data_5H4D # _model_server_result.job_id YFakXkkuRL97Z36o0iq3gA _model_server_result.datetime_utc '2024-11-27 18:25:40' _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 5h4d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":404}' # _entry.id 5H4D # _exptl.entry_id 5H4D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 5H4D _cell.length_a 114.56 _cell.length_b 114.56 _cell.length_c 123.404 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5H4D _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 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,D,E,F,G,H,P 1 1 B,C,I,J,K,L,M,N,O 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 ? 6 H N N ? 6 O 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 B C LYS 3 D LYS 3 1_555 B N ALY 4 D ALY 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.267 ? covale ? covale2 B C ALY 4 D ALY 4 1_555 I N MCM . D MCM 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale3 D C LYS 3 C LYS 3 1_555 D N ALY 4 C ALY 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.264 ? covale ? covale4 D C ALY 4 C ALY 4 1_555 P N MCM . C MCM 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? metalc ? metalc1 A SG CYS 136 A CYS 256 1_555 E ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc2 A SG CYS 160 A CYS 280 1_555 E ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc3 A SG CYS 163 A CYS 283 1_555 E ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc4 C SG CYS 136 H CYS 256 1_555 K ZN ZN . H ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc5 C SG CYS 139 H CYS 259 1_555 K ZN ZN . H ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc6 C SG CYS 160 H CYS 280 1_555 K ZN ZN . H ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc7 C SG CYS 163 H CYS 283 1_555 K ZN ZN . H ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? # _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 ? # _atom_sites.entry_id 5H4D _atom_sites.fract_transf_matrix[1][1] 0.008729 _atom_sites.fract_transf_matrix[1][2] 0.00504 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010079 _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] 0.008103 _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 3 ZN A 1 401 401 ZN ZN . F 4 MG A 1 402 405 MG MG . G 5 BBI A 1 403 1 BBI LIG . H 6 NAD A 1 404 702 NAD NAD . I 7 MCM D 1 101 4 MCM FDL . J 8 PEG H 1 401 403 PEG PEG . K 3 ZN H 1 402 401 ZN ZN . L 8 PEG H 1 403 404 PEG PEG . M 4 MG H 1 404 405 MG MG . N 5 BBI H 1 405 2 BBI LIG . O 6 NAD H 1 406 703 NAD NAD . P 7 MCM C 1 101 4 MCM FDL . # 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 . . . H 6 26.527 20.98 -9.941 1 117.44 ? PA NAD 404 A 1 HETATM 2 O O1A NAD . . . H 6 26.145 22.439 -10.102 1 112.11 -1 O1A NAD 404 A 1 HETATM 3 O O2A NAD . . . H 6 26.292 20.022 -11.09 1 115.92 ? O2A NAD 404 A 1 HETATM 4 O O5B NAD . . . H 6 28.081 20.886 -9.498 1 117.42 ? O5B NAD 404 A 1 HETATM 5 C C5B NAD . . . H 6 28.696 19.63 -9.182 1 112.85 ? C5B NAD 404 A 1 HETATM 6 C C4B NAD . . . H 6 30.209 19.779 -9.016 1 109.67 ? C4B NAD 404 A 1 HETATM 7 O O4B NAD . . . H 6 30.806 18.507 -8.726 1 109.07 ? O4B NAD 404 A 1 HETATM 8 C C3B NAD . . . H 6 30.888 20.307 -10.274 1 109 ? C3B NAD 404 A 1 HETATM 9 O O3B NAD . . . H 6 31.823 21.334 -9.932 1 103.29 ? O3B NAD 404 A 1 HETATM 10 C C2B NAD . . . H 6 31.602 19.11 -10.87 1 110.02 ? C2B NAD 404 A 1 HETATM 11 O O2B NAD . . . H 6 32.827 19.469 -11.523 1 111.31 ? O2B NAD 404 A 1 HETATM 12 C C1B NAD . . . H 6 31.857 18.225 -9.662 1 109.25 ? C1B NAD 404 A 1 HETATM 13 N N9A NAD . . . H 6 31.921 16.783 -10.031 1 109.88 ? N9A NAD 404 A 1 HETATM 14 C C8A NAD . . . H 6 30.976 16.041 -10.654 1 110.01 ? C8A NAD 404 A 1 HETATM 15 N N7A NAD . . . H 6 31.4 14.754 -10.814 1 108.86 ? N7A NAD 404 A 1 HETATM 16 C C5A NAD . . . H 6 32.64 14.657 -10.294 1 107.03 ? C5A NAD 404 A 1 HETATM 17 C C6A NAD . . . H 6 33.673 13.597 -10.132 1 100.55 ? C6A NAD 404 A 1 HETATM 18 N N6A NAD . . . H 6 33.472 12.329 -10.566 1 95.01 ? N6A NAD 404 A 1 HETATM 19 N N1A NAD . . . H 6 34.835 13.947 -9.526 1 101.57 ? N1A NAD 404 A 1 HETATM 20 C C2A NAD . . . H 6 35.072 15.203 -9.081 1 101.75 ? C2A NAD 404 A 1 HETATM 21 N N3A NAD . . . H 6 34.18 16.204 -9.193 1 104.69 ? N3A NAD 404 A 1 HETATM 22 C C4A NAD . . . H 6 32.973 16.001 -9.779 1 108.86 ? C4A NAD 404 A 1 HETATM 23 O O3 NAD . . . H 6 25.796 20.374 -8.637 1 108.67 ? O3 NAD 404 A 1 HETATM 24 P PN NAD . . . H 6 25.371 21.281 -7.373 1 103.74 ? PN NAD 404 A 1 HETATM 25 O O1N NAD . . . H 6 26.44 22.326 -7.134 1 99.95 -1 O1N NAD 404 A 1 HETATM 26 O O2N NAD . . . H 6 25.013 20.329 -6.257 1 102.36 ? O2N NAD 404 A 1 HETATM 27 O O5D NAD . . . H 6 24.004 21.992 -7.885 1 105.06 ? O5D NAD 404 A 1 HETATM 28 C C5D NAD . . . H 6 23.086 21.329 -8.773 1 101.72 ? C5D NAD 404 A 1 HETATM 29 C C4D NAD . . . H 6 21.617 21.65 -8.479 1 96.51 ? C4D NAD 404 A 1 HETATM 30 O O4D NAD . . . H 6 20.749 20.73 -9.153 1 92.72 ? O4D NAD 404 A 1 HETATM 31 C C3D NAD . . . H 6 21.238 21.521 -7.022 1 95.33 ? C3D NAD 404 A 1 HETATM 32 O O3D NAD . . . H 6 20.168 22.431 -6.765 1 96.94 ? O3D NAD 404 A 1 HETATM 33 C C2D NAD . . . H 6 20.793 20.076 -6.878 1 93.56 ? C2D NAD 404 A 1 HETATM 34 O O2D NAD . . . H 6 19.719 19.938 -5.944 1 94.51 ? O2D NAD 404 A 1 HETATM 35 C C1D NAD . . . H 6 20.352 19.662 -8.279 1 90.75 ? C1D NAD 404 A 1 HETATM 36 N N1N NAD . . . H 6 20.959 18.385 -8.694 1 89.54 ? N1N NAD 404 A 1 HETATM 37 C C2N NAD . . . H 6 20.865 17.302 -7.892 1 86.17 ? C2N NAD 404 A 1 HETATM 38 C C3N NAD . . . H 6 21.434 16.08 -8.268 1 85.24 ? C3N NAD 404 A 1 HETATM 39 C C7N NAD . . . H 6 21.335 14.876 -7.373 1 81 ? C7N NAD 404 A 1 HETATM 40 O O7N NAD . . . H 6 20.315 14.685 -6.734 1 77.46 ? O7N NAD 404 A 1 HETATM 41 N N7N NAD . . . H 6 22.371 14.04 -7.291 1 80.75 ? N7N NAD 404 A 1 HETATM 42 C C4N NAD . . . H 6 22.101 15.986 -9.49 1 88.02 ? C4N NAD 404 A 1 HETATM 43 C C5N NAD . . . H 6 22.185 17.108 -10.306 1 89.34 ? C5N NAD 404 A 1 HETATM 44 C C6N NAD . . . H 6 21.6 18.301 -9.883 1 90.88 ? C6N NAD 404 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #