data_1XLT # _model_server_result.job_id kNgMAhqWPL0q2Bz-cxV14Q _model_server_result.datetime_utc '2024-11-09 01:34:50' _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 1xlt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":400}' # _entry.id 1XLT # _exptl.entry_id 1XLT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _entity.pdbx_number_of_molecules 5 _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 1XLT _cell.length_a 95.372 _cell.length_b 171.082 _cell.length_c 203.181 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XLT _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 trimeric 3 author_and_software_defined_assembly 2 PISA trimeric 3 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,J,K,P,Q,R,S 1 1 D,E,F,L,M,T,U,V 2 1 G,H,I,N,O,W,X,Y,Z 3 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 ? 4 P N N ? 4 R N N ? 4 T N N ? 4 W N N ? 4 Y N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n J GLC 1 J 1 GLC A 600 SUC 3 n J FRU 2 J 2 FRU A 600 SUC 3 n K GLC 1 K 1 GLC B 600 SUC 3 n K FRU 2 K 2 FRU B 600 SUC 3 n L GLC 1 L 1 GLC D 600 SUC 3 n L FRU 2 L 2 FRU D 600 SUC 3 n M GLC 1 M 1 GLC E 600 SUC 3 n M FRU 2 M 2 FRU E 600 SUC 3 n N GLC 1 N 1 GLC G 600 SUC 3 n N FRU 2 N 2 FRU G 600 SUC 3 n O GLC 1 O 1 GLC H 600 SUC 3 n O FRU 2 O 2 FRU H 600 SUC # 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 J C1 GLC . J GLC 1 1_555 J O2 FRU . J FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 sing covale ? covale2 K C1 GLC . K GLC 1 1_555 K O2 FRU . K FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 sing covale ? covale3 L C1 GLC . L GLC 1 1_555 L O2 FRU . L FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 sing covale ? covale4 M C1 GLC . M GLC 1 1_555 M O2 FRU . M FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 sing covale ? covale5 N C1 GLC . N GLC 1 1_555 N O2 FRU . N FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 sing covale ? covale6 O C1 GLC . O GLC 1 1_555 O O2 FRU . O FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 sing metalc ? metalc1 A O ALA 159 A ALA 159 1_555 Q NA NA . A NA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? metalc ? metalc2 A O PRO 171 A PRO 171 1_555 Q NA NA . A NA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc3 Q NA NA . A NA 601 1_555 B OD2 ASP 330 B ASP 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? metalc ? metalc4 D O ALA 159 D ALA 159 1_555 U NA NA . D NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc5 D O PRO 171 D PRO 171 1_555 U NA NA . D NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc6 U NA NA . D NA 602 1_555 E OD2 ASP 330 E ASP 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc7 G O ALA 159 G ALA 159 1_555 X NA NA . G NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc8 G O PRO 171 G PRO 171 1_555 X NA NA . G NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc9 X NA NA . G NA 603 1_555 H OD2 ASP 330 H ASP 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? # _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 283 n n PA O2A NAD sing 284 n n PA O5B NAD sing 285 n n PA O3 NAD sing 286 n n O2A HOA2 NAD sing 287 n n O5B C5B NAD sing 288 n n C5B C4B NAD sing 289 n n C5B H51A NAD sing 290 n n C5B H52A NAD sing 291 n n C4B O4B NAD sing 292 n n C4B C3B NAD sing 293 n n C4B H4B NAD sing 294 n n O4B C1B NAD sing 295 n n C3B O3B NAD sing 296 n n C3B C2B NAD sing 297 n n C3B H3B NAD sing 298 n n O3B HO3A NAD sing 299 n n C2B O2B NAD sing 300 n n C2B C1B NAD sing 301 n n C2B H2B NAD sing 302 n n O2B HO2A NAD sing 303 n n C1B N9A NAD sing 304 n n C1B H1B NAD sing 305 n n N9A C8A NAD sing 306 n y N9A C4A NAD sing 307 n y C8A N7A NAD doub 308 n y C8A H8A NAD sing 309 n n N7A C5A NAD sing 310 n y C5A C6A NAD sing 311 n y C5A C4A NAD doub 312 n y C6A N6A NAD sing 313 n n C6A N1A NAD doub 314 n y N6A H61A NAD sing 315 n n N6A H62A NAD sing 316 n n N1A C2A NAD sing 317 n y C2A N3A NAD doub 318 n y C2A H2A NAD sing 319 n n N3A C4A NAD sing 320 n y O3 PN NAD sing 321 n n PN O1N NAD doub 322 n n PN O2N NAD sing 323 n n PN O5D NAD sing 324 n n O5D C5D NAD sing 325 n n C5D C4D NAD sing 326 n n C5D H51N NAD sing 327 n n C5D H52N NAD sing 328 n n C4D O4D NAD sing 329 n n C4D C3D NAD sing 330 n n C4D H4D NAD sing 331 n n O4D C1D NAD sing 332 n n C3D O3D NAD sing 333 n n C3D C2D NAD sing 334 n n C3D H3D NAD sing 335 n n O3D HO3N NAD sing 336 n n C2D O2D NAD sing 337 n n C2D C1D NAD sing 338 n n C2D H2D NAD sing 339 n n O2D HO2N NAD sing 340 n n C1D N1N NAD sing 341 n n C1D H1D NAD sing 342 n n N1N C2N NAD sing 343 n y N1N C6N NAD doub 344 n y C2N C3N NAD doub 345 n y C2N H2N NAD sing 346 n n C3N C7N NAD sing 347 n n C3N C4N NAD sing 348 n y C7N O7N NAD doub 349 n n C7N N7N NAD sing 350 n n N7N H71N NAD sing 351 n n N7N H72N NAD sing 352 n n C4N C5N NAD doub 353 n y C4N H4N NAD sing 354 n n C5N C6N NAD sing 355 n y C5N H5N NAD sing 356 n n C6N H6N NAD sing 357 n n # _atom_sites.entry_id 1XLT _atom_sites.fract_transf_matrix[1][1] 0.010485 _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] 0.005845 _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] 0.004922 _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 P 4 NAD A 1 400 400 NAD NAD . Q 5 NA A 1 601 601 NA NA . R 4 NAD B 1 400 400 NAD NAD . S 6 NDP C 1 500 500 NDP NDP . T 4 NAD D 1 400 400 NAD NAD . U 5 NA D 1 602 602 NA NA . V 6 NDP F 1 500 500 NDP NDP . W 4 NAD G 1 400 400 NAD NAD . X 5 NA G 1 603 603 NA NA . Y 4 NAD H 1 400 400 NAD NAD . Z 6 NDP I 1 500 500 NDP NDP . # 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 . . . W 4 130.423 -8.278 26.989 1 72.12 ? PA NAD 400 G 1 HETATM 2 O O1A NAD . . . W 4 130.273 -6.833 26.701 1 72.49 ? O1A NAD 400 G 1 HETATM 3 O O2A NAD . . . W 4 131.239 -9.153 26.115 1 72.72 ? O2A NAD 400 G 1 HETATM 4 O O5B NAD . . . W 4 128.955 -8.848 27.058 1 72.28 ? O5B NAD 400 G 1 HETATM 5 C C5B NAD . . . W 4 128.298 -9.888 26.405 1 70.55 ? C5B NAD 400 G 1 HETATM 6 C C4B NAD . . . W 4 128.046 -11.213 27.048 1 68.65 ? C4B NAD 400 G 1 HETATM 7 O O4B NAD . . . W 4 127.522 -12.298 26.238 1 68.5 ? O4B NAD 400 G 1 HETATM 8 C C3B NAD . . . W 4 129.187 -11.871 27.677 1 67.86 ? C3B NAD 400 G 1 HETATM 9 O O3B NAD . . . W 4 129.427 -11.256 28.98 1 68.04 ? O3B NAD 400 G 1 HETATM 10 C C2B NAD . . . W 4 128.957 -13.313 27.785 1 67.26 ? C2B NAD 400 G 1 HETATM 11 O O2B NAD . . . W 4 129 -14.03 28.941 1 65.01 ? O2B NAD 400 G 1 HETATM 12 C C1B NAD . . . W 4 127.648 -13.465 27.174 1 68.18 ? C1B NAD 400 G 1 HETATM 13 N N9A NAD . . . W 4 127.327 -14.703 26.254 1 69.09 ? N9A NAD 400 G 1 HETATM 14 C C8A NAD . . . W 4 126.52 -15.79 26.639 1 69.11 ? C8A NAD 400 G 1 HETATM 15 N N7A NAD . . . W 4 126.41 -16.669 25.663 1 69.19 ? N7A NAD 400 G 1 HETATM 16 C C5A NAD . . . W 4 127.123 -16.217 24.596 1 68.31 ? C5A NAD 400 G 1 HETATM 17 C C6A NAD . . . W 4 127.427 -16.616 23.27 1 67.96 ? C6A NAD 400 G 1 HETATM 18 N N6A NAD . . . W 4 126.918 -17.778 22.808 1 67.42 ? N6A NAD 400 G 1 HETATM 19 N N1A NAD . . . W 4 128.231 -15.819 22.474 1 68.04 ? N1A NAD 400 G 1 HETATM 20 C C2A NAD . . . W 4 128.765 -14.619 22.927 1 68.4 ? C2A NAD 400 G 1 HETATM 21 N N3A NAD . . . W 4 128.547 -14.124 24.173 1 67.91 ? N3A NAD 400 G 1 HETATM 22 C C4A NAD . . . W 4 127.756 -14.89 24.972 1 68.22 ? C4A NAD 400 G 1 HETATM 23 O O3 NAD . . . W 4 130.928 -8.569 28.475 1 73.1 ? O3 NAD 400 G 1 HETATM 24 P PN NAD . . . W 4 130.722 -7.477 29.749 1 75.69 ? PN NAD 400 G 1 HETATM 25 O O1N NAD . . . W 4 129.526 -6.605 29.64 1 75.91 ? O1N NAD 400 G 1 HETATM 26 O O2N NAD . . . W 4 132.059 -6.836 29.787 1 75.96 ? O2N NAD 400 G 1 HETATM 27 O O5D NAD . . . W 4 130.587 -8.238 31.066 1 76.96 ? O5D NAD 400 G 1 HETATM 28 C C5D NAD . . . W 4 131.262 -9.109 31.895 1 79.99 ? C5D NAD 400 G 1 HETATM 29 C C4D NAD . . . W 4 132.261 -9.162 33.067 1 81.72 ? C4D NAD 400 G 1 HETATM 30 O O4D NAD . . . W 4 133.182 -8.093 32.725 1 82.95 ? O4D NAD 400 G 1 HETATM 31 C C3D NAD . . . W 4 131.409 -8.884 34.333 1 82.69 ? C3D NAD 400 G 1 HETATM 32 O O3D NAD . . . W 4 131.234 -9.942 35.323 1 82.71 ? O3D NAD 400 G 1 HETATM 33 C C2D NAD . . . W 4 132.196 -7.622 34.908 1 83.49 ? C2D NAD 400 G 1 HETATM 34 O O2D NAD . . . W 4 132.473 -7.577 36.268 1 82.64 ? O2D NAD 400 G 1 HETATM 35 C C1D NAD . . . W 4 133.342 -7.467 33.973 1 84.32 ? C1D NAD 400 G 1 HETATM 36 N N1N NAD . . . W 4 134.106 -6.159 33.662 1 85.93 ? N1N NAD 400 G 1 HETATM 37 C C2N NAD . . . W 4 135.03 -5.629 34.617 1 86.56 ? C2N NAD 400 G 1 HETATM 38 C C3N NAD . . . W 4 135.712 -4.37 34.352 1 87.39 ? C3N NAD 400 G 1 HETATM 39 C C7N NAD . . . W 4 136.677 -3.817 35.36 1 87.31 ? C7N NAD 400 G 1 HETATM 40 O O7N NAD . . . W 4 136.503 -3.956 36.579 1 86.04 ? O7N NAD 400 G 1 HETATM 41 N N7N NAD . . . W 4 137.725 -3.178 34.786 1 87.5 ? N7N NAD 400 G 1 HETATM 42 C C4N NAD . . . W 4 135.469 -3.642 33.13 1 87 ? C4N NAD 400 G 1 HETATM 43 C C5N NAD . . . W 4 134.578 -4.15 32.199 1 85.94 ? C5N NAD 400 G 1 HETATM 44 C C6N NAD . . . W 4 133.93 -5.348 32.453 1 86.22 ? C6N NAD 400 G 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 118 _model_server_stats.query_time_ms 372 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 44 #