data_6KDY # _model_server_result.job_id J8Met0n0fHbHBo0uxUOClw _model_server_result.datetime_utc '2024-12-21 12:01:27' _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 6kdy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 6KDY # _exptl.entry_id 6KDY _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.31 _cell.angle_gamma 90 _cell.entry_id 6KDY _cell.length_a 99.46 _cell.length_b 162.979 _cell.length_c 114.407 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KDY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J 1 1 C,D,K,L,M 2 1 E,F,N,O 3 1 G,H,P,Q 4 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 ? 3 I N N ? 3 K N N ? 3 N N N ? 3 P 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 300 n n PA O2A NAD sing 301 n n PA O5B NAD sing 302 n n PA O3 NAD sing 303 n n O2A HOA2 NAD sing 304 n n O5B C5B NAD sing 305 n n C5B C4B NAD sing 306 n n C5B H51A NAD sing 307 n n C5B H52A NAD sing 308 n n C4B O4B NAD sing 309 n n C4B C3B NAD sing 310 n n C4B H4B NAD sing 311 n n O4B C1B NAD sing 312 n n C3B O3B NAD sing 313 n n C3B C2B NAD sing 314 n n C3B H3B NAD sing 315 n n O3B HO3A NAD sing 316 n n C2B O2B NAD sing 317 n n C2B C1B NAD sing 318 n n C2B H2B NAD sing 319 n n O2B HO2A NAD sing 320 n n C1B N9A NAD sing 321 n n C1B H1B NAD sing 322 n n N9A C8A NAD sing 323 n y N9A C4A NAD sing 324 n y C8A N7A NAD doub 325 n y C8A H8A NAD sing 326 n n N7A C5A NAD sing 327 n y C5A C6A NAD sing 328 n y C5A C4A NAD doub 329 n y C6A N6A NAD sing 330 n n C6A N1A NAD doub 331 n y N6A H61A NAD sing 332 n n N6A H62A NAD sing 333 n n N1A C2A NAD sing 334 n y C2A N3A NAD doub 335 n y C2A H2A NAD sing 336 n n N3A C4A NAD sing 337 n y O3 PN NAD sing 338 n n PN O1N NAD doub 339 n n PN O2N NAD sing 340 n n PN O5D NAD sing 341 n n O5D C5D NAD sing 342 n n C5D C4D NAD sing 343 n n C5D H51N NAD sing 344 n n C5D H52N NAD sing 345 n n C4D O4D NAD sing 346 n n C4D C3D NAD sing 347 n n C4D H4D NAD sing 348 n n O4D C1D NAD sing 349 n n C3D O3D NAD sing 350 n n C3D C2D NAD sing 351 n n C3D H3D NAD sing 352 n n O3D HO3N NAD sing 353 n n C2D O2D NAD sing 354 n n C2D C1D NAD sing 355 n n C2D H2D NAD sing 356 n n O2D HO2N NAD sing 357 n n C1D N1N NAD sing 358 n n C1D H1D NAD sing 359 n n N1N C2N NAD sing 360 n y N1N C6N NAD doub 361 n y C2N C3N NAD doub 362 n y C2N H2N NAD sing 363 n n C3N C7N NAD sing 364 n n C3N C4N NAD sing 365 n y C7N O7N NAD doub 366 n n C7N N7N NAD sing 367 n n N7N H71N NAD sing 368 n n N7N H72N NAD sing 369 n n C4N C5N NAD doub 370 n y C4N H4N NAD sing 371 n n C5N C6N NAD sing 372 n y C5N H5N NAD sing 373 n n C6N H6N NAD sing 374 n n # _atom_sites.entry_id 6KDY _atom_sites.fract_transf_matrix[1][1] 0.010054 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001828 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006136 _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] 0.008884 _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 I 3 NAD A 1 401 3 NAD NAD . J 4 PG4 B 1 401 2 PG4 PG4 . K 3 NAD C 1 401 2 NAD NAD . L 5 2PE D 1 401 1 2PE 2PE . M 4 PG4 D 1 402 1 PG4 PG4 . N 3 NAD E 1 401 1 NAD NAD . O 6 PE7 F 1 401 1 PE7 PE7 . P 3 NAD G 1 401 4 NAD NAD . Q 7 P6G H 1 401 1 P6G P6G . # 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 . . . I 3 -8.856 0.248 -9.116 1 52.93 ? PA NAD 401 A 1 HETATM 2 O O1A NAD . . . I 3 -10.217 0.461 -9.728 1 57.35 ? O1A NAD 401 A 1 HETATM 3 O O2A NAD . . . I 3 -8.944 -0.8 -8.026 1 64.78 ? O2A NAD 401 A 1 HETATM 4 O O5B NAD . . . I 3 -7.788 -0.244 -10.257 1 60.61 ? O5B NAD 401 A 1 HETATM 5 C C5B NAD . . . I 3 -6.489 0.242 -10.085 1 63.6 ? C5B NAD 401 A 1 HETATM 6 C C4B NAD . . . I 3 -5.494 -0.624 -10.941 1 60.42 ? C4B NAD 401 A 1 HETATM 7 O O4B NAD . . . I 3 -5.635 -1.948 -10.797 1 57.36 ? O4B NAD 401 A 1 HETATM 8 C C3B NAD . . . I 3 -5.796 -0.31 -12.388 1 58.25 ? C3B NAD 401 A 1 HETATM 9 O O3B NAD . . . I 3 -4.639 -0.566 -13.103 1 67.62 ? O3B NAD 401 A 1 HETATM 10 C C2B NAD . . . I 3 -6.842 -1.391 -12.701 1 58.12 ? C2B NAD 401 A 1 HETATM 11 O O2B NAD . . . I 3 -6.981 -1.643 -14.153 1 75.94 ? O2B NAD 401 A 1 HETATM 12 C C1B NAD . . . I 3 -6.345 -2.439 -12.147 1 58.23 ? C1B NAD 401 A 1 HETATM 13 N N9A NAD . . . I 3 -7.344 -3.431 -11.763 1 61.6 ? N9A NAD 401 A 1 HETATM 14 C C8A NAD . . . I 3 -8.217 -3.201 -10.804 1 59.67 ? C8A NAD 401 A 1 HETATM 15 N N7A NAD . . . I 3 -9.035 -4.221 -10.716 1 60.56 ? N7A NAD 401 A 1 HETATM 16 C C5A NAD . . . I 3 -8.656 -5.137 -11.632 1 54.44 ? C5A NAD 401 A 1 HETATM 17 C C6A NAD . . . I 3 -9.137 -6.37 -11.98 1 55.53 ? C6A NAD 401 A 1 HETATM 18 N N6A NAD . . . I 3 -10.269 -6.996 -11.368 1 54.33 ? N6A NAD 401 A 1 HETATM 19 N N1A NAD . . . I 3 -8.559 -7.078 -12.938 1 59.92 ? N1A NAD 401 A 1 HETATM 20 C C2A NAD . . . I 3 -7.478 -6.568 -13.58 1 53.56 ? C2A NAD 401 A 1 HETATM 21 N N3A NAD . . . I 3 -7.01 -5.376 -13.26 1 55.53 ? N3A NAD 401 A 1 HETATM 22 C C4A NAD . . . I 3 -7.576 -4.644 -12.291 1 58.74 ? C4A NAD 401 A 1 HETATM 23 O O3 NAD . . . I 3 -8.244 1.659 -8.536 1 61.2 ? O3 NAD 401 A 1 HETATM 24 P PN NAD . . . I 3 -8.464 3.174 -9.118 1 65.24 ? PN NAD 401 A 1 HETATM 25 O O1N NAD . . . I 3 -7.857 3.374 -10.495 1 70.94 ? O1N NAD 401 A 1 HETATM 26 O O2N NAD . . . I 3 -7.875 4.202 -8.174 1 55.65 ? O2N NAD 401 A 1 HETATM 27 O O5D NAD . . . I 3 -10.072 3.341 -9.285 1 53.01 ? O5D NAD 401 A 1 HETATM 28 C C5D NAD . . . I 3 -10.765 3.56 -8.099 1 51.44 ? C5D NAD 401 A 1 HETATM 29 C C4D NAD . . . I 3 -12.124 4.09 -8.39 1 57.51 ? C4D NAD 401 A 1 HETATM 30 O O4D NAD . . . I 3 -12.97 3.11 -8.117 1 62.9 ? O4D NAD 401 A 1 HETATM 31 C C3D NAD . . . I 3 -12.518 5.338 -7.386 1 59.59 ? C3D NAD 401 A 1 HETATM 32 O O3D NAD . . . I 3 -13.719 6.03 -7.829 1 62.74 ? O3D NAD 401 A 1 HETATM 33 C C2D NAD . . . I 3 -12.79 4.732 -6.284 1 60.43 ? C2D NAD 401 A 1 HETATM 34 O O2D NAD . . . I 3 -13.694 5.483 -5.356 1 65.84 ? O2D NAD 401 A 1 HETATM 35 C C1D NAD . . . I 3 -13.425 3.324 -6.707 1 56.57 ? C1D NAD 401 A 1 HETATM 36 N N1N NAD . . . I 3 -13.071 2.346 -5.895 1 57.04 ? N1N NAD 401 A 1 HETATM 37 C C2N NAD . . . I 3 -14.061 1.501 -5.437 1 60.43 ? C2N NAD 401 A 1 HETATM 38 C C3N NAD . . . I 3 -13.782 0.561 -4.488 1 54.08 ? C3N NAD 401 A 1 HETATM 39 C C7N NAD . . . I 3 -14.922 -0.37 -4.028 1 60.62 ? C7N NAD 401 A 1 HETATM 40 O O7N NAD . . . I 3 -14.744 -1.123 -3.107 1 78.49 ? O7N NAD 401 A 1 HETATM 41 N N7N NAD . . . I 3 -16.241 -0.377 -4.624 1 56.57 ? N7N NAD 401 A 1 HETATM 42 C C4N NAD . . . I 3 -12.513 0.398 -4.004 1 56.7 ? C4N NAD 401 A 1 HETATM 43 C C5N NAD . . . I 3 -11.556 1.267 -4.475 1 58.73 ? C5N NAD 401 A 1 HETATM 44 C C6N NAD . . . I 3 -11.824 2.215 -5.404 1 57.43 ? C6N NAD 401 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 63 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 44 #