data_4PGF # _model_server_result.job_id fE30AM-4ul6nv4Aa3TGtfA _model_server_result.datetime_utc '2025-02-16 15:01:03' _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 4pgf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4PGF # _exptl.entry_id 4PGF _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 4PGF _cell.length_a 97.597 _cell.length_b 102.74 _cell.length_c 175.018 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PGF _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 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 97.597 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 # 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 THR 407 A THR 407 1_555 A N ALY 408 A ALY 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C ALY 408 A ALY 408 1_555 A N LEU 409 A LEU 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale3 B C THR 407 B THR 407 1_555 B N ALY 408 B ALY 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 B C ALY 408 B ALY 408 1_555 B N LEU 409 B LEU 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _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 299 n n PA O2A NAD sing 300 n n PA O5B NAD sing 301 n n PA O3 NAD sing 302 n n O2A HOA2 NAD sing 303 n n O5B C5B NAD sing 304 n n C5B C4B NAD sing 305 n n C5B H51A NAD sing 306 n n C5B H52A NAD sing 307 n n C4B O4B NAD sing 308 n n C4B C3B NAD sing 309 n n C4B H4B NAD sing 310 n n O4B C1B NAD sing 311 n n C3B O3B NAD sing 312 n n C3B C2B NAD sing 313 n n C3B H3B NAD sing 314 n n O3B HO3A NAD sing 315 n n C2B O2B NAD sing 316 n n C2B C1B NAD sing 317 n n C2B H2B NAD sing 318 n n O2B HO2A NAD sing 319 n n C1B N9A NAD sing 320 n n C1B H1B NAD sing 321 n n N9A C8A NAD sing 322 n y N9A C4A NAD sing 323 n y C8A N7A NAD doub 324 n y C8A H8A NAD sing 325 n n N7A C5A NAD sing 326 n y C5A C6A NAD sing 327 n y C5A C4A NAD doub 328 n y C6A N6A NAD sing 329 n n C6A N1A NAD doub 330 n y N6A H61A NAD sing 331 n n N6A H62A NAD sing 332 n n N1A C2A NAD sing 333 n y C2A N3A NAD doub 334 n y C2A H2A NAD sing 335 n n N3A C4A NAD sing 336 n y O3 PN NAD sing 337 n n PN O1N NAD doub 338 n n PN O2N NAD sing 339 n n PN O5D NAD sing 340 n n O5D C5D NAD sing 341 n n C5D C4D NAD sing 342 n n C5D H51N NAD sing 343 n n C5D H52N NAD sing 344 n n C4D O4D NAD sing 345 n n C4D C3D NAD sing 346 n n C4D H4D NAD sing 347 n n O4D C1D NAD sing 348 n n C3D O3D NAD sing 349 n n C3D C2D NAD sing 350 n n C3D H3D NAD sing 351 n n O3D HO3N NAD sing 352 n n C2D O2D NAD sing 353 n n C2D C1D NAD sing 354 n n C2D H2D NAD sing 355 n n O2D HO2N NAD sing 356 n n C1D N1N NAD sing 357 n n C1D H1D NAD sing 358 n n N1N C2N NAD sing 359 n y N1N C6N NAD doub 360 n y C2N C3N NAD doub 361 n y C2N H2N NAD sing 362 n n C3N C7N NAD sing 363 n n C3N C4N NAD sing 364 n y C7N O7N NAD doub 365 n n C7N N7N NAD sing 366 n n N7N H71N NAD sing 367 n n N7N H72N NAD sing 368 n n C4N C5N NAD doub 369 n y C4N H4N NAD sing 370 n n C5N C6N NAD sing 371 n y C5N H5N NAD sing 372 n n C6N H6N NAD sing 373 n n # _atom_sites.entry_id 4PGF _atom_sites.fract_transf_matrix[1][1] 0.010246 _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] 0.009733 _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] 0.005714 _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 1 501 501 NAD NAD . D 3 ADN A 1 502 502 ADN ADN . E 2 NAD B 1 501 501 NAD NAD . F 3 ADN B 1 502 502 ADN ADN . G 4 HOH A 1 601 610 HOH HOH . G 4 HOH A 2 602 612 HOH HOH . G 4 HOH A 3 603 601 HOH HOH . G 4 HOH A 4 604 611 HOH HOH . G 4 HOH A 5 605 607 HOH HOH . G 4 HOH A 6 606 606 HOH HOH . G 4 HOH A 7 607 602 HOH HOH . G 4 HOH A 8 608 609 HOH HOH . G 4 HOH A 9 609 613 HOH HOH . G 4 HOH A 10 610 603 HOH HOH . G 4 HOH A 11 611 604 HOH HOH . G 4 HOH A 12 612 608 HOH HOH . G 4 HOH A 13 613 605 HOH HOH . H 4 HOH B 1 601 609 HOH HOH . H 4 HOH B 2 602 608 HOH HOH . H 4 HOH B 3 603 601 HOH HOH . H 4 HOH B 4 604 602 HOH HOH . H 4 HOH B 5 605 606 HOH HOH . H 4 HOH B 6 606 607 HOH HOH . H 4 HOH B 7 607 603 HOH HOH . H 4 HOH B 8 608 611 HOH HOH . H 4 HOH B 9 609 610 HOH HOH . H 4 HOH B 10 610 605 HOH HOH . H 4 HOH B 11 611 604 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 . . . C 2 47.27 -11.448 -63.118 1 47.82 ? PA NAD 501 A 1 HETATM 2 O O1A NAD . . . C 2 47.641 -12.229 -64.34 1 51.11 ? O1A NAD 501 A 1 HETATM 3 O O2A NAD . . . C 2 47.587 -10.03 -62.754 1 51.92 ? O2A NAD 501 A 1 HETATM 4 O O5B NAD . . . C 2 48.099 -12.296 -61.831 1 50.06 ? O5B NAD 501 A 1 HETATM 5 C C5B NAD . . . C 2 48.952 -13.263 -62.324 1 52.23 ? C5B NAD 501 A 1 HETATM 6 C C4B NAD . . . C 2 50.13 -13.293 -61.418 1 53.34 ? C4B NAD 501 A 1 HETATM 7 O O4B NAD . . . C 2 50.478 -14.653 -61.177 1 54.31 ? O4B NAD 501 A 1 HETATM 8 C C3B NAD . . . C 2 51.299 -12.636 -62.233 1 53.56 ? C3B NAD 501 A 1 HETATM 9 O O3B NAD . . . C 2 52.013 -11.877 -61.328 1 53.26 ? O3B NAD 501 A 1 HETATM 10 C C2B NAD . . . C 2 52.05 -13.867 -62.694 1 55.92 ? C2B NAD 501 A 1 HETATM 11 O O2B NAD . . . C 2 53.407 -13.639 -62.856 1 55.04 ? O2B NAD 501 A 1 HETATM 12 C C1B NAD . . . C 2 51.863 -14.736 -61.421 1 56.6 ? C1B NAD 501 A 1 HETATM 13 N N9A NAD . . . C 2 52.196 -16.132 -61.673 1 56.71 ? N9A NAD 501 A 1 HETATM 14 C C8A NAD . . . C 2 51.963 -16.927 -62.797 1 57.36 ? C8A NAD 501 A 1 HETATM 15 N N7A NAD . . . C 2 52.426 -18.167 -62.655 1 57.15 ? N7A NAD 501 A 1 HETATM 16 C C5A NAD . . . C 2 52.994 -18.184 -61.368 1 57.48 ? C5A NAD 501 A 1 HETATM 17 C C6A NAD . . . C 2 53.649 -19.201 -60.619 1 57.86 ? C6A NAD 501 A 1 HETATM 18 N N6A NAD . . . C 2 53.81 -20.444 -61.163 1 58.62 ? N6A NAD 501 A 1 HETATM 19 N N1A NAD . . . C 2 54.113 -18.937 -59.36 1 56.76 ? N1A NAD 501 A 1 HETATM 20 C C2A NAD . . . C 2 53.906 -17.661 -58.896 1 56.93 ? C2A NAD 501 A 1 HETATM 21 N N3A NAD . . . C 2 53.305 -16.607 -59.489 1 54.32 ? N3A NAD 501 A 1 HETATM 22 C C4A NAD . . . C 2 52.859 -16.915 -60.742 1 55.79 ? C4A NAD 501 A 1 HETATM 23 O O3 NAD . . . C 2 45.723 -11.903 -63.096 1 49.67 ? O3 NAD 501 A 1 HETATM 24 P PN NAD . . . C 2 44.909 -11.551 -61.785 1 48.62 ? PN NAD 501 A 1 HETATM 25 O O1N NAD . . . C 2 45.588 -11.548 -60.444 1 47.46 ? O1N NAD 501 A 1 HETATM 26 O O2N NAD . . . C 2 43.895 -10.601 -62.309 1 50 ? O2N NAD 501 A 1 HETATM 27 O O5D NAD . . . C 2 43.779 -12.907 -61.552 1 51.77 ? O5D NAD 501 A 1 HETATM 28 C C5D NAD . . . C 2 44.494 -14.075 -61.507 1 51.32 ? C5D NAD 501 A 1 HETATM 29 C C4D NAD . . . C 2 43.527 -15.25 -61.388 1 52.36 ? C4D NAD 501 A 1 HETATM 30 O O4D NAD . . . C 2 42.445 -14.866 -60.517 1 53.31 ? O4D NAD 501 A 1 HETATM 31 C C3D NAD . . . C 2 42.89 -15.507 -62.79 1 54.79 ? C3D NAD 501 A 1 HETATM 32 O O3D NAD . . . C 2 42.606 -16.871 -62.845 1 54.74 ? O3D NAD 501 A 1 HETATM 33 C C2D NAD . . . C 2 41.613 -14.656 -62.725 1 52.72 ? C2D NAD 501 A 1 HETATM 34 O O2D NAD . . . C 2 40.581 -15.127 -63.506 1 54.3 ? O2D NAD 501 A 1 HETATM 35 C C1D NAD . . . C 2 41.232 -14.976 -61.243 1 53.69 ? C1D NAD 501 A 1 HETATM 36 N N1N NAD . . . C 2 40.317 -13.945 -60.585 1 54.5 ? N1N NAD 501 A 1 HETATM 37 C C2N NAD . . . C 2 39.493 -14.44 -59.601 1 55.56 ? C2N NAD 501 A 1 HETATM 38 C C3N NAD . . . C 2 38.631 -13.561 -58.915 1 57.97 ? C3N NAD 501 A 1 HETATM 39 C C7N NAD . . . C 2 37.721 -14.131 -57.861 1 58.34 ? C7N NAD 501 A 1 HETATM 40 O O7N NAD . . . C 2 36.735 -13.505 -57.494 1 57.61 ? O7N NAD 501 A 1 HETATM 41 N N7N NAD . . . C 2 38.02 -15.361 -57.321 1 59.01 ? N7N NAD 501 A 1 HETATM 42 C C4N NAD . . . C 2 38.636 -12.196 -59.225 1 55.37 ? C4N NAD 501 A 1 HETATM 43 C C5N NAD . . . C 2 39.481 -11.716 -60.213 1 54.23 ? C5N NAD 501 A 1 HETATM 44 C C6N NAD . . . C 2 40.341 -12.592 -60.898 1 55.04 ? C6N NAD 501 A 1 HETATM 45 H H51A NAD . . . C 2 49.244 -13.082 -63.39 1 62.67 ? H51A NAD 501 A 1 HETATM 46 H H52A NAD . . . C 2 48.457 -14.273 -62.29 1 62.67 ? H52A NAD 501 A 1 HETATM 47 H H4B NAD . . . C 2 49.891 -12.813 -60.438 1 64.01 ? H4B NAD 501 A 1 HETATM 48 H H3B NAD . . . C 2 50.939 -12.025 -63.107 1 64.28 ? H3B NAD 501 A 1 HETATM 49 H HO3A NAD . . . C 2 52.381 -11.137 -61.802 1 63.92 ? HO3A NAD 501 A 1 HETATM 50 H H2B NAD . . . C 2 51.569 -14.334 -63.591 1 67.11 ? H2B NAD 501 A 1 HETATM 51 H HO2A NAD . . . C 2 53.553 -12.738 -62.567 1 66.05 ? HO2A NAD 501 A 1 HETATM 52 H H1B NAD . . . C 2 52.432 -14.363 -60.532 1 67.92 ? H1B NAD 501 A 1 HETATM 53 H H8A NAD . . . C 2 51.441 -16.523 -63.696 1 68.84 ? H8A NAD 501 A 1 HETATM 54 H H61A NAD . . . C 2 53.478 -20.643 -62.078 1 70.34 ? H61A NAD 501 A 1 HETATM 55 H H62A NAD . . . C 2 54.265 -21.168 -60.641 1 70.34 ? H62A NAD 501 A 1 HETATM 56 H H2A NAD . . . C 2 54.292 -17.483 -57.879 1 68.32 ? H2A NAD 501 A 1 HETATM 57 H H51N NAD . . . C 2 45.14 -14.117 -60.588 1 61.58 ? H51N NAD 501 A 1 HETATM 58 H H52N NAD . . . C 2 45.177 -14.178 -62.386 1 61.58 ? H52N NAD 501 A 1 HETATM 59 H H4D NAD . . . C 2 44.036 -16.132 -60.926 1 62.84 ? H4D NAD 501 A 1 HETATM 60 H H3D NAD . . . C 2 43.563 -15.156 -63.622 1 65.75 ? H3D NAD 501 A 1 HETATM 61 H HO3N NAD . . . C 2 41.682 -16.951 -63.074 1 65.68 ? HO3N NAD 501 A 1 HETATM 62 H H2D NAD . . . C 2 41.821 -13.571 -62.913 1 63.26 ? H2D NAD 501 A 1 HETATM 63 H HO2N NAD . . . C 2 39.774 -14.739 -63.165 1 65.17 ? HO2N NAD 501 A 1 HETATM 64 H H1D NAD . . . C 2 40.799 -15.999 -61.075 1 64.43 ? H1D NAD 501 A 1 HETATM 65 H H2N NAD . . . C 2 39.519 -15.526 -59.379 1 66.67 ? H2N NAD 501 A 1 HETATM 66 H H71N NAD . . . C 2 38.829 -15.867 -57.627 1 70.81 ? H71N NAD 501 A 1 HETATM 67 H H72N NAD . . . C 2 37.454 -15.789 -56.62 1 70.81 ? H72N NAD 501 A 1 HETATM 68 H H4N NAD . . . C 2 37.963 -11.504 -58.706 1 66.44 ? H4N NAD 501 A 1 HETATM 69 H H5N NAD . . . C 2 39.497 -10.651 -60.474 1 65.08 ? H5N NAD 501 A 1 HETATM 70 H H6N NAD . . . C 2 41.035 -12.23 -61.688 1 66.05 ? H6N NAD 501 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 70 #