data_4JK3 # _model_server_result.job_id eSt_n9WNK08KPcU4V8TtEw _model_server_result.datetime_utc '2024-10-19 10:18:56' _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 4jk3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":901}' # _entry.id 4JK3 # _exptl.entry_id 4JK3 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec 1.4.1.- # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 4JK3 _cell.length_a 79.65 _cell.length_b 155.4 _cell.length_c 39.57 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JK3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 1 A,B,C,D,E,F,G,H,I,J 3 1,2 # 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' 2_755 -x+2,-y,z -1 0 0 0 -1 0 0 0 1 159.3 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F 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 A C ASN 13 A ASN 13 1_555 A N MSE 14 A MSE 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C MSE 14 A MSE 14 1_555 A N GLN 15 A GLN 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C ASP 82 A ASP 82 1_555 A N MSE 83 A MSE 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 83 A MSE 83 1_555 A N PRO 84 A PRO 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale5 A C LEU 101 A LEU 101 1_555 A N MSE 102 A MSE 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale6 A C MSE 102 A MSE 102 1_555 A N ALA 103 A ALA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 A C LYS 117 A LYS 117 1_555 A N MSE 118 A MSE 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale8 A C MSE 118 A MSE 118 1_555 A N ALA 119 A ALA 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale9 A C SER 253 A SER 253 1_555 A N MSE 254 A MSE 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale10 A C MSE 254 A MSE 254 1_555 A N LEU 255 A LEU 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale11 B C ASN 13 B ASN 13 1_555 B N MSE 14 B MSE 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 B C MSE 14 B MSE 14 1_555 B N GLN 15 B GLN 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale13 B C ASP 82 B ASP 82 1_555 B N MSE 83 B MSE 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 B C MSE 83 B MSE 83 1_555 B N PRO 84 B PRO 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale15 B C LEU 101 B LEU 101 1_555 B N MSE 102 B MSE 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale16 B C MSE 102 B MSE 102 1_555 B N ALA 103 B ALA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 B C LYS 117 B LYS 117 1_555 B N MSE 118 B MSE 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale18 B C MSE 118 B MSE 118 1_555 B N ALA 119 B ALA 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale19 B C SER 253 B SER 253 1_555 B N MSE 254 B MSE 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale20 B C MSE 254 B MSE 254 1_555 B N LEU 255 B LEU 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? metalc ? metalc1 D NA NA . A NA 902 1_555 I O HOH . A HOH 1019 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc2 B O CYS 206 B CYS 206 1_555 G NA NA . B NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc3 A O THR 204 A THR 204 1_555 D NA NA . A NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc4 G NA NA . B NA 902 1_555 J O HOH . B HOH 1019 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc5 B O THR 204 B THR 204 1_555 G NA NA . B NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc6 A O PRO 227 A PRO 227 1_555 D NA NA . A NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc7 F O7N NAD . B NAD 901 1_555 H MG MG . B MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc8 A O CYS 206 A CYS 206 1_555 D NA NA . A NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? metalc ? metalc9 C O7N NAD . A NAD 901 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc10 A OE2 GLU 245 A GLU 245 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc11 B O PRO 227 B PRO 227 1_555 G NA NA . B NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc12 B OE1 GLU 202 B GLU 202 1_555 G NA NA . B NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? metalc ? metalc13 B OE2 GLU 245 B GLU 245 1_555 H MG MG . B MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc14 A OH TYR 129 A TYR 129 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc15 B OE2 GLU 202 B GLU 202 1_555 G NA NA . B NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc16 A OE2 GLU 202 A GLU 202 1_555 D NA NA . A NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc17 A OE1 GLU 202 A GLU 202 1_555 D NA NA . A NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? # _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 4JK3 _atom_sites.fract_transf_matrix[1][1] 0.012555 _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] 0.006435 _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] 0.025272 _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 2 NAD A 1 901 901 NAD NAD . D 3 NA A 1 902 903 NA NA . E 4 MG A 1 903 904 MG MG . F 2 NAD B 1 901 901 NAD NAD . G 3 NA B 1 902 903 NA NA . H 4 MG B 1 903 904 MG MG . I 5 HOH A 1 1001 3 HOH HOH . I 5 HOH A 2 1002 6 HOH HOH . I 5 HOH A 3 1003 8 HOH HOH . I 5 HOH A 4 1004 9 HOH HOH . I 5 HOH A 5 1005 12 HOH HOH . I 5 HOH A 6 1006 13 HOH HOH . I 5 HOH A 7 1007 14 HOH HOH . I 5 HOH A 8 1008 16 HOH HOH . I 5 HOH A 9 1009 17 HOH HOH . I 5 HOH A 10 1010 18 HOH HOH . I 5 HOH A 11 1011 19 HOH HOH . I 5 HOH A 12 1012 20 HOH HOH . I 5 HOH A 13 1013 21 HOH HOH . I 5 HOH A 14 1014 22 HOH HOH . I 5 HOH A 15 1015 23 HOH HOH . I 5 HOH A 16 1016 24 HOH HOH . I 5 HOH A 17 1017 25 HOH HOH . I 5 HOH A 18 1018 28 HOH HOH . I 5 HOH A 19 1019 29 HOH HOH . I 5 HOH A 20 1020 30 HOH HOH . I 5 HOH A 21 1021 34 HOH HOH . I 5 HOH A 22 1022 36 HOH HOH . I 5 HOH A 23 1023 37 HOH HOH . I 5 HOH A 24 1024 39 HOH HOH . I 5 HOH A 25 1025 40 HOH HOH . I 5 HOH A 26 1026 46 HOH HOH . I 5 HOH A 27 1027 47 HOH HOH . I 5 HOH A 28 1028 50 HOH HOH . I 5 HOH A 29 1029 52 HOH HOH . I 5 HOH A 30 1030 53 HOH HOH . J 5 HOH B 1 1001 5 HOH HOH . J 5 HOH B 2 1002 7 HOH HOH . J 5 HOH B 3 1003 10 HOH HOH . J 5 HOH B 4 1004 11 HOH HOH . J 5 HOH B 5 1005 15 HOH HOH . J 5 HOH B 6 1006 26 HOH HOH . J 5 HOH B 7 1007 27 HOH HOH . J 5 HOH B 8 1008 32 HOH HOH . J 5 HOH B 9 1009 33 HOH HOH . J 5 HOH B 10 1010 35 HOH HOH . J 5 HOH B 11 1011 38 HOH HOH . J 5 HOH B 12 1012 41 HOH HOH . J 5 HOH B 13 1013 42 HOH HOH . J 5 HOH B 14 1014 43 HOH HOH . J 5 HOH B 15 1015 44 HOH HOH . J 5 HOH B 16 1016 45 HOH HOH . J 5 HOH B 17 1017 48 HOH HOH . J 5 HOH B 18 1018 49 HOH HOH . J 5 HOH B 19 1019 51 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 . . . F 2 98.716 13.77 -23.276 1 39.45 ? PA NAD 901 B 1 HETATM 2 O O1A NAD . . . F 2 97.565 14.673 -22.92 1 41.47 ? O1A NAD 901 B 1 HETATM 3 O O2A NAD . . . F 2 99.143 12.578 -22.455 1 39.64 ? O2A NAD 901 B 1 HETATM 4 O O5B NAD . . . F 2 99.995 14.739 -23.397 1 42.78 ? O5B NAD 901 B 1 HETATM 5 C C5B NAD . . . F 2 99.896 16.038 -23.973 1 41.3 ? C5B NAD 901 B 1 HETATM 6 C C4B NAD . . . F 2 100.705 16.945 -23.074 1 43.32 ? C4B NAD 901 B 1 HETATM 7 O O4B NAD . . . F 2 100.866 18.235 -23.667 1 44.8 ? O4B NAD 901 B 1 HETATM 8 C C3B NAD . . . F 2 100.027 17.149 -21.726 1 44.07 ? C3B NAD 901 B 1 HETATM 9 O O3B NAD . . . F 2 101.008 16.812 -20.755 1 43.43 ? O3B NAD 901 B 1 HETATM 10 C C2B NAD . . . F 2 99.714 18.631 -21.665 1 44.74 ? C2B NAD 901 B 1 HETATM 11 O O2B NAD . . . F 2 99.908 19.107 -20.337 1 45.28 ? O2B NAD 901 B 1 HETATM 12 C C1B NAD . . . F 2 100.737 19.208 -22.638 1 44.17 ? C1B NAD 901 B 1 HETATM 13 N N9A NAD . . . F 2 100.456 20.539 -23.228 1 43.39 ? N9A NAD 901 B 1 HETATM 14 C C8A NAD . . . F 2 99.319 21.054 -23.72 1 44.37 ? C8A NAD 901 B 1 HETATM 15 N N7A NAD . . . F 2 99.524 22.332 -24.162 1 45.46 ? N7A NAD 901 B 1 HETATM 16 C C5A NAD . . . F 2 100.817 22.642 -23.952 1 43.56 ? C5A NAD 901 B 1 HETATM 17 C C6A NAD . . . F 2 101.723 23.798 -24.183 1 43.49 ? C6A NAD 901 B 1 HETATM 18 N N6A NAD . . . F 2 101.319 24.964 -24.742 1 43.2 ? N6A NAD 901 B 1 HETATM 19 N N1A NAD . . . F 2 103.01 23.661 -23.796 1 44.18 ? N1A NAD 901 B 1 HETATM 20 C C2A NAD . . . F 2 103.488 22.528 -23.24 1 43.83 ? C2A NAD 901 B 1 HETATM 21 N N3A NAD . . . F 2 102.735 21.442 -23.011 1 42.57 ? N3A NAD 901 B 1 HETATM 22 C C4A NAD . . . F 2 101.418 21.446 -23.338 1 43.51 ? C4A NAD 901 B 1 HETATM 23 O O3 NAD . . . F 2 98.556 13.346 -24.814 1 39.39 ? O3 NAD 901 B 1 HETATM 24 P PN NAD . . . F 2 99.541 12.292 -25.512 1 39.54 ? PN NAD 901 B 1 HETATM 25 O O1N NAD . . . F 2 98.936 10.929 -25.275 1 39.47 ? O1N NAD 901 B 1 HETATM 26 O O2N NAD . . . F 2 100.965 12.54 -25.066 1 38.11 ? O2N NAD 901 B 1 HETATM 27 O O5D NAD . . . F 2 99.364 12.666 -27.078 1 39.67 ? O5D NAD 901 B 1 HETATM 28 C C5D NAD . . . F 2 100.054 13.776 -27.651 1 40.82 ? C5D NAD 901 B 1 HETATM 29 C C4D NAD . . . F 2 99.497 14.115 -29.034 1 42.37 ? C4D NAD 901 B 1 HETATM 30 O O4D NAD . . . F 2 100.013 13.239 -30.042 1 42.4 ? O4D NAD 901 B 1 HETATM 31 C C3D NAD . . . F 2 97.982 14.001 -29.106 1 42.91 ? C3D NAD 901 B 1 HETATM 32 O O3D NAD . . . F 2 97.544 15.074 -29.927 1 42.69 ? O3D NAD 901 B 1 HETATM 33 C C2D NAD . . . F 2 97.718 12.709 -29.843 1 43.46 ? C2D NAD 901 B 1 HETATM 34 O O2D NAD . . . F 2 96.52 12.788 -30.611 1 45.96 ? O2D NAD 901 B 1 HETATM 35 C C1D NAD . . . F 2 98.927 12.616 -30.757 1 43.16 ? C1D NAD 901 B 1 HETATM 36 N N1N NAD . . . F 2 99.245 11.243 -31.16 1 42.98 ? N1N NAD 901 B 1 HETATM 37 C C2N NAD . . . F 2 99.668 11.052 -32.418 1 42.43 ? C2N NAD 901 B 1 HETATM 38 C C3N NAD . . . F 2 100.009 9.788 -32.898 1 41.4 ? C3N NAD 901 B 1 HETATM 39 C C7N NAD . . . F 2 100.498 9.652 -34.313 1 42.5 ? C7N NAD 901 B 1 HETATM 40 O O7N NAD . . . F 2 100.654 8.554 -34.819 1 43.94 ? O7N NAD 901 B 1 HETATM 41 N N7N NAD . . . F 2 100.789 10.759 -34.989 1 42.77 ? N7N NAD 901 B 1 HETATM 42 C C4N NAD . . . F 2 99.907 8.691 -32.053 1 41.07 ? C4N NAD 901 B 1 HETATM 43 C C5N NAD . . . F 2 99.464 8.909 -30.744 1 43.77 ? C5N NAD 901 B 1 HETATM 44 C C6N NAD . . . F 2 99.14 10.2 -30.308 1 43.57 ? C6N NAD 901 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 44 #