data_2DBR # _model_server_result.job_id f5AiuaYJLB5hmWo1TPT8Ew _model_server_result.datetime_utc '2024-11-22 20:48:55' _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 2dbr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":403}' # _entry.id 2DBR # _exptl.entry_id 2DBR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 113.76 _cell.angle_beta 91.17 _cell.angle_gamma 94 _cell.entry_id 2DBR _cell.length_a 68.052 _cell.length_b 85.443 _cell.length_c 107.132 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DBR _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J,K,L,Y,Z 1 1 C,D,M,N,O,P,Q,R,AA,BA 2 1 E,F,S,T,U,V,W,X,CA,DA 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 ? 3 I N N ? 3 L N N ? 3 O N N ? 3 R N N ? 3 U N N ? 3 X N N # _chem_comp.formula 'C21 H28 N7 O17 P3' _chem_comp.formula_weight 743.405 _chem_comp.id NAP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" # 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 NAP doub 224 n n PA O2A NAP sing 225 n n PA O5B NAP sing 226 n n PA O3 NAP sing 227 n n O2A HOA2 NAP sing 228 n n O5B C5B NAP sing 229 n n C5B C4B NAP sing 230 n n C5B H51A NAP sing 231 n n C5B H52A NAP sing 232 n n C4B O4B NAP sing 233 n n C4B C3B NAP sing 234 n n C4B H4B NAP sing 235 n n O4B C1B NAP sing 236 n n C3B O3B NAP sing 237 n n C3B C2B NAP sing 238 n n C3B H3B NAP sing 239 n n O3B HO3A NAP sing 240 n n C2B O2B NAP sing 241 n n C2B C1B NAP sing 242 n n C2B H2B NAP sing 243 n n O2B P2B NAP sing 244 n n C1B N9A NAP sing 245 n n C1B H1B NAP sing 246 n n N9A C8A NAP sing 247 n y N9A C4A NAP sing 248 n y C8A N7A NAP doub 249 n y C8A H8A NAP sing 250 n n N7A C5A NAP sing 251 n y C5A C6A NAP sing 252 n y C5A C4A NAP doub 253 n y C6A N6A NAP sing 254 n n C6A N1A NAP doub 255 n y N6A H61A NAP sing 256 n n N6A H62A NAP sing 257 n n N1A C2A NAP sing 258 n y C2A N3A NAP doub 259 n y C2A H2A NAP sing 260 n n N3A C4A NAP sing 261 n y O3 PN NAP sing 262 n n PN O1N NAP doub 263 n n PN O2N NAP sing 264 n n PN O5D NAP sing 265 n n O5D C5D NAP sing 266 n n C5D C4D NAP sing 267 n n C5D H51N NAP sing 268 n n C5D H52N NAP sing 269 n n C4D O4D NAP sing 270 n n C4D C3D NAP sing 271 n n C4D H4D NAP sing 272 n n O4D C1D NAP sing 273 n n C3D O3D NAP sing 274 n n C3D C2D NAP sing 275 n n C3D H3D NAP sing 276 n n O3D HO3N NAP sing 277 n n C2D O2D NAP sing 278 n n C2D C1D NAP sing 279 n n C2D H2D NAP sing 280 n n O2D HO2N NAP sing 281 n n C1D N1N NAP sing 282 n n C1D H1D NAP sing 283 n n N1N C2N NAP sing 284 n y N1N C6N NAP doub 285 n y C2N C3N NAP doub 286 n y C2N H2N NAP sing 287 n n C3N C7N NAP sing 288 n n C3N C4N NAP sing 289 n y C7N O7N NAP doub 290 n n C7N N7N NAP sing 291 n n N7N H71N NAP sing 292 n n N7N H72N NAP sing 293 n n C4N C5N NAP doub 294 n y C4N H4N NAP sing 295 n n C5N C6N NAP sing 296 n y C5N H5N NAP sing 297 n n C6N H6N NAP sing 298 n n P2B O1X NAP doub 299 n n P2B O2X NAP sing 300 n n P2B O3X NAP sing 301 n n O2X HOP2 NAP sing 302 n n O3X HOP3 NAP sing 303 n n # _atom_sites.entry_id 2DBR _atom_sites.fract_transf_matrix[1][1] 0.014695 _atom_sites.fract_transf_matrix[1][2] 0.001028 _atom_sites.fract_transf_matrix[1][3] 0.000784 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011732 _atom_sites.fract_transf_matrix[2][3] 0.005203 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.010213 _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 G 2 SO4 A 1 501 501 SO4 SO4 . H 2 SO4 A 1 507 507 SO4 SO4 . I 3 NAP A 1 401 401 NAP NAP . J 2 SO4 B 1 503 503 SO4 SO4 . K 2 SO4 B 1 509 509 SO4 SO4 . L 3 NAP B 1 402 402 NAP NAP . M 2 SO4 C 1 502 502 SO4 SO4 . N 2 SO4 C 1 508 508 SO4 SO4 . O 3 NAP C 1 403 403 NAP NAP . P 2 SO4 D 1 504 504 SO4 SO4 . Q 2 SO4 D 1 510 510 SO4 SO4 . R 3 NAP D 1 404 404 NAP NAP . S 2 SO4 E 1 505 505 SO4 SO4 . T 2 SO4 E 1 511 511 SO4 SO4 . U 3 NAP E 1 405 405 NAP NAP . V 2 SO4 F 1 506 506 SO4 SO4 . W 2 SO4 F 1 512 512 SO4 SO4 . X 3 NAP F 1 406 406 NAP NAP . Y 4 HOH A 1 508 1 HOH HOH . Y 4 HOH A 2 509 4 HOH HOH . Y 4 HOH A 3 510 13 HOH HOH . Y 4 HOH A 4 511 21 HOH HOH . Y 4 HOH A 5 512 22 HOH HOH . Y 4 HOH A 6 513 24 HOH HOH . Y 4 HOH A 7 514 31 HOH HOH . Y 4 HOH A 8 515 37 HOH HOH . Y 4 HOH A 9 516 57 HOH HOH . Y 4 HOH A 10 517 65 HOH HOH . Y 4 HOH A 11 518 67 HOH HOH . Z 4 HOH B 1 510 9 HOH HOH . Z 4 HOH B 2 511 11 HOH HOH . Z 4 HOH B 3 512 14 HOH HOH . Z 4 HOH B 4 513 16 HOH HOH . Z 4 HOH B 5 514 17 HOH HOH . Z 4 HOH B 6 515 18 HOH HOH . Z 4 HOH B 7 516 28 HOH HOH . Z 4 HOH B 8 517 30 HOH HOH . Z 4 HOH B 9 518 32 HOH HOH . Z 4 HOH B 10 519 34 HOH HOH . Z 4 HOH B 11 520 40 HOH HOH . Z 4 HOH B 12 521 41 HOH HOH . Z 4 HOH B 13 522 43 HOH HOH . Z 4 HOH B 14 523 45 HOH HOH . Z 4 HOH B 15 524 46 HOH HOH . Z 4 HOH B 16 525 49 HOH HOH . Z 4 HOH B 17 526 52 HOH HOH . Z 4 HOH B 18 527 54 HOH HOH . Z 4 HOH B 19 528 55 HOH HOH . Z 4 HOH B 20 529 56 HOH HOH . Z 4 HOH B 21 530 59 HOH HOH . Z 4 HOH B 22 531 76 HOH HOH . AA 4 HOH C 1 509 6 HOH HOH . AA 4 HOH C 2 510 7 HOH HOH . AA 4 HOH C 3 511 19 HOH HOH . AA 4 HOH C 4 512 20 HOH HOH . AA 4 HOH C 5 513 25 HOH HOH . AA 4 HOH C 6 514 26 HOH HOH . AA 4 HOH C 7 515 27 HOH HOH . AA 4 HOH C 8 516 33 HOH HOH . AA 4 HOH C 9 517 35 HOH HOH . AA 4 HOH C 10 518 42 HOH HOH . AA 4 HOH C 11 519 50 HOH HOH . AA 4 HOH C 12 520 51 HOH HOH . AA 4 HOH C 13 521 53 HOH HOH . AA 4 HOH C 14 522 70 HOH HOH . AA 4 HOH C 15 523 75 HOH HOH . AA 4 HOH C 16 524 78 HOH HOH . AA 4 HOH C 17 525 79 HOH HOH . AA 4 HOH C 18 526 80 HOH HOH . BA 4 HOH D 1 511 3 HOH HOH . BA 4 HOH D 2 512 5 HOH HOH . BA 4 HOH D 3 513 12 HOH HOH . BA 4 HOH D 4 514 23 HOH HOH . BA 4 HOH D 5 515 29 HOH HOH . BA 4 HOH D 6 516 44 HOH HOH . BA 4 HOH D 7 517 60 HOH HOH . BA 4 HOH D 8 518 61 HOH HOH . BA 4 HOH D 9 519 62 HOH HOH . BA 4 HOH D 10 520 63 HOH HOH . BA 4 HOH D 11 521 64 HOH HOH . BA 4 HOH D 12 522 68 HOH HOH . BA 4 HOH D 13 523 69 HOH HOH . BA 4 HOH D 14 524 74 HOH HOH . BA 4 HOH D 15 525 77 HOH HOH . BA 4 HOH D 16 526 81 HOH HOH . BA 4 HOH D 17 527 82 HOH HOH . CA 4 HOH E 1 512 8 HOH HOH . CA 4 HOH E 2 513 36 HOH HOH . CA 4 HOH E 3 514 38 HOH HOH . CA 4 HOH E 4 515 47 HOH HOH . CA 4 HOH E 5 516 48 HOH HOH . CA 4 HOH E 6 517 72 HOH HOH . DA 4 HOH F 1 513 2 HOH HOH . DA 4 HOH F 2 514 10 HOH HOH . DA 4 HOH F 3 515 15 HOH HOH . DA 4 HOH F 4 516 39 HOH HOH . DA 4 HOH F 5 517 58 HOH HOH . DA 4 HOH F 6 518 66 HOH HOH . DA 4 HOH F 7 519 71 HOH HOH . DA 4 HOH F 8 520 73 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 NAP . . . O 3 -17.554 17.509 -45.771 1 60.36 ? PA NAP 403 C 1 HETATM 2 O O1A NAP . . . O 3 -18.146 18.783 -45.305 1 57.2 ? O1A NAP 403 C 1 HETATM 3 O O2A NAP . . . O 3 -16.783 17.519 -47.033 1 69.18 ? O2A NAP 403 C 1 HETATM 4 O O5B NAP . . . O 3 -18.716 16.398 -45.875 1 62.05 ? O5B NAP 403 C 1 HETATM 5 C C5B NAP . . . O 3 -18.619 15.254 -46.73 1 61.8 ? C5B NAP 403 C 1 HETATM 6 C C4B NAP . . . O 3 -18.644 15.577 -48.23 1 59.48 ? C4B NAP 403 C 1 HETATM 7 O O4B NAP . . . O 3 -18.896 14.354 -48.95 1 63.12 ? O4B NAP 403 C 1 HETATM 8 C C3B NAP . . . O 3 -19.814 16.486 -48.612 1 60.51 ? C3B NAP 403 C 1 HETATM 9 O O3B NAP . . . O 3 -19.619 16.997 -49.934 1 51.29 ? O3B NAP 403 C 1 HETATM 10 C C2B NAP . . . O 3 -20.948 15.463 -48.617 1 59.07 ? C2B NAP 403 C 1 HETATM 11 O O2B NAP . . . O 3 -22.065 15.973 -49.349 1 63.28 ? O2B NAP 403 C 1 HETATM 12 C C1B NAP . . . O 3 -20.255 14.368 -49.428 1 57.44 ? C1B NAP 403 C 1 HETATM 13 N N9A NAP . . . O 3 -20.942 13.062 -49.279 1 55.81 ? N9A NAP 403 C 1 HETATM 14 C C8A NAP . . . O 3 -21.362 12.517 -48.138 1 53.77 ? C8A NAP 403 C 1 HETATM 15 N N7A NAP . . . O 3 -21.956 11.351 -48.382 1 50.19 ? N7A NAP 403 C 1 HETATM 16 C C5A NAP . . . O 3 -21.913 11.145 -49.694 1 50.08 ? C5A NAP 403 C 1 HETATM 17 C C6A NAP . . . O 3 -22.361 10.131 -50.533 1 45.88 ? C6A NAP 403 C 1 HETATM 18 N N6A NAP . . . O 3 -23.002 9.076 -50.038 1 43.7 ? N6A NAP 403 C 1 HETATM 19 N N1A NAP . . . O 3 -22.149 10.237 -51.853 1 46.87 ? N1A NAP 403 C 1 HETATM 20 C C2A NAP . . . O 3 -21.529 11.286 -52.367 1 50.97 ? C2A NAP 403 C 1 HETATM 21 N N3A NAP . . . O 3 -21.093 12.269 -51.596 1 52.63 ? N3A NAP 403 C 1 HETATM 22 C C4A NAP . . . O 3 -21.266 12.232 -50.267 1 53.51 ? C4A NAP 403 C 1 HETATM 23 O O3 NAP . . . O 3 -16.603 16.96 -44.594 1 57.42 ? O3 NAP 403 C 1 HETATM 24 P PN NAP . . . O 3 -15.007 17.17 -44.657 1 56.31 ? PN NAP 403 C 1 HETATM 25 O O1N NAP . . . O 3 -14.599 18.067 -43.553 1 51.08 ? O1N NAP 403 C 1 HETATM 26 O O2N NAP . . . O 3 -14.593 17.528 -46.032 1 52.25 ? O2N NAP 403 C 1 HETATM 27 O O5D NAP . . . O 3 -14.433 15.705 -44.314 1 50.54 ? O5D NAP 403 C 1 HETATM 28 C C5D NAP . . . O 3 -15.012 14.523 -44.873 1 49.89 ? C5D NAP 403 C 1 HETATM 29 C C4D NAP . . . O 3 -14.327 13.275 -44.313 1 52.21 ? C4D NAP 403 C 1 HETATM 30 O O4D NAP . . . O 3 -12.923 13.264 -44.612 1 55.65 ? O4D NAP 403 C 1 HETATM 31 C C3D NAP . . . O 3 -14.346 13.231 -42.787 1 51.57 ? C3D NAP 403 C 1 HETATM 32 O O3D NAP . . . O 3 -15.624 12.807 -42.305 1 50.19 ? O3D NAP 403 C 1 HETATM 33 C C2D NAP . . . O 3 -13.312 12.134 -42.544 1 51.51 ? C2D NAP 403 C 1 HETATM 34 O O2D NAP . . . O 3 -13.888 10.831 -42.672 1 52.27 ? O2D NAP 403 C 1 HETATM 35 C C1D NAP . . . O 3 -12.295 12.379 -43.664 1 56.43 ? C1D NAP 403 C 1 HETATM 36 N N1N NAP . . . O 3 -11.057 13.023 -43.169 1 59.14 ? N1N NAP 403 C 1 HETATM 37 C C2N NAP . . . O 3 -9.907 12.247 -42.967 1 53.63 ? C2N NAP 403 C 1 HETATM 38 C C3N NAP . . . O 3 -8.726 12.856 -42.553 1 52.45 ? C3N NAP 403 C 1 HETATM 39 C C7N NAP . . . O 3 -7.472 12.019 -42.295 1 50.71 ? C7N NAP 403 C 1 HETATM 40 O O7N NAP . . . O 3 -6.663 12.347 -41.429 1 51.8 ? O7N NAP 403 C 1 HETATM 41 N N7N NAP . . . O 3 -7.357 10.922 -43.038 1 49.02 ? N7N NAP 403 C 1 HETATM 42 C C4N NAP . . . O 3 -8.696 14.229 -42.342 1 52.92 ? C4N NAP 403 C 1 HETATM 43 C C5N NAP . . . O 3 -9.833 15.009 -42.54 1 58.01 ? C5N NAP 403 C 1 HETATM 44 C C6N NAP . . . O 3 -11.017 14.409 -42.953 1 56.67 ? C6N NAP 403 C 1 HETATM 45 P P2B NAP . . . O 3 -23.036 17.074 -48.687 1 64.1 ? P2B NAP 403 C 1 HETATM 46 O O1X NAP . . . O 3 -24.534 16.684 -49.124 1 61.85 ? O1X NAP 403 C 1 HETATM 47 O O2X NAP . . . O 3 -22.935 16.846 -47.096 1 63.55 ? O2X NAP 403 C 1 HETATM 48 O O3X NAP . . . O 3 -22.67 18.455 -49.075 1 60.01 ? O3X NAP 403 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #