data_1PSD # _model_server_result.job_id f24d5jWQpMuy3QwWtoftEw _model_server_result.datetime_utc '2024-11-25 22:50:27' _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 1psd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":450}' # _entry.id 1PSD # _exptl.entry_id 1PSD _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 90 _cell.angle_gamma 90 _cell.entry_id 1PSD _cell.length_a 136.1 _cell.length_b 146.3 _cell.length_c 53.3 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PSD _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 136.1 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 C N N ? 2 E 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 1PSD _atom_sites.fract_transf_matrix[1][1] 0.007348 _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] 0.006835 _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] 0.018762 _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 C 2 NAD A 1 450 450 NAD NAD . D 3 SER A 1 451 451 SER SER . E 2 NAD B 1 450 450 NAD NAD . F 3 SER B 1 451 451 SER SER . G 4 HOH A 1 500 500 HOH HOH . G 4 HOH A 2 501 501 HOH HOH . G 4 HOH A 3 502 502 HOH HOH . G 4 HOH A 4 503 503 HOH HOH . G 4 HOH A 5 504 504 HOH HOH . G 4 HOH A 6 505 505 HOH HOH . G 4 HOH A 7 506 506 HOH HOH . G 4 HOH A 8 507 507 HOH HOH . G 4 HOH A 9 508 508 HOH HOH . G 4 HOH A 10 509 509 HOH HOH . G 4 HOH A 11 511 511 HOH HOH . G 4 HOH A 12 512 512 HOH HOH . G 4 HOH A 13 513 513 HOH HOH . G 4 HOH A 14 516 516 HOH HOH . G 4 HOH A 15 518 518 HOH HOH . G 4 HOH A 16 519 519 HOH HOH . G 4 HOH A 17 523 523 HOH HOH . G 4 HOH A 18 525 525 HOH HOH . G 4 HOH A 19 526 526 HOH HOH . G 4 HOH A 20 530 530 HOH HOH . G 4 HOH A 21 531 531 HOH HOH . G 4 HOH A 22 532 532 HOH HOH . G 4 HOH A 23 533 533 HOH HOH . G 4 HOH A 24 534 534 HOH HOH . G 4 HOH A 25 535 535 HOH HOH . G 4 HOH A 26 538 538 HOH HOH . G 4 HOH A 27 562 562 HOH HOH . G 4 HOH A 28 563 563 HOH HOH . G 4 HOH A 29 564 564 HOH HOH . G 4 HOH A 30 566 566 HOH HOH . G 4 HOH A 31 567 567 HOH HOH . G 4 HOH A 32 571 571 HOH HOH . G 4 HOH A 33 572 572 HOH HOH . G 4 HOH A 34 574 574 HOH HOH . H 4 HOH B 1 510 510 HOH HOH . H 4 HOH B 2 514 514 HOH HOH . H 4 HOH B 3 515 515 HOH HOH . H 4 HOH B 4 517 517 HOH HOH . H 4 HOH B 5 520 520 HOH HOH . H 4 HOH B 6 521 521 HOH HOH . H 4 HOH B 7 522 522 HOH HOH . H 4 HOH B 8 524 524 HOH HOH . H 4 HOH B 9 527 527 HOH HOH . H 4 HOH B 10 528 528 HOH HOH . H 4 HOH B 11 529 529 HOH HOH . H 4 HOH B 12 536 536 HOH HOH . H 4 HOH B 13 537 537 HOH HOH . H 4 HOH B 14 539 539 HOH HOH . H 4 HOH B 15 540 540 HOH HOH . H 4 HOH B 16 541 541 HOH HOH . H 4 HOH B 17 542 542 HOH HOH . H 4 HOH B 18 543 543 HOH HOH . H 4 HOH B 19 544 544 HOH HOH . H 4 HOH B 20 545 545 HOH HOH . H 4 HOH B 21 546 546 HOH HOH . H 4 HOH B 22 547 547 HOH HOH . H 4 HOH B 23 548 548 HOH HOH . H 4 HOH B 24 549 549 HOH HOH . H 4 HOH B 25 550 550 HOH HOH . H 4 HOH B 26 551 551 HOH HOH . H 4 HOH B 27 552 552 HOH HOH . H 4 HOH B 28 553 553 HOH HOH . H 4 HOH B 29 554 554 HOH HOH . H 4 HOH B 30 555 555 HOH HOH . H 4 HOH B 31 556 556 HOH HOH . H 4 HOH B 32 557 557 HOH HOH . H 4 HOH B 33 558 558 HOH HOH . H 4 HOH B 34 559 559 HOH HOH . H 4 HOH B 35 560 560 HOH HOH . H 4 HOH B 36 561 561 HOH HOH . H 4 HOH B 37 565 565 HOH HOH . H 4 HOH B 38 568 568 HOH HOH . H 4 HOH B 39 569 569 HOH HOH . H 4 HOH B 40 570 570 HOH HOH . H 4 HOH B 41 573 573 HOH HOH . H 4 HOH B 42 575 575 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 . . . E 2 82.084 20.874 26.43 1 18.82 ? PA NAD 450 B 1 HETATM 2 O O1A NAD . . . E 2 83.18 21.687 25.865 1 24.01 ? O1A NAD 450 B 1 HETATM 3 O O2A NAD . . . E 2 82.331 19.758 27.374 1 20.91 ? O2A NAD 450 B 1 HETATM 4 O O5B NAD . . . E 2 81.213 20.233 25.241 1 12.93 ? O5B NAD 450 B 1 HETATM 5 C C5B NAD . . . E 2 81.013 20.991 24.061 1 8.48 ? C5B NAD 450 B 1 HETATM 6 C C4B NAD . . . E 2 80.721 19.958 23.024 1 18.13 ? C4B NAD 450 B 1 HETATM 7 O O4B NAD . . . E 2 80.499 20.684 21.806 1 26.91 ? O4B NAD 450 B 1 HETATM 8 C C3B NAD . . . E 2 81.929 19.065 22.766 1 24.98 ? C3B NAD 450 B 1 HETATM 9 O O3B NAD . . . E 2 81.642 17.681 22.932 1 13.44 ? O3B NAD 450 B 1 HETATM 10 C C2B NAD . . . E 2 82.365 19.469 21.355 1 27.45 ? C2B NAD 450 B 1 HETATM 11 O O2B NAD . . . E 2 83.018 18.475 20.568 1 28.9 ? O2B NAD 450 B 1 HETATM 12 C C1B NAD . . . E 2 81.04 19.868 20.764 1 25.73 ? C1B NAD 450 B 1 HETATM 13 N N9A NAD . . . E 2 81.151 20.637 19.527 1 22.06 ? N9A NAD 450 B 1 HETATM 14 C C8A NAD . . . E 2 81.934 21.715 19.339 1 22 ? C8A NAD 450 B 1 HETATM 15 N N7A NAD . . . E 2 81.508 22.444 18.306 1 26.99 ? N7A NAD 450 B 1 HETATM 16 C C5A NAD . . . E 2 80.448 21.772 17.879 1 23.64 ? C5A NAD 450 B 1 HETATM 17 C C6A NAD . . . E 2 79.797 22.037 16.684 1 26.48 ? C6A NAD 450 B 1 HETATM 18 N N6A NAD . . . E 2 80.244 22.99 15.866 1 34.59 ? N6A NAD 450 B 1 HETATM 19 N N1A NAD . . . E 2 78.884 21.126 16.288 1 23.52 ? N1A NAD 450 B 1 HETATM 20 C C2A NAD . . . E 2 78.668 20.017 16.989 1 21.98 ? C2A NAD 450 B 1 HETATM 21 N N3A NAD . . . E 2 79.34 19.745 18.109 1 21.81 ? N3A NAD 450 B 1 HETATM 22 C C4A NAD . . . E 2 80.226 20.623 18.589 1 17.86 ? C4A NAD 450 B 1 HETATM 23 O O3 NAD . . . E 2 81.241 21.974 27.204 1 19.05 ? O3 NAD 450 B 1 HETATM 24 P PN NAD . . . E 2 80.093 22.002 28.296 1 19.96 ? PN NAD 450 B 1 HETATM 25 O O1N NAD . . . E 2 80.674 22.362 29.616 1 17.83 ? O1N NAD 450 B 1 HETATM 26 O O2N NAD . . . E 2 79.28 20.759 28.129 1 9.48 ? O2N NAD 450 B 1 HETATM 27 O O5D NAD . . . E 2 79.304 23.329 27.859 1 18.65 ? O5D NAD 450 B 1 HETATM 28 C C5D NAD . . . E 2 78.721 23.514 26.571 1 25.25 ? C5D NAD 450 B 1 HETATM 29 C C4D NAD . . . E 2 78.235 24.947 26.538 1 21.79 ? C4D NAD 450 B 1 HETATM 30 O O4D NAD . . . E 2 77.393 25.152 27.686 1 20.38 ? O4D NAD 450 B 1 HETATM 31 C C3D NAD . . . E 2 79.383 25.934 26.639 1 21.17 ? C3D NAD 450 B 1 HETATM 32 O O3D NAD . . . E 2 79.172 27.025 25.748 1 25.4 ? O3D NAD 450 B 1 HETATM 33 C C2D NAD . . . E 2 79.237 26.522 28.025 1 22.68 ? C2D NAD 450 B 1 HETATM 34 O O2D NAD . . . E 2 79.669 27.888 28.068 1 22.73 ? O2D NAD 450 B 1 HETATM 35 C C1D NAD . . . E 2 77.745 26.452 28.189 1 25.08 ? C1D NAD 450 B 1 HETATM 36 N N1N NAD . . . E 2 77.316 26.776 29.575 1 29.89 ? N1N NAD 450 B 1 HETATM 37 C C2N NAD . . . E 2 76.202 27.621 29.786 1 29.33 ? C2N NAD 450 B 1 HETATM 38 C C3N NAD . . . E 2 75.776 27.906 31.087 1 21.43 ? C3N NAD 450 B 1 HETATM 39 C C7N NAD . . . E 2 74.544 28.762 31.388 1 11.61 ? C7N NAD 450 B 1 HETATM 40 O O7N NAD . . . E 2 74.531 29.426 32.425 1 11.95 ? O7N NAD 450 B 1 HETATM 41 N N7N NAD . . . E 2 73.626 28.843 30.438 1 2 ? N7N NAD 450 B 1 HETATM 42 C C4N NAD . . . E 2 76.485 27.378 32.168 1 26.41 ? C4N NAD 450 B 1 HETATM 43 C C5N NAD . . . E 2 77.592 26.553 31.972 1 27.29 ? C5N NAD 450 B 1 HETATM 44 C C6N NAD . . . E 2 78.007 26.243 30.68 1 25.08 ? C6N NAD 450 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 660 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 44 #