data_6ZDI # _model_server_result.job_id ANuPKdQAVU1kj11BZTlqBQ _model_server_result.datetime_utc '2025-01-05 12:22:27' _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 6zdi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6ZDI # _exptl.entry_id 6ZDI _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 1 _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 6ZDI _cell.length_a 91.254 _cell.length_b 91.254 _cell.length_c 133.167 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ZDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall 'I 4 2' _symmetry.space_group_name_H-M 'I 4 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 91.254 0 3 'crystal symmetry operation' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 6_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 91.254 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 A SG CYS 255 A CYS 255 1_555 A SG CYS 255 A CYS 255 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A O GLU 50 A GLU 50 1_555 C NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc2 A O LEU 53 A LEU 53 1_555 C NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc3 A O PRO 54 A PRO 54 1_555 C NA NA . A NA 302 1_555 ? B ? ? ? ? ? ? ? ? ? ? 3.114 ? metalc ? metalc4 A O ALA 56 A ALA 56 1_555 C NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc5 C NA NA . A NA 302 1_555 E O HOH . A HOH 447 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.251 ? metalc ? metalc6 C NA NA . A NA 302 1_555 E O HOH . A HOH 447 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.388 ? # _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 6ZDI _atom_sites.fract_transf_matrix[1][1] 0.010958 _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] 0.010958 _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] 0.007509 _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 B 2 NAD A 1 301 1 NAD NAD . C 3 NA A 1 302 1 NA NA . D 4 QFT A 1 303 1 QFT B27 . E 5 HOH A 1 401 14 HOH HOH . E 5 HOH A 2 402 22 HOH HOH . E 5 HOH A 3 403 5 HOH HOH . E 5 HOH A 4 404 10 HOH HOH . E 5 HOH A 5 405 42 HOH HOH . E 5 HOH A 6 406 47 HOH HOH . E 5 HOH A 7 407 7 HOH HOH . E 5 HOH A 8 408 60 HOH HOH . E 5 HOH A 9 409 53 HOH HOH . E 5 HOH A 10 410 30 HOH HOH . E 5 HOH A 11 411 51 HOH HOH . E 5 HOH A 12 412 6 HOH HOH . E 5 HOH A 13 413 55 HOH HOH . E 5 HOH A 14 414 19 HOH HOH . E 5 HOH A 15 415 17 HOH HOH . E 5 HOH A 16 416 12 HOH HOH . E 5 HOH A 17 417 48 HOH HOH . E 5 HOH A 18 418 16 HOH HOH . E 5 HOH A 19 419 59 HOH HOH . E 5 HOH A 20 420 25 HOH HOH . E 5 HOH A 21 421 21 HOH HOH . E 5 HOH A 22 422 39 HOH HOH . E 5 HOH A 23 423 57 HOH HOH . E 5 HOH A 24 424 61 HOH HOH . E 5 HOH A 25 425 50 HOH HOH . E 5 HOH A 26 426 35 HOH HOH . E 5 HOH A 27 427 40 HOH HOH . E 5 HOH A 28 428 41 HOH HOH . E 5 HOH A 29 429 28 HOH HOH . E 5 HOH A 30 430 29 HOH HOH . E 5 HOH A 31 431 18 HOH HOH . E 5 HOH A 32 432 13 HOH HOH . E 5 HOH A 33 433 58 HOH HOH . E 5 HOH A 34 434 36 HOH HOH . E 5 HOH A 35 435 24 HOH HOH . E 5 HOH A 36 436 49 HOH HOH . E 5 HOH A 37 437 56 HOH HOH . E 5 HOH A 38 438 38 HOH HOH . E 5 HOH A 39 439 27 HOH HOH . E 5 HOH A 40 440 54 HOH HOH . E 5 HOH A 41 441 26 HOH HOH . E 5 HOH A 42 442 8 HOH HOH . E 5 HOH A 43 443 15 HOH HOH . E 5 HOH A 44 444 46 HOH HOH . E 5 HOH A 45 445 34 HOH HOH . E 5 HOH A 46 446 31 HOH HOH . E 5 HOH A 47 447 52 HOH HOH . E 5 HOH A 48 448 32 HOH HOH . E 5 HOH A 49 449 23 HOH HOH . E 5 HOH A 50 450 37 HOH HOH . E 5 HOH A 51 451 43 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 . . . B 2 -15.696 32.865 -18.597 1 27.93 ? PA NAD 301 A 1 HETATM 2 O O1A NAD . . . B 2 -14.841 32.275 -19.644 1 27.37 ? O1A NAD 301 A 1 HETATM 3 O O2A NAD . . . B 2 -16.626 31.793 -17.953 1 24.21 ? O2A NAD 301 A 1 HETATM 4 O O5B NAD . . . B 2 -16.64 34.041 -19.158 1 21.27 ? O5B NAD 301 A 1 HETATM 5 C C5B NAD . . . B 2 -16.05 35.189 -19.797 1 28.33 ? C5B NAD 301 A 1 HETATM 6 C C4B NAD . . . B 2 -17.066 35.797 -20.725 1 24.35 ? C4B NAD 301 A 1 HETATM 7 O O4B NAD . . . B 2 -16.464 36.895 -21.447 1 27.94 ? O4B NAD 301 A 1 HETATM 8 C C3B NAD . . . B 2 -17.623 34.829 -21.776 1 30.68 ? C3B NAD 301 A 1 HETATM 9 O O3B NAD . . . B 2 -19.042 34.923 -21.86 1 28.82 ? O3B NAD 301 A 1 HETATM 10 C C2B NAD . . . B 2 -16.926 35.273 -23.067 1 27.37 ? C2B NAD 301 A 1 HETATM 11 O O2B NAD . . . B 2 -17.749 35.046 -24.204 1 28.81 ? O2B NAD 301 A 1 HETATM 12 C C1B NAD . . . B 2 -16.761 36.767 -22.82 1 24.4 ? C1B NAD 301 A 1 HETATM 13 N N9A NAD . . . B 2 -15.694 37.392 -23.592 1 30.87 ? N9A NAD 301 A 1 HETATM 14 C C8A NAD . . . B 2 -14.439 36.898 -23.835 1 28.02 ? C8A NAD 301 A 1 HETATM 15 N N7A NAD . . . B 2 -13.723 37.633 -24.652 1 27.59 ? N7A NAD 301 A 1 HETATM 16 C C5A NAD . . . B 2 -14.562 38.693 -24.961 1 28.5 ? C5A NAD 301 A 1 HETATM 17 C C6A NAD . . . B 2 -14.421 39.793 -25.824 1 27.3 ? C6A NAD 301 A 1 HETATM 18 N N6A NAD . . . B 2 -13.341 40.014 -26.575 1 31.02 ? N6A NAD 301 A 1 HETATM 19 N N1A NAD . . . B 2 -15.467 40.641 -25.938 1 29.15 ? N1A NAD 301 A 1 HETATM 20 C C2A NAD . . . B 2 -16.575 40.394 -25.234 1 27.52 ? C2A NAD 301 A 1 HETATM 21 N N3A NAD . . . B 2 -16.824 39.392 -24.387 1 26.87 ? N3A NAD 301 A 1 HETATM 22 C C4A NAD . . . B 2 -15.776 38.565 -24.302 1 31.73 ? C4A NAD 301 A 1 HETATM 23 O O3 NAD . . . B 2 -14.707 33.411 -17.474 1 24.91 ? O3 NAD 301 A 1 HETATM 24 P PN NAD . . . B 2 -14.845 33.877 -15.951 1 25.3 ? PN NAD 301 A 1 HETATM 25 O O1N NAD . . . B 2 -14.219 32.842 -15.096 1 20.2 ? O1N NAD 301 A 1 HETATM 26 O O2N NAD . . . B 2 -16.24 34.295 -15.687 1 20.24 ? O2N NAD 301 A 1 HETATM 27 O O5D NAD . . . B 2 -13.972 35.207 -15.958 1 25.96 ? O5D NAD 301 A 1 HETATM 28 C C5D NAD . . . B 2 -14.599 36.501 -16.008 1 21.58 ? C5D NAD 301 A 1 HETATM 29 C C4D NAD . . . B 2 -13.581 37.513 -15.545 1 22.77 ? C4D NAD 301 A 1 HETATM 30 O O4D NAD . . . B 2 -13.169 37.182 -14.199 1 26.22 ? O4D NAD 301 A 1 HETATM 31 C C3D NAD . . . B 2 -12.283 37.597 -16.375 1 22.7 ? C3D NAD 301 A 1 HETATM 32 O O3D NAD . . . B 2 -11.792 38.939 -16.454 1 22.58 ? O3D NAD 301 A 1 HETATM 33 C C2D NAD . . . B 2 -11.321 36.745 -15.552 1 23.51 ? C2D NAD 301 A 1 HETATM 34 O O2D NAD . . . B 2 -9.94 37.023 -15.775 1 24.81 ? O2D NAD 301 A 1 HETATM 35 C C1D NAD . . . B 2 -11.765 37.174 -14.164 1 23.91 ? C1D NAD 301 A 1 HETATM 36 N N1N NAD . . . B 2 -11.312 36.278 -13.034 1 25.01 ? N1N NAD 301 A 1 HETATM 37 C C2N NAD . . . B 2 -11.777 35.016 -12.994 1 24.04 ? C2N NAD 301 A 1 HETATM 38 C C3N NAD . . . B 2 -11.413 34.18 -11.957 1 21.56 ? C3N NAD 301 A 1 HETATM 39 C C7N NAD . . . B 2 -11.835 32.742 -11.891 1 25.92 ? C7N NAD 301 A 1 HETATM 40 O O7N NAD . . . B 2 -12.534 32.253 -12.816 1 32.59 ? O7N NAD 301 A 1 HETATM 41 N N7N NAD . . . B 2 -11.433 32.038 -10.857 1 26.65 ? N7N NAD 301 A 1 HETATM 42 C C4N NAD . . . B 2 -10.577 34.679 -10.965 1 26.6 ? C4N NAD 301 A 1 HETATM 43 C C5N NAD . . . B 2 -10.097 35.977 -11.047 1 26.6 ? C5N NAD 301 A 1 HETATM 44 C C6N NAD . . . B 2 -10.47 36.765 -12.1 1 23.5 ? C6N NAD 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 44 #