data_5H4D # _model_server_result.job_id 7bwR854DstDOCcK0l_WKBA _model_server_result.datetime_utc '2024-11-24 00:45:11' _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":"O","auth_seq_id":406}' # _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 . . . O 6 4.966 33.498 34.633 1 71.63 ? PA NAD 406 H 1 HETATM 2 O O1A NAD . . . O 6 6.325 34.166 34.733 1 67.09 -1 O1A NAD 406 H 1 HETATM 3 O O2A NAD . . . O 6 4.575 32.459 35.673 1 68.63 ? O2A NAD 406 H 1 HETATM 4 O O5B NAD . . . O 6 3.829 34.661 34.568 1 72.05 ? O5B NAD 406 H 1 HETATM 5 C C5B NAD . . . O 6 2.553 34.553 33.899 1 69.25 ? C5B NAD 406 H 1 HETATM 6 C C4B NAD . . . O 6 1.956 35.943 33.66 1 69.56 ? C4B NAD 406 H 1 HETATM 7 O O4B NAD . . . O 6 0.566 35.885 33.302 1 70.52 ? O4B NAD 406 H 1 HETATM 8 C C3B NAD . . . O 6 2.011 36.815 34.908 1 70.39 ? C3B NAD 406 H 1 HETATM 9 O O3B NAD . . . O 6 2.313 38.158 34.496 1 67.61 ? O3B NAD 406 H 1 HETATM 10 C C2B NAD . . . O 6 0.629 36.647 35.528 1 71.24 ? C2B NAD 406 H 1 HETATM 11 O O2B NAD . . . O 6 0.195 37.732 36.355 1 70.23 ? O2B NAD 406 H 1 HETATM 12 C C1B NAD . . . O 6 -0.248 36.545 34.299 1 72.4 ? C1B NAD 406 H 1 HETATM 13 N N9A NAD . . . O 6 -1.529 35.813 34.531 1 74.74 ? N9A NAD 406 H 1 HETATM 14 C C8A NAD . . . O 6 -1.727 34.629 35.17 1 74.81 ? C8A NAD 406 H 1 HETATM 15 N N7A NAD . . . O 6 -3.045 34.277 35.14 1 73.18 ? N7A NAD 406 H 1 HETATM 16 C C5A NAD . . . O 6 -3.712 35.245 34.474 1 72.82 ? C5A NAD 406 H 1 HETATM 17 C C6A NAD . . . O 6 -5.12 35.517 34.077 1 70.6 ? C6A NAD 406 H 1 HETATM 18 N N6A NAD . . . O 6 -6.116 34.654 34.393 1 69.96 ? N6A NAD 406 H 1 HETATM 19 N N1A NAD . . . O 6 -5.374 36.66 33.392 1 68.28 ? N1A NAD 406 H 1 HETATM 20 C C2A NAD . . . O 6 -4.394 37.532 33.069 1 68.54 ? C2A NAD 406 H 1 HETATM 21 N N3A NAD . . . O 6 -3.098 37.347 33.384 1 69.96 ? N3A NAD 406 H 1 HETATM 22 C C4A NAD . . . O 6 -2.705 36.25 34.076 1 73 ? C4A NAD 406 H 1 HETATM 23 O O3 NAD . . . O 6 4.767 32.825 33.17 1 71.48 ? O3 NAD 406 H 1 HETATM 24 P PN NAD . . . O 6 5.74 32.969 31.883 1 70.34 ? PN NAD 406 H 1 HETATM 25 O O1N NAD . . . O 6 6.178 34.416 31.68 1 64.09 -1 O1N NAD 406 H 1 HETATM 26 O O2N NAD . . . O 6 5.077 32.186 30.772 1 68.3 ? O2N NAD 406 H 1 HETATM 27 O O5D NAD . . . O 6 6.954 32.044 32.387 1 67.95 ? O5D NAD 406 H 1 HETATM 28 C C5D NAD . . . O 6 6.603 30.85 33.086 1 66.21 ? C5D NAD 406 H 1 HETATM 29 C C4D NAD . . . O 6 7.604 29.789 32.724 1 64.94 ? C4D NAD 406 H 1 HETATM 30 O O4D NAD . . . O 6 7.364 28.593 33.482 1 64.59 ? O4D NAD 406 H 1 HETATM 31 C C3D NAD . . . O 6 7.52 29.436 31.265 1 64.48 ? C3D NAD 406 H 1 HETATM 32 O O3D NAD . . . O 6 8.855 29.488 30.763 1 65.78 ? O3D NAD 406 H 1 HETATM 33 C C2D NAD . . . O 6 6.861 28.065 31.25 1 63.99 ? C2D NAD 406 H 1 HETATM 34 O O2D NAD . . . O 6 7.525 27.113 30.411 1 63.35 ? O2D NAD 406 H 1 HETATM 35 C C1D NAD . . . O 6 6.868 27.521 32.669 1 63.94 ? C1D NAD 406 H 1 HETATM 36 N N1N NAD . . . O 6 5.524 27.103 33.1 1 64.54 ? N1N NAD 406 H 1 HETATM 37 C C2N NAD . . . O 6 4.637 26.547 32.243 1 64.37 ? C2N NAD 406 H 1 HETATM 38 C C3N NAD . . . O 6 3.363 26.157 32.678 1 64.86 ? C3N NAD 406 H 1 HETATM 39 C C7N NAD . . . O 6 2.349 25.568 31.744 1 63.81 ? C7N NAD 406 H 1 HETATM 40 O O7N NAD . . . O 6 2.644 24.631 31.028 1 62.11 ? O7N NAD 406 H 1 HETATM 41 N N7N NAD . . . O 6 1.131 26.114 31.705 1 63.93 ? N7N NAD 406 H 1 HETATM 42 C C4N NAD . . . O 6 3.004 26.339 34.005 1 64.81 ? C4N NAD 406 H 1 HETATM 43 C C5N NAD . . . O 6 3.93 26.908 34.868 1 66.73 ? C5N NAD 406 H 1 HETATM 44 C C6N NAD . . . O 6 5.188 27.28 34.392 1 66 ? C6N NAD 406 H 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #