . . . F 2 -11.044 -1.8 78.204 1 66.2 ? C2A NAD 301 D 1 HETATM 21 N N3A NAD . . . F 2 -11.181 -1.51 79.538 1 67.08 ? N3A NAD 301 D 1 HETATM 22 C C4A NAD . . . F 2 -11.789 -2.409 80.359 1 68.98 ? C4A NAD 301 D 1 HETATM 23 O O3 NAD . . . F 2 -11.076 -2.411 88.97 1 70.8 ? O3 NAD 301 D 1 HETATM 24 P PN NAD . . . F 2 -9.619 -2.363 89.653 1 67.38 ? PN NAD 301 D 1 HETATM 25 O O1N NAD . . . F 2 -9.766 -2.929 91.07 1 71.96 ? O1N NAD 301 D 1 HETATM 26 O O2N NAD . . . F 2 -9.046 -0.95 89.7 1 65.8 -1 O2N NAD 301 D 1 HETATM 27 O O5D NAD . . . F 2 -8.616 -3.349 88.831 1 69.08 ? O5D NAD 301 D 1 HETATM 28 C C5D NAD . . . F 2 -7.605 -2.841 88.005 1 62.61 ? C5D NAD 301 D 1 HETATM 29 C C4D NAD . . . F 2 -6.414 -3.827 87.898 1 61.14 ? C4D NAD 301 D 1 HETATM 30 O O4D NAD . . . F 2 -5.781 -3.954 89.055 1 64.78 ? O4D NAD 301 D 1 HETATM 31 C C3D NAD . . . F 2 -6.854 -5.214 87.514 1 62.81 ? C3D NAD 301 D 1 HETATM 32 O O3D NAD . . . F 2 -5.977 -5.777 86.636 1 63.38 ? O3D NAD 301 D 1 HETATM 33 C C2D NAD . . . F 2 -6.81 -5.989 88.869 1 58.01 ? C2D NAD 301 D 1 HETATM 34 O O2D NAD . . . F 2 -6.646 -7.418 88.604 1 60.34 ? O2D NAD 301 D 1 HETATM 35 C C1D NAD . . . F 2 -5.77 -5.519 89.429 1 56.64 ? C1D NAD 301 D 1 HETATM 36 N N1N NAD . . . F 2 -5.831 -5.733 90.855 1 63.34 1 N1N NAD 301 D 1 HETATM 37 C C2N NAD . . . F 2 -6.901 -5.279 91.6 1 66.82 ? C2N NAD 301 D 1 HETATM 38 C C3N NAD . . . F 2 -6.959 -5.498 92.978 1 64.03 ? C3N NAD 301 D 1 HETATM 39 C C7N NAD . . . F 2 -8.166 -4.971 93.841 1 63.7 ? C7N NAD 301 D 1 HETATM 40 O O7N NAD . . . F 2 -8.246 -5.239 95.035 1 57.01 ? O7N NAD 301 D 1 HETATM 41 N N7N NAD . . . F 2 -9.207 -4.147 93.217 1 64.57 ? N7N NAD 301 D 1 HETATM 42 C C4N NAD . . . F 2 -5.934 -6.18 93.586 1 58.21 ? C4N NAD 301 D 1 HETATM 43 C C5N NAD . . . F 2 -4.874 -6.646 92.847 1 62.98 ? C5N NAD 301 D 1 HETATM 44 C C6N NAD . . . F 2 -4.815 -6.422 91.476 1 62.24 ? C6N NAD 301 D 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 44 #