data_2VNA # _model_server_result.job_id RYu2S2gJ8QP7HSOgzTS41A _model_server_result.datetime_utc '2024-10-12 21:22:52' _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 2vna # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 2VNA # _exptl.entry_id 2VNA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 108.43 _cell.angle_gamma 90 _cell.entry_id 2VNA _cell.length_a 70.335 _cell.length_b 83.505 _cell.length_c 72.585 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VNA _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C21 H28 N7 O17 P3' _chem_comp.formula_weight 743.405 _chem_comp.id NAP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" # 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 NAP doub 237 n n PA O2A NAP sing 238 n n PA O5B NAP sing 239 n n PA O3 NAP sing 240 n n O2A HOA2 NAP sing 241 n n O5B C5B NAP sing 242 n n C5B C4B NAP sing 243 n n C5B H51A NAP sing 244 n n C5B H52A NAP sing 245 n n C4B O4B NAP sing 246 n n C4B C3B NAP sing 247 n n C4B H4B NAP sing 248 n n O4B C1B NAP sing 249 n n C3B O3B NAP sing 250 n n C3B C2B NAP sing 251 n n C3B H3B NAP sing 252 n n O3B HO3A NAP sing 253 n n C2B O2B NAP sing 254 n n C2B C1B NAP sing 255 n n C2B H2B NAP sing 256 n n O2B P2B NAP sing 257 n n C1B N9A NAP sing 258 n n C1B H1B NAP sing 259 n n N9A C8A NAP sing 260 n y N9A C4A NAP sing 261 n y C8A N7A NAP doub 262 n y C8A H8A NAP sing 263 n n N7A C5A NAP sing 264 n y C5A C6A NAP sing 265 n y C5A C4A NAP doub 266 n y C6A N6A NAP sing 267 n n C6A N1A NAP doub 268 n y N6A H61A NAP sing 269 n n N6A H62A NAP sing 270 n n N1A C2A NAP sing 271 n y C2A N3A NAP doub 272 n y C2A H2A NAP sing 273 n n N3A C4A NAP sing 274 n y O3 PN NAP sing 275 n n PN O1N NAP doub 276 n n PN O2N NAP sing 277 n n PN O5D NAP sing 278 n n O5D C5D NAP sing 279 n n C5D C4D NAP sing 280 n n C5D H51N NAP sing 281 n n C5D H52N NAP sing 282 n n C4D O4D NAP sing 283 n n C4D C3D NAP sing 284 n n C4D H4D NAP sing 285 n n O4D C1D NAP sing 286 n n C3D O3D NAP sing 287 n n C3D C2D NAP sing 288 n n C3D H3D NAP sing 289 n n O3D HO3N NAP sing 290 n n C2D O2D NAP sing 291 n n C2D C1D NAP sing 292 n n C2D H2D NAP sing 293 n n O2D HO2N NAP sing 294 n n C1D N1N NAP sing 295 n n C1D H1D NAP sing 296 n n N1N C2N NAP sing 297 n y N1N C6N NAP doub 298 n y C2N C3N NAP doub 299 n y C2N H2N NAP sing 300 n n C3N C7N NAP sing 301 n n C3N C4N NAP sing 302 n y C7N O7N NAP doub 303 n n C7N N7N NAP sing 304 n n N7N H71N NAP sing 305 n n N7N H72N NAP sing 306 n n C4N C5N NAP doub 307 n y C4N H4N NAP sing 308 n n C5N C6N NAP sing 309 n y C5N H5N NAP sing 310 n n C6N H6N NAP sing 311 n n P2B O1X NAP doub 312 n n P2B O2X NAP sing 313 n n P2B O3X NAP sing 314 n n O2X HOP2 NAP sing 315 n n O3X HOP3 NAP sing 316 n n # _atom_sites.entry_id 2VNA _atom_sites.fract_transf_matrix[1][1] 0.014218 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004738 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011975 _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] 0.014522 _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 B 2 NAP A 1 801 801 NAP NAP . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 HOH HOH . C 3 HOH A 8 2008 2008 HOH HOH . C 3 HOH A 9 2009 2009 HOH HOH . C 3 HOH A 10 2010 2010 HOH HOH . C 3 HOH A 11 2011 2011 HOH HOH . C 3 HOH A 12 2012 2012 HOH HOH . C 3 HOH A 13 2013 2013 HOH HOH . C 3 HOH A 14 2014 2014 HOH HOH . C 3 HOH A 15 2015 2015 HOH HOH . C 3 HOH A 16 2016 2016 HOH HOH . C 3 HOH A 17 2017 2017 HOH HOH . C 3 HOH A 18 2018 2018 HOH HOH . C 3 HOH A 19 2019 2019 HOH HOH . C 3 HOH A 20 2020 2020 HOH HOH . C 3 HOH A 21 2021 2021 HOH HOH . C 3 HOH A 22 2022 2022 HOH HOH . C 3 HOH A 23 2023 2023 HOH HOH . C 3 HOH A 24 2024 2024 HOH HOH . C 3 HOH A 25 2025 2025 HOH HOH . C 3 HOH A 26 2026 2026 HOH HOH . C 3 HOH A 27 2027 2027 HOH HOH . C 3 HOH A 28 2028 2028 HOH HOH . C 3 HOH A 29 2029 2029 HOH HOH . C 3 HOH A 30 2030 2030 HOH HOH . C 3 HOH A 31 2031 2031 HOH HOH . C 3 HOH A 32 2032 2032 HOH HOH . C 3 HOH A 33 2033 2033 HOH HOH . C 3 HOH A 34 2034 2034 HOH HOH . C 3 HOH A 35 2035 2035 HOH HOH . C 3 HOH A 36 2036 2036 HOH HOH . C 3 HOH A 37 2037 2037 HOH HOH . C 3 HOH A 38 2038 2038 HOH HOH . C 3 HOH A 39 2039 2039 HOH HOH . C 3 HOH A 40 2040 2040 HOH HOH . C 3 HOH A 41 2041 2041 HOH HOH . C 3 HOH A 42 2042 2042 HOH HOH . C 3 HOH A 43 2043 2043 HOH HOH . C 3 HOH A 44 2044 2044 HOH HOH . C 3 HOH A 45 2045 2045 HOH HOH . C 3 HOH A 46 2046 2046 HOH HOH . C 3 HOH A 47 2047 2047 HOH HOH . C 3 HOH A 48 2048 2048 HOH HOH . C 3 HOH A 49 2049 2049 HOH HOH . C 3 HOH A 50 2050 2050 HOH HOH . C 3 HOH A 51 2051 2051 HOH HOH . C 3 HOH A 52 2052 2052 HOH HOH . C 3 HOH A 53 2053 2053 HOH HOH . C 3 HOH A 54 2054 2054 HOH HOH . C 3 HOH A 55 2055 2055 HOH HOH . C 3 HOH A 56 2056 2056 HOH HOH . C 3 HOH A 57 2057 2057 HOH HOH . C 3 HOH A 58 2058 2058 HOH HOH . C 3 HOH A 59 2059 2059 HOH HOH . C 3 HOH A 60 2060 2060 HOH HOH . C 3 HOH A 61 2061 2061 HOH HOH . C 3 HOH A 62 2062 2062 HOH HOH . C 3 HOH A 63 2063 2063 HOH HOH . C 3 HOH A 64 2064 2064 HOH HOH . C 3 HOH A 65 2065 2065 HOH HOH . C 3 HOH A 66 2066 2066 HOH HOH . C 3 HOH A 67 2067 2067 HOH HOH . C 3 HOH A 68 2068 2068 HOH HOH . C 3 HOH A 69 2069 2069 HOH HOH . C 3 HOH A 70 2070 2070 HOH HOH . C 3 HOH A 71 2071 2071 HOH HOH . C 3 HOH A 72 2072 2072 HOH HOH . C 3 HOH A 73 2073 2073 HOH HOH . C 3 HOH A 74 2074 2074 HOH HOH . C 3 HOH A 75 2075 2075 HOH HOH . C 3 HOH A 76 2076 2076 HOH HOH . C 3 HOH A 77 2077 2077 HOH HOH . C 3 HOH A 78 2078 2078 HOH HOH . C 3 HOH A 79 2079 2079 HOH HOH . C 3 HOH A 80 2080 2080 HOH HOH . C 3 HOH A 81 2081 2081 HOH HOH . C 3 HOH A 82 2082 2082 HOH HOH . C 3 HOH A 83 2083 2083 HOH HOH . C 3 HOH A 84 2084 2084 HOH HOH . C 3 HOH A 85 2085 2085 HOH HOH . C 3 HOH A 86 2086 2086 HOH HOH . C 3 HOH A 87 2087 2087 HOH HOH . C 3 HOH A 88 2088 2088 HOH HOH . C 3 HOH A 89 2089 2089 HOH HOH . C 3 HOH A 90 2090 2090 HOH HOH . C 3 HOH A 91 2091 2091 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 NAP . . . B 2 20.88 -10.836 -18.906 1 29.77 ? PA NAP 801 A 1 HETATM 2 O O1A NAP . . . B 2 19.509 -10.161 -18.311 1 44.09 ? O1A NAP 801 A 1 HETATM 3 O O2A NAP . . . B 2 21.583 -9.905 -19.789 1 35.65 ? O2A NAP 801 A 1 HETATM 4 O O5B NAP . . . B 2 20.608 -12.262 -19.659 1 42.72 ? O5B NAP 801 A 1 HETATM 5 C C5B NAP . . . B 2 21.743 -12.904 -20.194 1 39.57 ? C5B NAP 801 A 1 HETATM 6 C C4B NAP . . . B 2 21.713 -12.73 -21.698 1 48.6 ? C4B NAP 801 A 1 HETATM 7 O O4B NAP . . . B 2 22.942 -12.887 -22.38 1 39.04 ? O4B NAP 801 A 1 HETATM 8 C C3B NAP . . . B 2 20.646 -13.554 -22.436 1 40.47 ? C3B NAP 801 A 1 HETATM 9 O O3B NAP . . . B 2 19.368 -13.018 -22.194 1 36.35 ? O3B NAP 801 A 1 HETATM 10 C C2B NAP . . . B 2 21.112 -13.532 -23.915 1 44.82 ? C2B NAP 801 A 1 HETATM 11 O O2B NAP . . . B 2 20.318 -12.661 -24.711 1 38.4 ? O2B NAP 801 A 1 HETATM 12 C C1B NAP . . . B 2 22.588 -13.072 -23.774 1 37.61 ? C1B NAP 801 A 1 HETATM 13 N N9A NAP . . . B 2 23.443 -14.162 -24.231 1 38.83 ? N9A NAP 801 A 1 HETATM 14 C C8A NAP . . . B 2 23.532 -15.418 -23.681 1 46.04 ? C8A NAP 801 A 1 HETATM 15 N N7A NAP . . . B 2 24.528 -16.122 -24.437 1 40.56 ? N7A NAP 801 A 1 HETATM 16 C C5A NAP . . . B 2 25.024 -15.236 -25.431 1 43.04 ? C5A NAP 801 A 1 HETATM 17 C C6A NAP . . . B 2 26.039 -15.391 -26.483 1 30.17 ? C6A NAP 801 A 1 HETATM 18 N N6A NAP . . . B 2 26.74 -16.644 -26.592 1 25.73 ? N6A NAP 801 A 1 HETATM 19 N N1A NAP . . . B 2 26.321 -14.396 -27.292 1 42.05 ? N1A NAP 801 A 1 HETATM 20 C C2A NAP . . . B 2 25.668 -13.153 -27.175 1 43.14 ? C2A NAP 801 A 1 HETATM 21 N N3A NAP . . . B 2 24.665 -12.998 -26.134 1 32.77 ? N3A NAP 801 A 1 HETATM 22 C C4A NAP . . . B 2 24.386 -14.027 -25.323 1 32.22 ? C4A NAP 801 A 1 HETATM 23 O O3 NAP . . . B 2 21.824 -11.228 -17.622 1 36.44 ? O3 NAP 801 A 1 HETATM 24 P PN NAP . . . B 2 22.547 -9.99 -16.776 1 26.08 ? PN NAP 801 A 1 HETATM 25 O O1N NAP . . . B 2 22.129 -8.496 -17.26 1 28.67 ? O1N NAP 801 A 1 HETATM 26 O O2N NAP . . . B 2 22.23 -10.214 -15.36 1 26.94 ? O2N NAP 801 A 1 HETATM 27 O O5D NAP . . . B 2 24.178 -10.081 -17.029 1 33.19 ? O5D NAP 801 A 1 HETATM 28 C C5D NAP . . . B 2 24.631 -9.767 -18.322 1 28.49 ? C5D NAP 801 A 1 HETATM 29 C C4D NAP . . . B 2 26.153 -9.627 -18.261 1 35.38 ? C4D NAP 801 A 1 HETATM 30 O O4D NAP . . . B 2 26.584 -8.685 -17.159 1 34.69 ? O4D NAP 801 A 1 HETATM 31 C C3D NAP . . . B 2 26.907 -10.964 -17.918 1 36 ? C3D NAP 801 A 1 HETATM 32 O O3D NAP . . . B 2 28.081 -11.13 -18.651 1 33.88 ? O3D NAP 801 A 1 HETATM 33 C C2D NAP . . . B 2 27.152 -10.849 -16.443 1 48.51 ? C2D NAP 801 A 1 HETATM 34 O O2D NAP . . . B 2 28.056 -11.779 -15.943 1 34.48 ? O2D NAP 801 A 1 HETATM 35 C C1D NAP . . . B 2 27.545 -9.404 -16.365 1 25.44 ? C1D NAP 801 A 1 HETATM 36 N N1N NAP . . . B 2 27.466 -8.885 -14.981 1 24.82 ? N1N NAP 801 A 1 HETATM 37 C C2N NAP . . . B 2 28.642 -8.222 -14.416 1 27.79 ? C2N NAP 801 A 1 HETATM 38 C C3N NAP . . . B 2 28.605 -7.65 -12.995 1 23.66 ? C3N NAP 801 A 1 HETATM 39 C C7N NAP . . . B 2 29.929 -7.104 -12.425 1 30.15 ? C7N NAP 801 A 1 HETATM 40 O O7N NAP . . . B 2 30.071 -6.789 -11.271 1 29.36 ? O7N NAP 801 A 1 HETATM 41 N N7N NAP . . . B 2 30.953 -6.82 -13.413 1 30.11 ? N7N NAP 801 A 1 HETATM 42 C C4N NAP . . . B 2 27.315 -7.646 -12.155 1 29.01 ? C4N NAP 801 A 1 HETATM 43 C C5N NAP . . . B 2 26.079 -8.214 -12.904 1 31.1 ? C5N NAP 801 A 1 HETATM 44 C C6N NAP . . . B 2 26.188 -8.82 -14.296 1 27.85 ? C6N NAP 801 A 1 HETATM 45 P P2B NAP . . . B 2 20.411 -12.469 -26.371 1 40.77 ? P2B NAP 801 A 1 HETATM 46 O O1X NAP . . . B 2 21.66 -13.327 -26.977 1 46.52 ? O1X NAP 801 A 1 HETATM 47 O O2X NAP . . . B 2 19.042 -13.08 -27.072 1 50.51 ? O2X NAP 801 A 1 HETATM 48 O O3X NAP . . . B 2 20.499 -11.032 -26.622 1 32.07 ? O3X NAP 801 A 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #