data_6JKP # _model_server_result.job_id XdgOZN8j3izjvGF012NLlw _model_server_result.datetime_utc '2025-07-03 16:51:41' _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 6jkp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 6JKP # _exptl.entry_id 6JKP _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.53 _cell.angle_gamma 90 _cell.entry_id 6JKP _cell.length_a 70.881 _cell.length_b 112.317 _cell.length_c 93.573 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JKP _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E 1 1 B,F 1 2 C,G,H,J 2 1 D,I 2 3 # 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' 1_655 x+1,y,z 1 0 0 0 1 0 0 0 1 70.881 0 0 3 'crystal symmetry operation' 2_545 -x,y-1/2,-z -1 0 0 0 1 0 0 0 -1 0 -56.1585 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 I N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id C _struct_conn.ptnr1_label_atom_id NE2 _struct_conn.ptnr1_label_comp_id GLN _struct_conn.ptnr1_label_seq_id 201 _struct_conn.ptnr1_auth_asym_id C _struct_conn.ptnr1_auth_comp_id GLN _struct_conn.ptnr1_auth_seq_id 196 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id H _struct_conn.ptnr2_label_atom_id ZN _struct_conn.ptnr2_label_comp_id ZN _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id C _struct_conn.ptnr2_auth_comp_id ZN _struct_conn.ptnr2_auth_seq_id 402 _struct_conn.ptnr2_symmetry 1_555 _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 2.533 _struct_conn.pdbx_value_order ? # _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 6JKP _atom_sites.fract_transf_matrix[1][1] 0.014108 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004456 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008903 _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] 0.011207 _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 NAD A 1 401 1 NAD NAD . F 2 NAD B 1 401 2 NAD NAD . G 2 NAD C 1 401 4 NAD NAD . H 3 ZN C 1 402 1 ZN ZN . I 2 NAD D 1 401 3 NAD NAD . J 4 HOH C 1 501 1 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 . . . I 2 -20.243 12.116 1.148 1 66.31 ? PA NAD 401 D 1 HETATM 2 O O1A NAD . . . I 2 -19.463 13.305 0.656 1 68.44 ? O1A NAD 401 D 1 HETATM 3 O O2A NAD . . . I 2 -21.27 11.265 0.474 1 77.19 ? O2A NAD 401 D 1 HETATM 4 O O5B NAD . . . I 2 -21.245 12.95 2.28 1 77.06 ? O5B NAD 401 D 1 HETATM 5 C C5B NAD . . . I 2 -22.071 12.001 2.838 1 73.95 ? C5B NAD 401 D 1 HETATM 6 C C4B NAD . . . I 2 -22.815 12.611 3.993 1 70.95 ? C4B NAD 401 D 1 HETATM 7 O O4B NAD . . . I 2 -21.878 12.866 5.022 1 57.71 ? O4B NAD 401 D 1 HETATM 8 C C3B NAD . . . I 2 -23.361 13.971 3.481 1 69.68 ? C3B NAD 401 D 1 HETATM 9 O O3B NAD . . . I 2 -24.733 13.915 3.697 1 75.98 ? O3B NAD 401 D 1 HETATM 10 C C2B NAD . . . I 2 -22.646 14.995 4.391 1 72.8 ? C2B NAD 401 D 1 HETATM 11 O O2B NAD . . . I 2 -23.514 15.969 4.875 1 82.06 ? O2B NAD 401 D 1 HETATM 12 C C1B NAD . . . I 2 -22.235 14.095 5.6 1 66.23 ? C1B NAD 401 D 1 HETATM 13 N N9A NAD . . . I 2 -21.025 14.595 6.247 1 60.56 ? N9A NAD 401 D 1 HETATM 14 C C8A NAD . . . I 2 -19.804 15.014 5.691 1 56.86 ? C8A NAD 401 D 1 HETATM 15 N N7A NAD . . . I 2 -18.926 15.404 6.614 1 58.76 ? N7A NAD 401 D 1 HETATM 16 C C5A NAD . . . I 2 -19.604 15.234 7.838 1 58.36 ? C5A NAD 401 D 1 HETATM 17 C C6A NAD . . . I 2 -19.229 15.466 9.191 1 54.3 ? C6A NAD 401 D 1 HETATM 18 N N6A NAD . . . I 2 -17.987 15.95 9.481 1 56.85 ? N6A NAD 401 D 1 HETATM 19 N N1A NAD . . . I 2 -20.11 15.204 10.207 1 50.76 ? N1A NAD 401 D 1 HETATM 20 C C2A NAD . . . I 2 -21.336 14.719 9.843 1 60.87 ? C2A NAD 401 D 1 HETATM 21 N N3A NAD . . . I 2 -21.831 14.451 8.616 1 69.57 ? N3A NAD 401 D 1 HETATM 22 C C4A NAD . . . I 2 -20.917 14.727 7.624 1 60.47 ? C4A NAD 401 D 1 HETATM 23 O O3 NAD . . . I 2 -19.064 11.38 1.972 1 70.63 ? O3 NAD 401 D 1 HETATM 24 P PN NAD . . . I 2 -18.233 10.301 1.153 1 75.4 ? PN NAD 401 D 1 HETATM 25 O O1N NAD . . . I 2 -18.387 8.833 1.466 1 75.68 ? O1N NAD 401 D 1 HETATM 26 O O2N NAD . . . I 2 -17.012 11.083 0.828 1 66.88 ? O2N NAD 401 D 1 HETATM 27 O O5D NAD . . . I 2 -18.944 10.315 -0.493 1 83.17 ? O5D NAD 401 D 1 HETATM 28 C C5D NAD . . . I 2 -18.096 9.638 -1.309 1 77.1 ? C5D NAD 401 D 1 HETATM 29 C C4D NAD . . . I 2 -18.128 10.282 -2.675 1 78.49 ? C4D NAD 401 D 1 HETATM 30 O O4D NAD . . . I 2 -16.769 10.32 -3.176 1 84.19 ? O4D NAD 401 D 1 HETATM 31 C C3D NAD . . . I 2 -18.943 9.345 -3.608 1 87.02 ? C3D NAD 401 D 1 HETATM 32 O O3D NAD . . . I 2 -19.57 10.168 -4.528 1 84.86 ? O3D NAD 401 D 1 HETATM 33 C C2D NAD . . . I 2 -17.844 8.505 -4.26 1 85.76 ? C2D NAD 401 D 1 HETATM 34 O O2D NAD . . . I 2 -18.125 8.113 -5.563 1 82.72 ? O2D NAD 401 D 1 HETATM 35 C C1D NAD . . . I 2 -16.739 9.593 -4.375 1 88.14 ? C1D NAD 401 D 1 HETATM 36 N N1N NAD . . . I 2 -15.382 8.921 -4.438 1 83.55 ? N1N NAD 401 D 1 HETATM 37 C C2N NAD . . . I 2 -14.377 9.648 -5.016 1 83.92 ? C2N NAD 401 D 1 HETATM 38 C C3N NAD . . . I 2 -13.102 9.09 -5.109 1 84.66 ? C3N NAD 401 D 1 HETATM 39 C C7N NAD . . . I 2 -12.055 9.941 -5.751 1 80.66 ? C7N NAD 401 D 1 HETATM 40 O O7N NAD . . . I 2 -12.298 11.076 -6.151 1 76.94 ? O7N NAD 401 D 1 HETATM 41 N N7N NAD . . . I 2 -10.802 9.39 -5.87 1 78.25 ? N7N NAD 401 D 1 HETATM 42 C C4N NAD . . . I 2 -12.872 7.806 -4.611 1 81.17 ? C4N NAD 401 D 1 HETATM 43 C C5N NAD . . . I 2 -13.913 7.092 -4.029 1 81.06 ? C5N NAD 401 D 1 HETATM 44 C C6N NAD . . . I 2 -15.187 7.661 -3.942 1 81.64 ? C6N NAD 401 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 44 #