data_6OFB # _model_server_result.job_id 601tYcxTFey7hMLNEpzaLQ _model_server_result.datetime_utc '2025-08-31 00:25:36' _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 6ofb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":901}' # _entry.id 6OFB # _exptl.entry_id 6OFB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 665.418 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICOTINIC ACID 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 90 _cell.entry_id 6OFB _cell.length_a 102.25 _cell.length_b 198.89 _cell.length_c 219.69 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6OFB _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall 'I 2 2' _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 198.89 0 3 'crystal symmetry operation' 3_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 219.69 4 'crystal symmetry operation' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 198.89 219.69 # 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 L 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 metalc ? metalc1 A N VAL 361 A VAL 360 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc2 A N ASP 362 A ASP 361 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? metalc ? metalc3 E O2 POP . A POP 903 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc4 E O3 POP . A POP 903 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc5 E O5 POP . A POP 903 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc6 B N VAL 361 B VAL 360 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? metalc ? metalc7 B N ASP 362 B ASP 361 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc8 N O1 POP . B POP 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc9 N O3 POP . B POP 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc10 N O5 POP . B POP 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? # _chem_comp.formula 'C21 H27 N6 O15 P2 1' _chem_comp.formula_weight 665.418 _chem_comp.id DND _chem_comp.mon_nstd_flag . _chem_comp.name 'NICOTINIC ACID ADENINE DINUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DEAMIDO-NAD+ # 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 O13 PA DND doub 122 n n O14 PA DND sing 123 n n PA O3P DND sing 124 n n PA O5B DND sing 125 n n O11 PN DND doub 126 n n O3P PN DND sing 127 n n O5B C5B DND sing 128 n n PN O12 DND sing 129 n n PN O5D DND sing 130 n n C5B C4B DND sing 131 n n N7A C8A DND doub 132 n y N7A C5A DND sing 133 n y C8A N9A DND sing 134 n y N6A C6A DND sing 135 n n O5D C5D DND sing 136 n n C5A C6A DND sing 137 n y C5A C4A DND doub 138 n y O4B C4B DND sing 139 n n O4B C1B DND sing 140 n n C6A N1A DND doub 141 n y C4B C3B DND sing 142 n n N9A C4A DND sing 143 n y N9A C1B DND sing 144 n n C5D C4D DND sing 145 n n C3D O3D DND sing 146 n n C3D C4D DND sing 147 n n C3D C2D DND sing 148 n n C4A N3A DND sing 149 n y C1B C2B DND sing 150 n n N1A C2A DND sing 151 n y C4D O4D DND sing 152 n n C2B C3B DND sing 153 n n C2B O2B DND sing 154 n n C2D O2D DND sing 155 n n C2D C1D DND sing 156 n n C3B O3B DND sing 157 n n N3A C2A DND doub 158 n y O4D C1D DND sing 159 n n C1D N1N DND sing 160 n n C6N N1N DND doub 161 n y C6N C5N DND sing 162 n y N1N C2N DND sing 163 n y C5N C4N DND doub 164 n y C2N C3N DND doub 165 n y C4N C3N DND sing 166 n y C3N C7N DND sing 167 n n C7N O7N DND doub 168 n n C7N O8N DND sing 169 n n O12 H1 DND sing 170 n n C5D H2 DND sing 171 n n C5D H3 DND sing 172 n n C4D H4 DND sing 173 n n C3D H5 DND sing 174 n n O3D H6 DND sing 175 n n C2D H7 DND sing 176 n n O2D H8 DND sing 177 n n C1D H9 DND sing 178 n n C6N H10 DND sing 179 n n C5N H11 DND sing 180 n n C4N H12 DND sing 181 n n C2N H13 DND sing 182 n n O8N H14 DND sing 183 n n O14 H15 DND sing 184 n n C5B H16 DND sing 185 n n C5B H17 DND sing 186 n n C4B H18 DND sing 187 n n C3B H19 DND sing 188 n n O3B H20 DND sing 189 n n C2B H21 DND sing 190 n n O2B H22 DND sing 191 n n C1B H23 DND sing 192 n n C2A H24 DND sing 193 n n C8A H25 DND sing 194 n n N6A H26 DND sing 195 n n N6A H27 DND sing 196 n n # _atom_sites.entry_id 6OFB _atom_sites.fract_transf_matrix[1][1] 0.00978 _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] 0.005028 _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] 0.004552 _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 DND A 1 901 901 DND NXX . D 3 AMP A 1 902 902 AMP AMP . E 4 POP A 1 903 903 POP POP . F 5 MG A 1 904 904 MG MG . G 6 CL A 1 905 905 CL CL . H 6 CL A 1 906 906 CL CL . I 6 CL A 1 907 907 CL CL . J 6 CL A 1 908 908 CL CL . K 6 CL A 1 909 909 CL CL . L 2 DND B 1 901 901 DND NXX . M 3 AMP B 1 902 902 AMP AMP . N 4 POP B 1 903 903 POP POP . O 5 MG B 1 904 904 MG MG . P 6 CL B 1 905 905 CL CL . Q 6 CL B 1 906 906 CL CL . R 6 CL B 1 907 907 CL CL . S 6 CL B 1 908 908 CL CL . T 7 HOH A 1 1001 1008 HOH HOH . T 7 HOH A 2 1002 1010 HOH HOH . T 7 HOH A 3 1003 1013 HOH HOH . T 7 HOH A 4 1004 1007 HOH HOH . T 7 HOH A 5 1005 1011 HOH HOH . T 7 HOH A 6 1006 1005 HOH HOH . T 7 HOH A 7 1007 1009 HOH HOH . T 7 HOH A 8 1008 1024 HOH HOH . T 7 HOH A 9 1009 1001 HOH HOH . T 7 HOH A 10 1010 1002 HOH HOH . T 7 HOH A 11 1011 1003 HOH HOH . T 7 HOH A 12 1012 1004 HOH HOH . T 7 HOH A 13 1013 1015 HOH HOH . T 7 HOH A 14 1014 1012 HOH HOH . T 7 HOH A 15 1015 1014 HOH HOH . T 7 HOH A 16 1016 1006 HOH HOH . U 7 HOH B 1 1001 1027 HOH HOH . U 7 HOH B 2 1002 1026 HOH HOH . U 7 HOH B 3 1003 1001 HOH HOH . U 7 HOH B 4 1004 1022 HOH HOH . U 7 HOH B 5 1005 1030 HOH HOH . U 7 HOH B 6 1006 1016 HOH HOH . U 7 HOH B 7 1007 1005 HOH HOH . U 7 HOH B 8 1008 1002 HOH HOH . U 7 HOH B 9 1009 1020 HOH HOH . U 7 HOH B 10 1010 1023 HOH HOH . U 7 HOH B 11 1011 1017 HOH HOH . U 7 HOH B 12 1012 1018 HOH HOH . U 7 HOH B 13 1013 1012 HOH HOH . U 7 HOH B 14 1014 1032 HOH HOH . U 7 HOH B 15 1015 1006 HOH HOH . U 7 HOH B 16 1016 1003 HOH HOH . U 7 HOH B 17 1017 1011 HOH HOH . U 7 HOH B 18 1018 1014 HOH HOH . U 7 HOH B 19 1019 1010 HOH HOH . U 7 HOH B 20 1020 1009 HOH HOH . U 7 HOH B 21 1021 1007 HOH HOH . U 7 HOH B 22 1022 1031 HOH HOH . U 7 HOH B 23 1023 1025 HOH HOH . U 7 HOH B 24 1024 1019 HOH HOH . U 7 HOH B 25 1025 1015 HOH HOH . U 7 HOH B 26 1026 1029 HOH HOH . U 7 HOH B 27 1027 1008 HOH HOH . U 7 HOH B 28 1028 1021 HOH HOH . U 7 HOH B 29 1029 1004 HOH HOH . U 7 HOH B 30 1030 1028 HOH HOH . U 7 HOH B 31 1031 1013 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 PN DND . . . L 2 -13.188 57.011 60.016 1 206.89 ? PN DND 901 B 1 HETATM 2 O O11 DND . . . L 2 -11.739 57.445 60.038 1 206.68 ? O11 DND 901 B 1 HETATM 3 O O12 DND . . . L 2 -14.119 57.354 61.158 1 205.6 ? O12 DND 901 B 1 HETATM 4 O O3P DND . . . L 2 -13.224 55.41 59.81 1 233.63 ? O3P DND 901 B 1 HETATM 5 O O5D DND . . . L 2 -13.855 57.608 58.668 1 167.73 ? O5D DND 901 B 1 HETATM 6 C C5D DND . . . L 2 -13.031 58.308 57.726 1 171.36 ? C5D DND 901 B 1 HETATM 7 C C4D DND . . . L 2 -13.633 59.621 57.209 1 175.54 ? C4D DND 901 B 1 HETATM 8 O O4D DND . . . L 2 -12.736 60.211 56.258 1 176.76 ? O4D DND 901 B 1 HETATM 9 C C3D DND . . . L 2 -14.98 59.473 56.505 1 176.19 ? C3D DND 901 B 1 HETATM 10 O O3D DND . . . L 2 -15.96 60.258 57.199 1 173.21 ? O3D DND 901 B 1 HETATM 11 C C2D DND . . . L 2 -14.769 59.996 55.087 1 175.76 ? C2D DND 901 B 1 HETATM 12 O O2D DND . . . L 2 -15.847 60.828 54.634 1 171.22 ? O2D DND 901 B 1 HETATM 13 C C1D DND . . . L 2 -13.472 60.781 55.17 1 178.06 ? C1D DND 901 B 1 HETATM 14 N N1N DND . . . L 2 -12.681 60.678 53.944 1 181.43 ? N1N DND 901 B 1 HETATM 15 C C6N DND . . . L 2 -12.994 59.823 52.954 1 181.83 ? C6N DND 901 B 1 HETATM 16 C C5N DND . . . L 2 -12.209 59.753 51.803 1 183.4 ? C5N DND 901 B 1 HETATM 17 C C4N DND . . . L 2 -11.091 60.574 51.69 1 186.17 ? C4N DND 901 B 1 HETATM 18 C C3N DND . . . L 2 -10.808 61.449 52.734 1 188.06 ? C3N DND 901 B 1 HETATM 19 C C2N DND . . . L 2 -11.616 61.472 53.854 1 184.35 ? C2N DND 901 B 1 HETATM 20 C C7N DND . . . L 2 -9.627 62.367 52.715 1 191.89 ? C7N DND 901 B 1 HETATM 21 O O7N DND . . . L 2 -9.822 63.603 52.678 1 191.66 ? O7N DND 901 B 1 HETATM 22 O O8N DND . . . L 2 -8.484 61.864 52.781 1 194.31 ? O8N DND 901 B 1 HETATM 23 P PA DND . . . L 2 -12.238 54.326 60.513 1 251.09 ? PA DND 901 B 1 HETATM 24 O O13 DND . . . L 2 -13.108 53.179 60.972 1 250.03 ? O13 DND 901 B 1 HETATM 25 O O14 DND . . . L 2 -11.153 54.015 59.508 1 251.15 ? O14 DND 901 B 1 HETATM 26 O O5B DND . . . L 2 -11.531 54.956 61.831 1 157.06 ? O5B DND 901 B 1 HETATM 27 C C5B DND . . . L 2 -12.256 55.324 63.01 1 155.9 ? C5B DND 901 B 1 HETATM 28 C C4B DND . . . L 2 -12.15 54.291 64.14 1 154.29 ? C4B DND 901 B 1 HETATM 29 O O4B DND . . . L 2 -12.344 54.928 65.418 1 155.64 ? O4B DND 901 B 1 HETATM 30 C C3B DND . . . L 2 -13.241 53.233 64.019 1 150.03 ? C3B DND 901 B 1 HETATM 31 O O3B DND . . . L 2 -12.692 51.916 64.149 1 142.87 ? O3B DND 901 B 1 HETATM 32 C C2B DND . . . L 2 -14.188 53.498 65.174 1 151.21 ? C2B DND 901 B 1 HETATM 33 O O2B DND . . . L 2 -14.732 52.259 65.644 1 153.82 ? O2B DND 901 B 1 HETATM 34 C C1B DND . . . L 2 -13.308 54.206 66.209 1 147.59 ? C1B DND 901 B 1 HETATM 35 N N9A DND . . . L 2 -14.072 55.055 67.201 1 131.72 ? N9A DND 901 B 1 HETATM 36 C C4A DND . . . L 2 -13.666 55.446 68.429 1 118.85 ? C4A DND 901 B 1 HETATM 37 N N3A DND . . . L 2 -12.533 55.274 69.13 1 112.11 ? N3A DND 901 B 1 HETATM 38 C C2A DND . . . L 2 -12.367 55.786 70.369 1 106.09 ? C2A DND 901 B 1 HETATM 39 N N1A DND . . . L 2 -13.313 56.508 70.995 1 102.28 ? N1A DND 901 B 1 HETATM 40 C C6A DND . . . L 2 -14.491 56.744 70.373 1 109.75 ? C6A DND 901 B 1 HETATM 41 C C5A DND . . . L 2 -14.692 56.184 69.009 1 116.53 ? C5A DND 901 B 1 HETATM 42 N N7A DND . . . L 2 -15.715 56.231 68.135 1 119.62 ? N7A DND 901 B 1 HETATM 43 C C8A DND . . . L 2 -15.327 55.526 67.042 1 128.46 ? C8A DND 901 B 1 HETATM 44 N N6A DND . . . L 2 -15.474 57.469 70.962 1 108.78 ? N6A DND 901 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 62 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 684 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #