data_1GYP # _model_server_result.job_id 73cx0V6rUzFPmaELsyJU1w _model_server_result.datetime_utc '2024-11-26 15:57:47' _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 1gyp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":361}' # _entry.id 1GYP # _exptl.entry_id 1GYP _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 90 _cell.angle_gamma 90 _cell.entry_id 1GYP _cell.length_a 99 _cell.length_b 126.5 _cell.length_c 138.9 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GYP _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,I,J,K,L,M,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 G N N ? 3 J N N ? 3 M 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 235 n n PA O2A NAD sing 236 n n PA O5B NAD sing 237 n n PA O3 NAD sing 238 n n O2A HOA2 NAD sing 239 n n O5B C5B NAD sing 240 n n C5B C4B NAD sing 241 n n C5B H51A NAD sing 242 n n C5B H52A NAD sing 243 n n C4B O4B NAD sing 244 n n C4B C3B NAD sing 245 n n C4B H4B NAD sing 246 n n O4B C1B NAD sing 247 n n C3B O3B NAD sing 248 n n C3B C2B NAD sing 249 n n C3B H3B NAD sing 250 n n O3B HO3A NAD sing 251 n n C2B O2B NAD sing 252 n n C2B C1B NAD sing 253 n n C2B H2B NAD sing 254 n n O2B HO2A NAD sing 255 n n C1B N9A NAD sing 256 n n C1B H1B NAD sing 257 n n N9A C8A NAD sing 258 n y N9A C4A NAD sing 259 n y C8A N7A NAD doub 260 n y C8A H8A NAD sing 261 n n N7A C5A NAD sing 262 n y C5A C6A NAD sing 263 n y C5A C4A NAD doub 264 n y C6A N6A NAD sing 265 n n C6A N1A NAD doub 266 n y N6A H61A NAD sing 267 n n N6A H62A NAD sing 268 n n N1A C2A NAD sing 269 n y C2A N3A NAD doub 270 n y C2A H2A NAD sing 271 n n N3A C4A NAD sing 272 n y O3 PN NAD sing 273 n n PN O1N NAD doub 274 n n PN O2N NAD sing 275 n n PN O5D NAD sing 276 n n O5D C5D NAD sing 277 n n C5D C4D NAD sing 278 n n C5D H51N NAD sing 279 n n C5D H52N NAD sing 280 n n C4D O4D NAD sing 281 n n C4D C3D NAD sing 282 n n C4D H4D NAD sing 283 n n O4D C1D NAD sing 284 n n C3D O3D NAD sing 285 n n C3D C2D NAD sing 286 n n C3D H3D NAD sing 287 n n O3D HO3N NAD sing 288 n n C2D O2D NAD sing 289 n n C2D C1D NAD sing 290 n n C2D H2D NAD sing 291 n n O2D HO2N NAD sing 292 n n C1D N1N NAD sing 293 n n C1D H1D NAD sing 294 n n N1N C2N NAD sing 295 n y N1N C6N NAD doub 296 n y C2N C3N NAD doub 297 n y C2N H2N NAD sing 298 n n C3N C7N NAD sing 299 n n C3N C4N NAD sing 300 n y C7N O7N NAD doub 301 n n C7N N7N NAD sing 302 n n N7N H71N NAD sing 303 n n N7N H72N NAD sing 304 n n C4N C5N NAD doub 305 n y C4N H4N NAD sing 306 n n C5N C6N NAD sing 307 n y C5N H5N NAD sing 308 n n C6N H6N NAD sing 309 n n # _atom_sites.entry_id 1GYP _atom_sites.fract_transf_matrix[1][1] 0.010101 _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] 0.007905 _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] 0.007199 _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 E 2 PO4 A 1 359 359 PO4 PO4 . F 2 PO4 A 1 360 360 PO4 PO4 . G 3 NAD A 1 361 361 NAD NAD . H 2 PO4 B 1 359 359 PO4 PO4 . I 2 PO4 B 1 360 360 PO4 PO4 . J 3 NAD B 1 361 361 NAD NAD . K 2 PO4 C 1 359 359 PO4 PO4 . L 2 PO4 C 1 360 360 PO4 PO4 . M 3 NAD C 1 361 361 NAD NAD . N 2 PO4 D 1 359 359 PO4 PO4 . O 2 PO4 D 1 360 360 PO4 PO4 . P 3 NAD D 1 361 361 NAD NAD . # 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 . . . J 3 55.364 48.931 74.896 1 19.84 ? PA NAD 361 B 1 HETATM 2 O O1A NAD . . . J 3 55.627 50.311 74.37 1 26 ? O1A NAD 361 B 1 HETATM 3 O O2A NAD . . . J 3 55.895 48.541 76.248 1 26.15 ? O2A NAD 361 B 1 HETATM 4 O O5B NAD . . . J 3 55.876 47.824 73.854 1 24.56 ? O5B NAD 361 B 1 HETATM 5 C C5B NAD . . . J 3 56.048 48.156 72.481 1 18.22 ? C5B NAD 361 B 1 HETATM 6 C C4B NAD . . . J 3 57.441 47.693 72.164 1 20.77 ? C4B NAD 361 B 1 HETATM 7 O O4B NAD . . . J 3 57.594 47.716 70.745 1 23.44 ? O4B NAD 361 B 1 HETATM 8 C C3B NAD . . . J 3 58.43 48.657 72.773 1 20.13 ? C3B NAD 361 B 1 HETATM 9 O O3B NAD . . . J 3 59.326 47.989 73.665 1 21.84 ? O3B NAD 361 B 1 HETATM 10 C C2B NAD . . . J 3 59.105 49.285 71.57 1 21.12 ? C2B NAD 361 B 1 HETATM 11 O O2B NAD . . . J 3 60.493 49.417 71.835 1 17.09 ? O2B NAD 361 B 1 HETATM 12 C C1B NAD . . . J 3 58.884 48.271 70.47 1 27.74 ? C1B NAD 361 B 1 HETATM 13 N N9A NAD . . . J 3 58.928 48.823 69.09 1 33.69 ? N9A NAD 361 B 1 HETATM 14 C C8A NAD . . . J 3 58.639 50.077 68.719 1 36.98 ? C8A NAD 361 B 1 HETATM 15 N N7A NAD . . . J 3 58.765 50.233 67.392 1 40.6 ? N7A NAD 361 B 1 HETATM 16 C C5A NAD . . . J 3 59.136 49.036 66.968 1 41.35 ? C5A NAD 361 B 1 HETATM 17 C C6A NAD . . . J 3 59.384 48.699 65.638 1 41.08 ? C6A NAD 361 B 1 HETATM 18 N N6A NAD . . . J 3 59.247 49.585 64.647 1 40.18 ? N6A NAD 361 B 1 HETATM 19 N N1A NAD . . . J 3 59.768 47.42 65.41 1 38.89 ? N1A NAD 361 B 1 HETATM 20 C C2A NAD . . . J 3 59.894 46.544 66.411 1 37.29 ? C2A NAD 361 B 1 HETATM 21 N N3A NAD . . . J 3 59.635 46.868 67.676 1 38.56 ? N3A NAD 361 B 1 HETATM 22 C C4A NAD . . . J 3 59.252 48.128 67.995 1 38.92 ? C4A NAD 361 B 1 HETATM 23 O O3 NAD . . . J 3 53.786 48.727 74.843 1 21.91 ? O3 NAD 361 B 1 HETATM 24 P PN NAD . . . J 3 52.809 47.492 75.036 1 20.91 ? PN NAD 361 B 1 HETATM 25 O O1N NAD . . . J 3 51.945 47.757 76.232 1 25.95 ? O1N NAD 361 B 1 HETATM 26 O O2N NAD . . . J 3 53.611 46.228 74.907 1 25.51 ? O2N NAD 361 B 1 HETATM 27 O O5D NAD . . . J 3 51.858 47.706 73.781 1 22.5 ? O5D NAD 361 B 1 HETATM 28 C C5D NAD . . . J 3 52.074 47.036 72.545 1 23.6 ? C5D NAD 361 B 1 HETATM 29 C C4D NAD . . . J 3 50.685 46.684 72.05 1 26.73 ? C4D NAD 361 B 1 HETATM 30 O O4D NAD . . . J 3 50.053 45.844 73.036 1 28.03 ? O4D NAD 361 B 1 HETATM 31 C C3D NAD . . . J 3 49.79 47.901 71.868 1 22.38 ? C3D NAD 361 B 1 HETATM 32 O O3D NAD . . . J 3 49.167 47.856 70.585 1 29.86 ? O3D NAD 361 B 1 HETATM 33 C C2D NAD . . . J 3 48.757 47.759 72.967 1 25.52 ? C2D NAD 361 B 1 HETATM 34 O O2D NAD . . . J 3 47.479 48.314 72.662 1 31.72 ? O2D NAD 361 B 1 HETATM 35 C C1D NAD . . . J 3 48.684 46.262 73.128 1 26.75 ? C1D NAD 361 B 1 HETATM 36 N N1N NAD . . . J 3 48.11 45.841 74.419 1 25.38 ? N1N NAD 361 B 1 HETATM 37 C C2N NAD . . . J 3 48.648 46.361 75.603 1 28.91 ? C2N NAD 361 B 1 HETATM 38 C C3N NAD . . . J 3 48.038 46.092 76.824 1 31.18 ? C3N NAD 361 B 1 HETATM 39 C C7N NAD . . . J 3 48.609 46.698 78.109 1 28.43 ? C7N NAD 361 B 1 HETATM 40 O O7N NAD . . . J 3 47.849 47.041 79.017 1 31.97 ? O7N NAD 361 B 1 HETATM 41 N N7N NAD . . . J 3 49.926 46.837 78.174 1 24.1 ? N7N NAD 361 B 1 HETATM 42 C C4N NAD . . . J 3 46.917 45.263 76.848 1 31.47 ? C4N NAD 361 B 1 HETATM 43 C C5N NAD . . . J 3 46.391 44.723 75.672 1 29.9 ? C5N NAD 361 B 1 HETATM 44 C C6N NAD . . . J 3 46.982 45.015 74.448 1 26.88 ? C6N NAD 361 B 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #