data_4J9U # _model_server_result.job_id rugFIjX-HdzY4JRvZHDaEw _model_server_result.datetime_utc '2025-03-04 23:32:13' _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 4j9u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":501}' # _entry.id 4J9U # _exptl.entry_id 4J9U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 5 _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 99.32 _cell.angle_gamma 90 _cell.entry_id 4J9U _cell.length_a 133.725 _cell.length_b 146.627 _cell.length_c 163.672 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4J9U _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,K,L,M,N,O,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA 1 1 C,D,E,F,G,H,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA 2 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 ? 5 W N N ? 5 Z N N ? 5 CA N N ? 5 FA 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 disulf ? disulf1 A SG CYS 251 A CYS 251 1_555 A SG CYS 348 A CYS 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 B SG CYS 251 B CYS 251 1_555 B SG CYS 348 B CYS 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 C SG CYS 251 C CYS 251 1_555 C SG CYS 348 C CYS 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf4 D SG CYS 251 D CYS 251 1_555 D SG CYS 348 D CYS 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc1 A O THR 111 A THR 111 1_555 L K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc2 A O THR 112 A THR 112 1_555 L K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc3 A O ILE 220 A ILE 220 1_555 L K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.264 ? metalc ? metalc4 A O GLY 221 A GLY 221 1_555 L K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc5 A O THR 320 A THR 320 1_555 L K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc6 A O ALA 321 A ALA 321 1_555 L K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc7 A O ASN 437 A ASN 437 1_555 L K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc8 A O LEU 438 A LEU 438 1_555 L K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc9 B O THR 111 B THR 111 1_555 O K K . B K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.102 ? metalc ? metalc10 B O THR 112 B THR 112 1_555 O K K . B K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc11 B O GLY 221 B GLY 221 1_555 O K K . B K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc12 B O THR 320 B THR 320 1_555 O K K . B K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc13 B O ALA 321 B ALA 321 1_555 O K K . B K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? metalc ? metalc14 B O ASN 437 B ASN 437 1_555 O K K . B K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc15 B O LEU 438 B LEU 438 1_555 O K K . B K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? metalc ? metalc16 C O THR 111 C THR 111 1_555 R K K . C K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc17 C O THR 112 C THR 112 1_555 R K K . C K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc18 C O ILE 220 C ILE 220 1_555 R K K . C K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.267 ? metalc ? metalc19 C O GLY 221 C GLY 221 1_555 R K K . C K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc20 C O THR 320 C THR 320 1_555 R K K . C K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc21 C O ALA 321 C ALA 321 1_555 R K K . C K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc22 C O ASN 437 C ASN 437 1_555 R K K . C K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.85 ? metalc ? metalc23 C O LEU 438 C LEU 438 1_555 R K K . C K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc24 D O THR 111 D THR 111 1_555 V K K . D K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc25 D O THR 112 D THR 112 1_555 V K K . D K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.905 ? metalc ? metalc26 D O ILE 220 D ILE 220 1_555 V K K . D K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.3 ? metalc ? metalc27 D O GLY 221 D GLY 221 1_555 V K K . D K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc28 D O THR 320 D THR 320 1_555 V K K . D K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc29 D O ALA 321 D ALA 321 1_555 V K K . D K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.857 ? metalc ? metalc30 D O ASN 437 D ASN 437 1_555 V K K . D K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc31 D O LEU 438 D LEU 438 1_555 V K K . D K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? # _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 4J9U _atom_sites.fract_transf_matrix[1][1] 0.007478 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001227 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00682 _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] 0.006191 _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 I 3 TBR A 1 501 501 TBR TBR . J 3 TBR A 1 502 502 TBR TBR . K 3 TBR A 1 503 503 TBR TBR . L 4 K A 1 504 601 K K . M 3 TBR B 1 501 501 TBR TBR . N 3 TBR B 1 502 502 TBR TBR . O 4 K B 1 503 601 K K . P 3 TBR C 1 501 501 TBR TBR . Q 3 TBR C 1 502 502 TBR TBR . R 4 K C 1 503 601 K K . S 3 TBR D 1 501 501 TBR TBR . T 3 TBR D 1 502 502 TBR TBR . U 3 TBR D 1 503 503 TBR TBR . V 4 K D 1 504 601 K K . W 5 NAD E 1 501 501 NAD NAD . X 3 TBR E 1 502 601 TBR TBR . Y 3 TBR E 1 503 602 TBR TBR . Z 5 NAD F 1 501 501 NAD NAD . AA 3 TBR F 1 502 601 TBR TBR . BA 3 TBR F 1 503 602 TBR TBR . CA 5 NAD G 1 501 501 NAD NAD . DA 3 TBR G 1 502 601 TBR TBR . EA 3 TBR G 1 503 602 TBR TBR . FA 5 NAD H 1 501 501 NAD NAD . GA 3 TBR H 1 502 601 TBR TBR . HA 3 TBR H 1 503 602 TBR TBR . # 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 . . . Z 5 31.373 75.971 121.309 1 41.79 ? PA NAD 501 F 1 HETATM 2 O O1A NAD . . . Z 5 30.832 74.643 121.787 1 59.68 ? O1A NAD 501 F 1 HETATM 3 O O2A NAD . . . Z 5 31.346 77.134 122.262 1 42.07 ? O2A NAD 501 F 1 HETATM 4 O O5B NAD . . . Z 5 30.541 76.324 119.969 1 65.65 ? O5B NAD 501 F 1 HETATM 5 C C5B NAD . . . Z 5 30.986 77.221 118.947 1 67.3 ? C5B NAD 501 F 1 HETATM 6 C C4B NAD . . . Z 5 29.844 78.151 118.514 1 71.06 ? C4B NAD 501 F 1 HETATM 7 O O4B NAD . . . Z 5 29.885 78.521 117.124 1 70.32 ? O4B NAD 501 F 1 HETATM 8 C C3B NAD . . . Z 5 28.465 77.544 118.721 1 72.32 ? C3B NAD 501 F 1 HETATM 9 O O3B NAD . . . Z 5 27.683 78.506 119.439 1 70.41 ? O3B NAD 501 F 1 HETATM 10 C C2B NAD . . . Z 5 27.889 77.406 117.328 1 71.06 ? C2B NAD 501 F 1 HETATM 11 O O2B NAD . . . Z 5 26.469 77.533 117.351 1 77.49 ? O2B NAD 501 F 1 HETATM 12 C C1B NAD . . . Z 5 28.523 78.618 116.681 1 68.95 ? C1B NAD 501 F 1 HETATM 13 N N9A NAD . . . Z 5 28.343 78.801 115.204 1 75.71 ? N9A NAD 501 F 1 HETATM 14 C C8A NAD . . . Z 5 28.314 80.022 114.633 1 82.31 ? C8A NAD 501 F 1 HETATM 15 N N7A NAD . . . Z 5 28.125 79.968 113.293 1 46.15 ? N7A NAD 501 F 1 HETATM 16 C C5A NAD . . . Z 5 28.015 78.675 112.976 1 46.25 ? C5A NAD 501 F 1 HETATM 17 C C6A NAD . . . Z 5 27.803 77.942 111.715 1 70.78 ? C6A NAD 501 F 1 HETATM 18 N N6A NAD . . . Z 5 27.674 78.603 110.537 1 71.26 ? N6A NAD 501 F 1 HETATM 19 N N1A NAD . . . Z 5 27.744 76.598 111.795 1 70.18 ? N1A NAD 501 F 1 HETATM 20 C C2A NAD . . . Z 5 27.872 75.951 112.972 1 63.22 ? C2A NAD 501 F 1 HETATM 21 N N3A NAD . . . Z 5 28.068 76.559 114.156 1 54.82 ? N3A NAD 501 F 1 HETATM 22 C C4A NAD . . . Z 5 28.142 77.904 114.23 1 45.49 ? C4A NAD 501 F 1 HETATM 23 O O3 NAD . . . Z 5 32.892 75.76 120.819 1 58.16 ? O3 NAD 501 F 1 HETATM 24 P PN NAD . . . Z 5 34.157 76.015 121.79 1 56.18 ? PN NAD 501 F 1 HETATM 25 O O1N NAD . . . Z 5 33.825 75.56 123.188 1 56.64 ? O1N NAD 501 F 1 HETATM 26 O O2N NAD . . . Z 5 34.624 77.433 121.577 1 41.38 ? O2N NAD 501 F 1 HETATM 27 O O5D NAD . . . Z 5 35.231 74.987 121.172 1 40.93 ? O5D NAD 501 F 1 HETATM 28 C C5D NAD . . . Z 5 35.357 74.866 119.76 1 40.96 ? C5D NAD 501 F 1 HETATM 29 C C4D NAD . . . Z 5 35.538 73.397 119.4 1 63.77 ? C4D NAD 501 F 1 HETATM 30 O O4D NAD . . . Z 5 36.89 72.981 119.602 1 73.35 ? O4D NAD 501 F 1 HETATM 31 C C3D NAD . . . Z 5 34.692 72.481 120.268 1 58.78 ? C3D NAD 501 F 1 HETATM 32 O O3D NAD . . . Z 5 33.565 72.038 119.526 1 51.46 ? O3D NAD 501 F 1 HETATM 33 C C2D NAD . . . Z 5 35.574 71.292 120.6 1 69.65 ? C2D NAD 501 F 1 HETATM 34 O O2D NAD . . . Z 5 35.072 70.077 120.037 1 76.85 ? O2D NAD 501 F 1 HETATM 35 C C1D NAD . . . Z 5 36.926 71.602 119.987 1 75.48 ? C1D NAD 501 F 1 HETATM 36 N N1N NAD . . . Z 5 37.901 71.418 121.048 1 78.62 ? N1N NAD 501 F 1 HETATM 37 C C2N NAD . . . Z 5 37.883 72.323 122.018 1 81.96 ? C2N NAD 501 F 1 HETATM 38 C C3N NAD . . . Z 5 38.758 72.225 123.077 1 92.14 ? C3N NAD 501 F 1 HETATM 39 C C7N NAD . . . Z 5 38.707 73.28 124.131 1 114.96 ? C7N NAD 501 F 1 HETATM 40 O O7N NAD . . . Z 5 37.633 73.662 124.572 1 119.13 ? O7N NAD 501 F 1 HETATM 41 N N7N NAD . . . Z 5 39.863 73.79 124.521 1 125.36 ? N7N NAD 501 F 1 HETATM 42 C C4N NAD . . . Z 5 39.677 71.183 123.127 1 79.4 ? C4N NAD 501 F 1 HETATM 43 C C5N NAD . . . Z 5 39.671 70.242 122.105 1 72.54 ? C5N NAD 501 F 1 HETATM 44 C C6N NAD . . . Z 5 38.758 70.386 121.064 1 76.7 ? C6N NAD 501 F 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 44 #