data_1XCB # _model_server_result.job_id ylM6Fr6a6lcC2bx4ByUhWw _model_server_result.datetime_utc '2024-12-21 12:34:48' _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 1xcb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":213}' # _entry.id 1XCB # _exptl.entry_id 1XCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _entity.pdbx_number_of_molecules 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 106.09 _cell.angle_gamma 90 _cell.entry_id 1XCB _cell.length_a 189.24 _cell.length_b 88.97 _cell.length_c 112.91 _cell.Z_PDB 28 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XCB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 ? dimeric 2 author_defined_assembly 4 PISA tetradecameric 14 software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,H,I,J,K 1 1 C,D,L,M,N,O,P 2 1 E,F,Q,R 3 1 G,S 4 1,2 A,B,G,H,I,J,K,S 5 4,5 C,D,E,F,L,M,N,O,P,Q,R 5 1,3 # 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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 157.947337 0 108.487038 3 'crystal symmetry operation' 2_756 -x+2,y,-z+1 -1 0 0 0 1 0 0 0 -1 347.187337 0 108.487038 4 'crystal symmetry operation' 3_545 x+1/2,y-1/2,z 1 0 0 0 1 0 0 0 1 94.62 -44.485 0 5 'crystal symmetry operation' 4_646 -x+3/2,y-1/2,-z+1 -1 0 0 0 1 0 0 0 -1 252.567337 -44.485 108.487038 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 K N N ? 3 M N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C GLY 87 A GLY 87 1_555 A N MSE 88 A MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C MSE 88 A MSE 88 1_555 A N GLY 89 A GLY 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C GLY 87 B GLY 87 1_555 B N MSE 88 B MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 B C MSE 88 B MSE 88 1_555 B N GLY 89 B GLY 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 C C GLY 87 C GLY 87 1_555 C N MSE 88 C MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale6 C C MSE 88 C MSE 88 1_555 C N GLY 89 C GLY 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 D C GLY 87 D GLY 87 1_555 D N MSE 88 D MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 D C MSE 88 D MSE 88 1_555 D N GLY 89 D GLY 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale9 E C MSE 1 E MSE 1 1_555 E N LYS 2 E LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 E C GLY 87 E GLY 87 1_555 E N MSE 88 E MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale11 E C MSE 88 E MSE 88 1_555 E N GLY 89 E GLY 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale12 F C GLY 87 F GLY 87 1_555 F N MSE 88 F MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale13 F C MSE 88 F MSE 88 1_555 F N GLY 89 F GLY 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 G C GLY 87 G GLY 87 1_555 G N MSE 88 G MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale15 G C MSE 88 G MSE 88 1_555 G N GLY 89 G GLY 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 B O GLY 139 B GLY 139 1_555 J CA CA . B CA 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.211 ? metalc ? metalc2 J CA CA . B CA 212 1_555 G O GLY 139 G GLY 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.317 ? metalc ? metalc3 D O GLY 139 D GLY 139 1_555 N CA CA . D CA 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.259 ? metalc ? metalc4 D O ASP 188 D ASP 188 1_555 O CA CA . D CA 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.378 ? # _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 254 n n PA O2A NAD sing 255 n n PA O5B NAD sing 256 n n PA O3 NAD sing 257 n n O2A HOA2 NAD sing 258 n n O5B C5B NAD sing 259 n n C5B C4B NAD sing 260 n n C5B H51A NAD sing 261 n n C5B H52A NAD sing 262 n n C4B O4B NAD sing 263 n n C4B C3B NAD sing 264 n n C4B H4B NAD sing 265 n n O4B C1B NAD sing 266 n n C3B O3B NAD sing 267 n n C3B C2B NAD sing 268 n n C3B H3B NAD sing 269 n n O3B HO3A NAD sing 270 n n C2B O2B NAD sing 271 n n C2B C1B NAD sing 272 n n C2B H2B NAD sing 273 n n O2B HO2A NAD sing 274 n n C1B N9A NAD sing 275 n n C1B H1B NAD sing 276 n n N9A C8A NAD sing 277 n y N9A C4A NAD sing 278 n y C8A N7A NAD doub 279 n y C8A H8A NAD sing 280 n n N7A C5A NAD sing 281 n y C5A C6A NAD sing 282 n y C5A C4A NAD doub 283 n y C6A N6A NAD sing 284 n n C6A N1A NAD doub 285 n y N6A H61A NAD sing 286 n n N6A H62A NAD sing 287 n n N1A C2A NAD sing 288 n y C2A N3A NAD doub 289 n y C2A H2A NAD sing 290 n n N3A C4A NAD sing 291 n y O3 PN NAD sing 292 n n PN O1N NAD doub 293 n n PN O2N NAD sing 294 n n PN O5D NAD sing 295 n n O5D C5D NAD sing 296 n n C5D C4D NAD sing 297 n n C5D H51N NAD sing 298 n n C5D H52N NAD sing 299 n n C4D O4D NAD sing 300 n n C4D C3D NAD sing 301 n n C4D H4D NAD sing 302 n n O4D C1D NAD sing 303 n n C3D O3D NAD sing 304 n n C3D C2D NAD sing 305 n n C3D H3D NAD sing 306 n n O3D HO3N NAD sing 307 n n C2D O2D NAD sing 308 n n C2D C1D NAD sing 309 n n C2D H2D NAD sing 310 n n O2D HO2N NAD sing 311 n n C1D N1N NAD sing 312 n n C1D H1D NAD sing 313 n n N1N C2N NAD sing 314 n y N1N C6N NAD doub 315 n y C2N C3N NAD doub 316 n y C2N H2N NAD sing 317 n n C3N C7N NAD sing 318 n n C3N C4N NAD sing 319 n y C7N O7N NAD doub 320 n n C7N N7N NAD sing 321 n n N7N H71N NAD sing 322 n n N7N H72N NAD sing 323 n n C4N C5N NAD doub 324 n y C4N H4N NAD sing 325 n n C5N C6N NAD sing 326 n y C5N H5N NAD sing 327 n n C6N H6N NAD sing 328 n n # _atom_sites.entry_id 1XCB _atom_sites.fract_transf_matrix[1][1] 0.005284 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001524 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01124 _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] 0.009218 _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 H 2 CA A 1 212 12 CA CA . I 3 NAD A 1 213 1 NAD NAD . J 2 CA B 1 212 8 CA CA . K 3 NAD B 1 213 2 NAD NAD . L 2 CA C 1 212 10 CA CA . M 3 NAD C 1 213 3 NAD NAD . N 2 CA D 1 212 9 CA CA . O 2 CA D 1 213 11 CA CA . P 3 NAD D 1 214 4 NAD NAD . Q 3 NAD E 1 212 5 NAD NAD . R 3 NAD F 1 212 6 NAD NAD . S 3 NAD G 1 212 7 NAD NAD . # 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 . . . K 3 32.637 112.962 39.487 1 30.15 ? PA NAD 213 B 1 HETATM 2 O O1A NAD . . . K 3 31.978 113.161 40.829 1 31.36 ? O1A NAD 213 B 1 HETATM 3 O O2A NAD . . . K 3 32.734 114.096 38.514 1 28.52 ? O2A NAD 213 B 1 HETATM 4 O O5B NAD . . . K 3 34.01 112.326 39.909 1 34.23 ? O5B NAD 213 B 1 HETATM 5 C C5B NAD . . . K 3 35.267 112.321 39.217 1 30.13 ? C5B NAD 213 B 1 HETATM 6 C C4B NAD . . . K 3 36.236 112.696 40.307 1 24.87 ? C4B NAD 213 B 1 HETATM 7 O O4B NAD . . . K 3 37.572 112.656 39.713 1 24.32 ? O4B NAD 213 B 1 HETATM 8 C C3B NAD . . . K 3 36.084 114.155 40.839 1 18.28 ? C3B NAD 213 B 1 HETATM 9 O O3B NAD . . . K 3 35.84 114.082 42.246 1 20.71 ? O3B NAD 213 B 1 HETATM 10 C C2B NAD . . . K 3 37.37 114.879 40.509 1 20.01 ? C2B NAD 213 B 1 HETATM 11 O O2B NAD . . . K 3 37.795 115.84 41.426 1 17.26 ? O2B NAD 213 B 1 HETATM 12 C C1B NAD . . . K 3 38.328 113.68 40.304 1 21.65 ? C1B NAD 213 B 1 HETATM 13 N N9A NAD . . . K 3 39.414 113.919 39.353 1 20.95 ? N9A NAD 213 B 1 HETATM 14 C C8A NAD . . . K 3 39.492 114.535 38.109 1 14.87 ? C8A NAD 213 B 1 HETATM 15 N N7A NAD . . . K 3 40.708 114.509 37.579 1 15.22 ? N7A NAD 213 B 1 HETATM 16 C C5A NAD . . . K 3 41.508 113.877 38.446 1 18.92 ? C5A NAD 213 B 1 HETATM 17 C C6A NAD . . . K 3 42.938 113.518 38.429 1 19.59 ? C6A NAD 213 B 1 HETATM 18 N N6A NAD . . . K 3 43.732 113.83 37.426 1 20.03 ? N6A NAD 213 B 1 HETATM 19 N N1A NAD . . . K 3 43.393 112.835 39.565 1 21.32 ? N1A NAD 213 B 1 HETATM 20 C C2A NAD . . . K 3 42.643 112.48 40.625 1 23.24 ? C2A NAD 213 B 1 HETATM 21 N N3A NAD . . . K 3 41.272 112.788 40.691 1 27.7 ? N3A NAD 213 B 1 HETATM 22 C C4A NAD . . . K 3 40.739 113.483 39.568 1 23.17 ? C4A NAD 213 B 1 HETATM 23 O O3 NAD . . . K 3 32.002 111.766 38.716 1 25.84 ? O3 NAD 213 B 1 HETATM 24 P PN NAD . . . K 3 31.447 110.353 39.228 1 26.22 ? PN NAD 213 B 1 HETATM 25 O O1N NAD . . . K 3 30.003 110.405 39 1 27.36 ? O1N NAD 213 B 1 HETATM 26 O O2N NAD . . . K 3 31.974 110.162 40.62 1 24.84 ? O2N NAD 213 B 1 HETATM 27 O O5D NAD . . . K 3 32.116 109.323 38.134 1 21.26 ? O5D NAD 213 B 1 HETATM 28 C C5D NAD . . . K 3 33.554 109.044 38.125 1 23.08 ? C5D NAD 213 B 1 HETATM 29 C C4D NAD . . . K 3 33.886 108.071 37.052 1 22.54 ? C4D NAD 213 B 1 HETATM 30 O O4D NAD . . . K 3 32.991 106.881 37.167 1 22.46 ? O4D NAD 213 B 1 HETATM 31 C C3D NAD . . . K 3 33.647 108.593 35.587 1 25.42 ? C3D NAD 213 B 1 HETATM 32 O O3D NAD . . . K 3 34.694 108.148 34.695 1 25.88 ? O3D NAD 213 B 1 HETATM 33 C C2D NAD . . . K 3 32.309 107.963 35.203 1 24.12 ? C2D NAD 213 B 1 HETATM 34 O O2D NAD . . . K 3 32.063 107.979 33.817 1 25.12 ? O2D NAD 213 B 1 HETATM 35 C C1D NAD . . . K 3 32.474 106.544 35.86 1 20.52 ? C1D NAD 213 B 1 HETATM 36 N N1N NAD . . . K 3 31.192 105.801 35.98 1 17.77 ? N1N NAD 213 B 1 HETATM 37 C C2N NAD . . . K 3 31.345 104.368 35.872 1 17.32 ? C2N NAD 213 B 1 HETATM 38 C C3N NAD . . . K 3 30.487 103.497 36.418 1 19.18 ? C3N NAD 213 B 1 HETATM 39 C C7N NAD . . . K 3 30.674 102 36.259 1 21.32 ? C7N NAD 213 B 1 HETATM 40 O O7N NAD . . . K 3 29.751 101.233 36.616 1 24.75 ? O7N NAD 213 B 1 HETATM 41 N N7N NAD . . . K 3 31.809 101.538 35.724 1 22.74 ? N7N NAD 213 B 1 HETATM 42 C C4N NAD . . . K 3 29.294 103.995 37.207 1 22.26 ? C4N NAD 213 B 1 HETATM 43 C C5N NAD . . . K 3 29.696 105.272 37.891 1 23.74 ? C5N NAD 213 B 1 HETATM 44 C C6N NAD . . . K 3 30.327 106.232 37.062 1 18.13 ? C6N NAD 213 B 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 44 #