data_5J33 # _model_server_result.job_id 6bpMa6FYcFGm3A-DGcLlHw _model_server_result.datetime_utc '2024-12-26 18:33:25' _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 5j33 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":501}' # _entry.id 5J33 # _exptl.entry_id 5J33 _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 8 _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 5J33 _cell.length_a 77.2 _cell.length_b 132.868 _cell.length_c 349.426 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5J33 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,K,L,M,N 1 1 C,H,O,P,Q,R,S,EA,FA,GA 2 1 D,F,T,U,V,W,X,Y 3 1 E,G,Z,AA,BA,CA,DA 4 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 ? 2 I N N ? 2 L N N ? 2 O N N ? 2 T N N ? 2 V N N ? 2 Z N N ? 2 CA N N ? 2 EA 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 I C4N NAD . A NAD 501 1_555 J O4 SO4 . A SO4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale2 L N7N NAD . A NAD 504 1_555 M O1 SO4 . A SO4 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? covale ? covale3 T C4N NAD . D NAD 501 1_555 U O2 SO4 . D SO4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale4 V N7N NAD . D NAD 503 1_555 W O3 SO4 . D SO4 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.306 ? covale ? covale5 Z C5N NAD . E NAD 501 1_555 AA O3 SO4 . E SO4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale6 H NH1 ARG 186 H ARG 186 1_555 H CG ASN 200 H ASN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.283 ? covale ? covale7 H NH2 ARG 186 H ARG 186 1_555 H OD1 ASN 200 H ASN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale8 EA C4N NAD . H NAD 501 1_555 GA O1 SO4 . H SO4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? metalc ? metalc1 A OD2 ASP 264 A ASP 264 1_555 N MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc2 A OD1 ASP 288 A ASP 288 1_555 K MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc3 K MG MG . A MG 503 1_555 B OD2 ASP 264 B ASP 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc4 M O2 SO4 . A SO4 505 1_555 N MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? metalc ? metalc5 N MG MG . A MG 506 1_555 B OD1 ASP 288 B ASP 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc6 C OD2 ASP 264 C ASP 264 1_555 R MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? metalc ? metalc7 C OD1 ASP 288 C ASP 288 1_555 S MG MG . C MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc8 P O1 SO4 . C SO4 502 1_555 S MG MG . C MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc9 R MG MG . C MG 504 1_555 H OD1 ASP 288 H ASP 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc10 R MG MG . C MG 504 1_555 H OD2 ASP 292 H ASP 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? metalc ? metalc11 S MG MG . C MG 505 1_555 H OD2 ASP 264 H ASP 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? metalc ? metalc12 D OD2 ASP 264 D ASP 264 1_555 X MG MG . D MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc13 D OD1 ASP 288 D ASP 288 1_555 Y MG MG . D MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc14 U O3 SO4 . D SO4 502 1_555 Y MG MG . D MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc15 W O2 SO4 . D SO4 504 1_555 X MG MG . D MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc16 X MG MG . D MG 505 1_555 F OD1 ASP 288 F ASP 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc17 X MG MG . D MG 505 1_555 F OD2 ASP 288 F ASP 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? metalc ? metalc18 Y MG MG . D MG 506 1_555 F OD2 ASP 264 F ASP 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc19 E OD1 ASP 288 E ASP 288 1_555 BA MG MG . E MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc20 E OD2 ASP 292 E ASP 292 1_555 BA MG MG . E MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc21 AA O1 SO4 . E SO4 502 1_555 BA MG MG . E MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? # _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 5J33 _atom_sites.fract_transf_matrix[1][1] 0.012953 _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] 0.007526 _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] 0.002862 _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 2 NAD A 1 501 900 NAD NAD . J 3 SO4 A 1 502 801 SO4 SO4 . K 4 MG A 1 503 702 MG MG . L 2 NAD A 1 504 900 NAD NAD . M 3 SO4 A 1 505 802 SO4 SO4 . N 4 MG A 1 506 703 MG MG . O 2 NAD C 1 501 900 NAD NAD . P 3 SO4 C 1 502 804 SO4 SO4 . Q 3 SO4 C 1 503 806 SO4 SO4 . R 4 MG C 1 504 701 MG MG . S 4 MG C 1 505 705 MG MG . T 2 NAD D 1 501 900 NAD NAD . U 3 SO4 D 1 502 810 SO4 SO4 . V 2 NAD D 1 503 900 NAD NAD . W 3 SO4 D 1 504 803 SO4 SO4 . X 4 MG D 1 505 704 MG MG . Y 4 MG D 1 506 707 MG MG . Z 2 NAD E 1 501 900 NAD NAD . AA 3 SO4 E 1 502 812 SO4 SO4 . BA 4 MG E 1 503 706 MG MG . CA 2 NAD G 1 501 900 NAD NAD . DA 3 SO4 G 1 502 813 SO4 SO4 . EA 2 NAD H 1 501 900 NAD NAD . FA 3 SO4 H 1 502 809 SO4 SO4 . GA 3 SO4 H 1 503 811 SO4 SO4 . # 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 2 50.487 -54.759 -51.629 1 41.69 ? PA NAD 501 E 1 HETATM 2 O O1A NAD . . . Z 2 51.067 -54.137 -52.862 1 44.63 ? O1A NAD 501 E 1 HETATM 3 O O2A NAD . . . Z 2 50.694 -53.752 -50.482 1 39.85 ? O2A NAD 501 E 1 HETATM 4 O O5B NAD . . . Z 2 51.365 -55.97 -51.37 1 40.99 ? O5B NAD 501 E 1 HETATM 5 C C5B NAD . . . Z 2 52.321 -56.218 -52.27 1 39.17 ? C5B NAD 501 E 1 HETATM 6 C C4B NAD . . . Z 2 53.26 -57.252 -51.808 1 39.56 ? C4B NAD 501 E 1 HETATM 7 O O4B NAD . . . Z 2 54.509 -56.784 -52.058 1 41.04 ? O4B NAD 501 E 1 HETATM 8 C C3B NAD . . . Z 2 53.154 -57.382 -50.356 1 40.75 ? C3B NAD 501 E 1 HETATM 9 O O3B NAD . . . Z 2 53.453 -58.672 -49.968 1 42.85 ? O3B NAD 501 E 1 HETATM 10 C C2B NAD . . . Z 2 54.167 -56.59 -49.782 1 40.79 ? C2B NAD 501 E 1 HETATM 11 O O2B NAD . . . Z 2 54.742 -57.394 -48.765 1 41.45 ? O2B NAD 501 E 1 HETATM 12 C C1B NAD . . . Z 2 55.093 -56.354 -50.85 1 42.44 ? C1B NAD 501 E 1 HETATM 13 N N9A NAD . . . Z 2 55.383 -54.984 -50.973 1 46.38 ? N9A NAD 501 E 1 HETATM 14 C C8A NAD . . . Z 2 54.513 -54.003 -51.238 1 51.81 ? C8A NAD 501 E 1 HETATM 15 N N7A NAD . . . Z 2 55.181 -52.826 -51.278 1 53.87 ? N7A NAD 501 E 1 HETATM 16 C C5A NAD . . . Z 2 56.486 -53.08 -51.039 1 50.65 ? C5A NAD 501 E 1 HETATM 17 C C6A NAD . . . Z 2 57.631 -52.3 -50.952 1 49.54 ? C6A NAD 501 E 1 HETATM 18 N N6A NAD . . . Z 2 57.538 -50.89 -51.14 1 50.06 ? N6A NAD 501 E 1 HETATM 19 N N1A NAD . . . Z 2 58.81 -52.855 -50.699 1 49.53 ? N1A NAD 501 E 1 HETATM 20 C C2A NAD . . . Z 2 58.891 -54.172 -50.521 1 48.44 ? C2A NAD 501 E 1 HETATM 21 N N3A NAD . . . Z 2 57.817 -54.957 -50.596 1 47.6 ? N3A NAD 501 E 1 HETATM 22 C C4A NAD . . . Z 2 56.613 -54.442 -50.85 1 47.55 ? C4A NAD 501 E 1 HETATM 23 O O3 NAD . . . Z 2 49.004 -55.125 -51.874 1 40.18 ? O3 NAD 501 E 1 HETATM 24 P PN NAD . . . Z 2 48.221 -55.978 -50.837 1 39.12 ? PN NAD 501 E 1 HETATM 25 O O1N NAD . . . Z 2 47.143 -56.743 -51.59 1 35.41 ? O1N NAD 501 E 1 HETATM 26 O O2N NAD . . . Z 2 49.145 -56.979 -50.197 1 39.58 ? O2N NAD 501 E 1 HETATM 27 O O5D NAD . . . Z 2 47.532 -55.141 -49.633 1 41.61 ? O5D NAD 501 E 1 HETATM 28 C C5D NAD . . . Z 2 47.808 -53.821 -49.232 1 47.07 ? C5D NAD 501 E 1 HETATM 29 C C4D NAD . . . Z 2 46.702 -52.848 -49.142 1 53.88 ? C4D NAD 501 E 1 HETATM 30 O O4D NAD . . . Z 2 46.854 -51.834 -50.149 1 62.89 ? O4D NAD 501 E 1 HETATM 31 C C3D NAD . . . Z 2 45.429 -53.498 -49.403 1 52.97 ? C3D NAD 501 E 1 HETATM 32 O O3D NAD . . . Z 2 44.514 -53.097 -48.442 1 51.4 ? O3D NAD 501 E 1 HETATM 33 C C2D NAD . . . Z 2 44.938 -52.984 -50.646 1 61.63 ? C2D NAD 501 E 1 HETATM 34 O O2D NAD . . . Z 2 43.602 -52.756 -50.378 1 65.3 ? O2D NAD 501 E 1 HETATM 35 C C1D NAD . . . Z 2 45.637 -51.7 -50.844 1 66.33 ? C1D NAD 501 E 1 HETATM 36 N N1N NAD . . . Z 2 45.782 -51.094 -52.201 1 69.12 ? N1N NAD 501 E 1 HETATM 37 C C2N NAD . . . Z 2 46.485 -49.955 -52.158 1 85.42 ? C2N NAD 501 E 1 HETATM 38 C C3N NAD . . . Z 2 46.731 -49.201 -53.293 1 88.45 ? C3N NAD 501 E 1 HETATM 39 C C7N NAD . . . Z 2 47.535 -47.939 -53.122 1 66.61 ? C7N NAD 501 E 1 HETATM 40 O O7N NAD . . . Z 2 47.495 -47.36 -52.043 1 66.74 ? O7N NAD 501 E 1 HETATM 41 N N7N NAD . . . Z 2 48.35 -47.371 -54.174 1 74.1 ? N7N NAD 501 E 1 HETATM 42 C C4N NAD . . . Z 2 46.228 -49.621 -54.546 1 99.03 ? C4N NAD 501 E 1 HETATM 43 C C5N NAD . . . Z 2 45.471 -50.808 -54.62 1 98.78 ? C5N NAD 501 E 1 HETATM 44 C C6N NAD . . . Z 2 45.26 -51.529 -53.402 1 91.72 ? C6N NAD 501 E 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 44 #