data_2H4F # _model_server_result.job_id FPTCW9IiKw591LgUkDggPQ _model_server_result.datetime_utc '2024-12-02 22:42:04' _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 2h4f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":702}' # _entry.id 2H4F # _exptl.entry_id 2H4F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _entity.pdbx_number_of_molecules 1 _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 2H4F _cell.length_a 45.821 _cell.length_b 59.331 _cell.length_c 106.66 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2H4F _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B C LYS 10 D LYS 10 1_555 B N ALY 11 D ALY 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.515 ? covale ? covale2 B C ALY 11 D ALY 11 1_555 B N LEU 12 D LEU 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 A SG CYS 124 A CYS 124 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc2 A SG CYS 127 A CYS 127 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc3 A SG CYS 148 A CYS 148 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc4 A SG CYS 151 A CYS 151 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? # _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 265 n n PA O2A NAD sing 266 n n PA O5B NAD sing 267 n n PA O3 NAD sing 268 n n O2A HOA2 NAD sing 269 n n O5B C5B NAD sing 270 n n C5B C4B NAD sing 271 n n C5B H51A NAD sing 272 n n C5B H52A NAD sing 273 n n C4B O4B NAD sing 274 n n C4B C3B NAD sing 275 n n C4B H4B NAD sing 276 n n O4B C1B NAD sing 277 n n C3B O3B NAD sing 278 n n C3B C2B NAD sing 279 n n C3B H3B NAD sing 280 n n O3B HO3A NAD sing 281 n n C2B O2B NAD sing 282 n n C2B C1B NAD sing 283 n n C2B H2B NAD sing 284 n n O2B HO2A NAD sing 285 n n C1B N9A NAD sing 286 n n C1B H1B NAD sing 287 n n N9A C8A NAD sing 288 n y N9A C4A NAD sing 289 n y C8A N7A NAD doub 290 n y C8A H8A NAD sing 291 n n N7A C5A NAD sing 292 n y C5A C6A NAD sing 293 n y C5A C4A NAD doub 294 n y C6A N6A NAD sing 295 n n C6A N1A NAD doub 296 n y N6A H61A NAD sing 297 n n N6A H62A NAD sing 298 n n N1A C2A NAD sing 299 n y C2A N3A NAD doub 300 n y C2A H2A NAD sing 301 n n N3A C4A NAD sing 302 n y O3 PN NAD sing 303 n n PN O1N NAD doub 304 n n PN O2N NAD sing 305 n n PN O5D NAD sing 306 n n O5D C5D NAD sing 307 n n C5D C4D NAD sing 308 n n C5D H51N NAD sing 309 n n C5D H52N NAD sing 310 n n C4D O4D NAD sing 311 n n C4D C3D NAD sing 312 n n C4D H4D NAD sing 313 n n O4D C1D NAD sing 314 n n C3D O3D NAD sing 315 n n C3D C2D NAD sing 316 n n C3D H3D NAD sing 317 n n O3D HO3N NAD sing 318 n n C2D O2D NAD sing 319 n n C2D C1D NAD sing 320 n n C2D H2D NAD sing 321 n n O2D HO2N NAD sing 322 n n C1D N1N NAD sing 323 n n C1D H1D NAD sing 324 n n N1N C2N NAD sing 325 n y N1N C6N NAD doub 326 n y C2N C3N NAD doub 327 n y C2N H2N NAD sing 328 n n C3N C7N NAD sing 329 n n C3N C4N NAD sing 330 n y C7N O7N NAD doub 331 n n C7N N7N NAD sing 332 n n N7N H71N NAD sing 333 n n N7N H72N NAD sing 334 n n C4N C5N NAD doub 335 n y C4N H4N NAD sing 336 n n C5N C6N NAD sing 337 n y C5N H5N NAD sing 338 n n C6N H6N NAD sing 339 n n # _atom_sites.entry_id 2H4F _atom_sites.fract_transf_matrix[1][1] 0.021824 _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] 0.016855 _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] 0.009376 _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 C 3 ZN A 1 1001 1001 ZN ZN . D 4 NAD A 1 702 702 NAD NAD . E 5 HOH A 1 1002 1 HOH HOH . E 5 HOH A 2 1003 2 HOH HOH . E 5 HOH A 3 1004 3 HOH HOH . E 5 HOH A 4 1005 4 HOH HOH . E 5 HOH A 5 1006 5 HOH HOH . E 5 HOH A 6 1007 6 HOH HOH . E 5 HOH A 7 1008 7 HOH HOH . E 5 HOH A 8 1009 8 HOH HOH . E 5 HOH A 9 1010 9 HOH HOH . E 5 HOH A 10 1011 10 HOH HOH . E 5 HOH A 11 1012 11 HOH HOH . E 5 HOH A 12 1013 14 HOH HOH . E 5 HOH A 13 1014 15 HOH HOH . E 5 HOH A 14 1015 16 HOH HOH . E 5 HOH A 15 1016 17 HOH HOH . E 5 HOH A 16 1017 19 HOH HOH . E 5 HOH A 17 1018 21 HOH HOH . E 5 HOH A 18 1019 22 HOH HOH . E 5 HOH A 19 1020 24 HOH HOH . E 5 HOH A 20 1021 26 HOH HOH . E 5 HOH A 21 1022 28 HOH HOH . E 5 HOH A 22 1023 29 HOH HOH . E 5 HOH A 23 1024 30 HOH HOH . E 5 HOH A 24 1025 32 HOH HOH . E 5 HOH A 25 1026 33 HOH HOH . E 5 HOH A 26 1027 34 HOH HOH . E 5 HOH A 27 1028 36 HOH HOH . E 5 HOH A 28 1029 37 HOH HOH . E 5 HOH A 29 1030 38 HOH HOH . E 5 HOH A 30 1031 39 HOH HOH . E 5 HOH A 31 1032 41 HOH HOH . E 5 HOH A 32 1033 42 HOH HOH . E 5 HOH A 33 1034 44 HOH HOH . E 5 HOH A 34 1035 45 HOH HOH . E 5 HOH A 35 1036 47 HOH HOH . E 5 HOH A 36 1037 48 HOH HOH . E 5 HOH A 37 1038 49 HOH HOH . E 5 HOH A 38 1039 52 HOH HOH . E 5 HOH A 39 1040 53 HOH HOH . E 5 HOH A 40 1041 55 HOH HOH . E 5 HOH A 41 1042 56 HOH HOH . E 5 HOH A 42 1043 57 HOH HOH . E 5 HOH A 43 1044 58 HOH HOH . E 5 HOH A 44 1045 59 HOH HOH . E 5 HOH A 45 1046 60 HOH HOH . E 5 HOH A 46 1047 61 HOH HOH . E 5 HOH A 47 1048 62 HOH HOH . E 5 HOH A 48 1049 64 HOH HOH . E 5 HOH A 49 1050 65 HOH HOH . E 5 HOH A 50 1051 66 HOH HOH . E 5 HOH A 51 1052 69 HOH HOH . E 5 HOH A 52 1053 71 HOH HOH . E 5 HOH A 53 1054 72 HOH HOH . E 5 HOH A 54 1055 73 HOH HOH . E 5 HOH A 55 1056 75 HOH HOH . E 5 HOH A 56 1057 76 HOH HOH . E 5 HOH A 57 1058 77 HOH HOH . E 5 HOH A 58 1059 84 HOH HOH . E 5 HOH A 59 1060 85 HOH HOH . E 5 HOH A 60 1061 86 HOH HOH . E 5 HOH A 61 1062 89 HOH HOH . E 5 HOH A 62 1063 90 HOH HOH . E 5 HOH A 63 1064 91 HOH HOH . E 5 HOH A 64 1065 92 HOH HOH . E 5 HOH A 65 1066 93 HOH HOH . E 5 HOH A 66 1067 95 HOH HOH . E 5 HOH A 67 1068 96 HOH HOH . F 5 HOH D 1 31 31 HOH HOH . F 5 HOH D 2 40 40 HOH HOH . F 5 HOH D 3 94 94 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 . . . D 4 10.517 21.056 12.279 1 31.33 ? PA NAD 702 A 1 HETATM 2 O O1A NAD . . . D 4 11.061 21.118 13.666 1 31.43 ? O1A NAD 702 A 1 HETATM 3 O O2A NAD . . . D 4 10.73 22.18 11.275 1 28.55 ? O2A NAD 702 A 1 HETATM 4 O O5B NAD . . . D 4 10.981 19.694 11.595 1 28.96 ? O5B NAD 702 A 1 HETATM 5 C C5B NAD . . . D 4 10.501 19.264 10.318 1 25.63 ? C5B NAD 702 A 1 HETATM 6 C C4B NAD . . . D 4 11.397 18.077 10.004 1 24.73 ? C4B NAD 702 A 1 HETATM 7 O O4B NAD . . . D 4 11.097 17.562 8.728 1 23.23 ? O4B NAD 702 A 1 HETATM 8 C C3B NAD . . . D 4 12.896 18.398 9.94 1 25.68 ? C3B NAD 702 A 1 HETATM 9 O O3B NAD . . . D 4 13.536 17.327 10.665 1 24.06 ? O3B NAD 702 A 1 HETATM 10 C C2B NAD . . . D 4 13.283 18.328 8.478 1 24.38 ? C2B NAD 702 A 1 HETATM 11 O O2B NAD . . . D 4 14.549 17.688 8.313 1 30.84 ? O2B NAD 702 A 1 HETATM 12 C C1B NAD . . . D 4 12.296 17.296 7.977 1 21.3 ? C1B NAD 702 A 1 HETATM 13 N N9A NAD . . . D 4 11.854 17.503 6.602 1 18.67 ? N9A NAD 702 A 1 HETATM 14 C C8A NAD . . . D 4 11.614 18.709 6.026 1 19.23 ? C8A NAD 702 A 1 HETATM 15 N N7A NAD . . . D 4 11.132 18.491 4.79 1 21.58 ? N7A NAD 702 A 1 HETATM 16 C C5A NAD . . . D 4 11.072 17.159 4.572 1 18.71 ? C5A NAD 702 A 1 HETATM 17 C C6A NAD . . . D 4 10.652 16.276 3.474 1 20.02 ? C6A NAD 702 A 1 HETATM 18 N N6A NAD . . . D 4 10.21 16.806 2.317 1 19.61 ? N6A NAD 702 A 1 HETATM 19 N N1A NAD . . . D 4 10.752 14.955 3.655 1 19.39 ? N1A NAD 702 A 1 HETATM 20 C C2A NAD . . . D 4 11.214 14.391 4.795 1 21.04 ? C2A NAD 702 A 1 HETATM 21 N N3A NAD . . . D 4 11.572 15.14 5.843 1 17.48 ? N3A NAD 702 A 1 HETATM 22 C C4A NAD . . . D 4 11.547 16.505 5.773 1 18.57 ? C4A NAD 702 A 1 HETATM 23 O O3 NAD . . . D 4 8.946 20.743 12.307 1 28.01 ? O3 NAD 702 A 1 HETATM 24 P PN NAD . . . D 4 8.07 19.979 13.383 1 30.53 ? PN NAD 702 A 1 HETATM 25 O O1N NAD . . . D 4 8.819 18.856 14.009 1 26.06 ? O1N NAD 702 A 1 HETATM 26 O O2N NAD . . . D 4 6.752 19.742 12.715 1 32.75 ? O2N NAD 702 A 1 HETATM 27 O O5D NAD . . . D 4 7.809 21.096 14.522 1 29.45 ? O5D NAD 702 A 1 HETATM 28 C C5D NAD . . . D 4 7.624 22.485 14.152 1 33.49 ? C5D NAD 702 A 1 HETATM 29 C C4D NAD . . . D 4 6.524 23.224 14.886 1 32.54 ? C4D NAD 702 A 1 HETATM 30 O O4D NAD . . . D 4 6.147 24.4 14.133 1 34.7 ? O4D NAD 702 A 1 HETATM 31 C C3D NAD . . . D 4 5.237 22.452 15.088 1 33.59 ? C3D NAD 702 A 1 HETATM 32 O O3D NAD . . . D 4 4.746 22.9 16.357 1 36.59 ? O3D NAD 702 A 1 HETATM 33 C C2D NAD . . . D 4 4.284 22.951 14.002 1 35.19 ? C2D NAD 702 A 1 HETATM 34 O O2D NAD . . . D 4 3.057 23.4 14.587 1 35.8 ? O2D NAD 702 A 1 HETATM 35 C C1D NAD . . . D 4 4.893 24.233 13.439 1 31.49 ? C1D NAD 702 A 1 HETATM 36 N N1N NAD . . . D 4 4.919 24.369 11.951 1 31.12 ? N1N NAD 702 A 1 HETATM 37 C C2N NAD . . . D 4 3.887 23.934 11.189 1 27.81 ? C2N NAD 702 A 1 HETATM 38 C C3N NAD . . . D 4 3.922 24.11 9.798 1 27.54 ? C3N NAD 702 A 1 HETATM 39 C C7N NAD . . . D 4 2.793 23.604 8.971 1 26.58 ? C7N NAD 702 A 1 HETATM 40 O O7N NAD . . . D 4 1.684 23.549 9.482 1 21.93 ? O7N NAD 702 A 1 HETATM 41 N N7N NAD . . . D 4 3.04 23.223 7.711 1 19.77 ? N7N NAD 702 A 1 HETATM 42 C C4N NAD . . . D 4 5.003 24.757 9.173 1 26.99 ? C4N NAD 702 A 1 HETATM 43 C C5N NAD . . . D 4 6.037 25.205 9.988 1 26.13 ? C5N NAD 702 A 1 HETATM 44 C C6N NAD . . . D 4 5.957 25.003 11.375 1 25.98 ? C6N NAD 702 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 44 #