data_2NVB
#
_model_server_result.job_id            y6YJN35Ggh020auwq2q7PQ 
_model_server_result.datetime_utc      '2024-11-15 07:34:36' 
_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          2nvb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":2353}' 
#
_entry.id    2NVB 
#
_exptl.entry_id    2NVB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              743.405 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_entity.pdbx_number_of_molecules    4 
_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            2NVB 
_cell.length_a            79.598 
_cell.length_b            125.008 
_cell.length_c            167.111 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2NVB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA tetrameric 4 author_and_software_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
PISA dimeric 2 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,B,C,D,E,F,G,H,I,J,K,L 1 1 
A,B,E,F,G,H 2 1 
C,D,I,J,K,L 3 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
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 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 SG CYS 37 A CYS 37 1_555 E ZN ZN . A ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? 
metalc ? metalc2 A NE2 HIS 59 A HIS 59 1_555 E ZN ZN . A ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc3 A OD2 ASP 150 A ASP 150 1_555 E ZN ZN . A ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
metalc ? metalc4 B SG CYS 37 B CYS 37 1_555 G ZN ZN . B ZN 1354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc5 B NE2 HIS 59 B HIS 59 1_555 G ZN ZN . B ZN 1354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc6 B OD2 ASP 150 B ASP 150 1_555 G ZN ZN . B ZN 1354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc7 C SG CYS 37 C CYS 37 1_555 I ZN ZN . C ZN 2354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? 
metalc ? metalc8 C NE2 HIS 59 C HIS 59 1_555 I ZN ZN . C ZN 2354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc9 C OD2 ASP 150 C ASP 150 1_555 I ZN ZN . C ZN 2354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc10 D SG CYS 37 D CYS 37 1_555 K ZN ZN . D ZN 3354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? 
metalc ? metalc11 D OD2 ASP 150 D ASP 150 1_555 K ZN ZN . D ZN 3354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
#
_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 235 n n 
PA O2A NAP sing 236 n n 
PA O5B NAP sing 237 n n 
PA O3 NAP sing 238 n n 
O2A HOA2 NAP sing 239 n n 
O5B C5B NAP sing 240 n n 
C5B C4B NAP sing 241 n n 
C5B H51A NAP sing 242 n n 
C5B H52A NAP sing 243 n n 
C4B O4B NAP sing 244 n n 
C4B C3B NAP sing 245 n n 
C4B H4B NAP sing 246 n n 
O4B C1B NAP sing 247 n n 
C3B O3B NAP sing 248 n n 
C3B C2B NAP sing 249 n n 
C3B H3B NAP sing 250 n n 
O3B HO3A NAP sing 251 n n 
C2B O2B NAP sing 252 n n 
C2B C1B NAP sing 253 n n 
C2B H2B NAP sing 254 n n 
O2B P2B NAP sing 255 n n 
C1B N9A NAP sing 256 n n 
C1B H1B NAP sing 257 n n 
N9A C8A NAP sing 258 n y 
N9A C4A NAP sing 259 n y 
C8A N7A NAP doub 260 n y 
C8A H8A NAP sing 261 n n 
N7A C5A NAP sing 262 n y 
C5A C6A NAP sing 263 n y 
C5A C4A NAP doub 264 n y 
C6A N6A NAP sing 265 n n 
C6A N1A NAP doub 266 n y 
N6A H61A NAP sing 267 n n 
N6A H62A NAP sing 268 n n 
N1A C2A NAP sing 269 n y 
C2A N3A NAP doub 270 n y 
C2A H2A NAP sing 271 n n 
N3A C4A NAP sing 272 n y 
O3 PN NAP sing 273 n n 
PN O1N NAP doub 274 n n 
PN O2N NAP sing 275 n n 
PN O5D NAP sing 276 n n 
O5D C5D NAP sing 277 n n 
C5D C4D NAP sing 278 n n 
C5D H51N NAP sing 279 n n 
C5D H52N NAP sing 280 n n 
C4D O4D NAP sing 281 n n 
C4D C3D NAP sing 282 n n 
C4D H4D NAP sing 283 n n 
O4D C1D NAP sing 284 n n 
C3D O3D NAP sing 285 n n 
C3D C2D NAP sing 286 n n 
C3D H3D NAP sing 287 n n 
O3D HO3N NAP sing 288 n n 
C2D O2D NAP sing 289 n n 
C2D C1D NAP sing 290 n n 
C2D H2D NAP sing 291 n n 
O2D HO2N NAP sing 292 n n 
C1D N1N NAP sing 293 n n 
C1D H1D NAP sing 294 n n 
N1N C2N NAP sing 295 n y 
N1N C6N NAP doub 296 n y 
C2N C3N NAP doub 297 n y 
C2N H2N NAP sing 298 n n 
C3N C7N NAP sing 299 n n 
C3N C4N NAP sing 300 n y 
C7N O7N NAP doub 301 n n 
C7N N7N NAP sing 302 n n 
N7N H71N NAP sing 303 n n 
N7N H72N NAP sing 304 n n 
C4N C5N NAP doub 305 n y 
C4N H4N NAP sing 306 n n 
C5N C6N NAP sing 307 n y 
C5N H5N NAP sing 308 n n 
C6N H6N NAP sing 309 n n 
P2B O1X NAP doub 310 n n 
P2B O2X NAP sing 311 n n 
P2B O3X NAP sing 312 n n 
O2X HOP2 NAP sing 313 n n 
O3X HOP3 NAP sing 314 n n 
#
_atom_sites.entry_id                     2NVB 
_atom_sites.fract_transf_matrix[1][1]    0.012563 
_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]    0.007999 
_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]    0.005984 
_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 2 ZN A 1 354 354 ZN ZN . 
F 3 NAP A 1 353 353 NAP NAP . 
G 2 ZN B 1 1354 1354 ZN ZN . 
H 3 NAP B 1 1353 1353 NAP NAP . 
I 2 ZN C 1 2354 2354 ZN ZN . 
J 3 NAP C 1 2353 2353 NAP NAP . 
K 2 ZN D 1 3354 3354 ZN ZN . 
L 3 NAP D 1 3353 3353 NAP NAP . 
#
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 . . . J 3 70.353 91.656 22.22 1 101.44 ? PA NAP 2353 C 1 
HETATM 2 O O1A NAP . . . J 3 68.908 91.574 21.884 1 101.78 ? O1A NAP 2353 C 1 
HETATM 3 O O2A NAP . . . J 3 70.961 92.913 22.654 1 94.2 ? O2A NAP 2353 C 1 
HETATM 4 O O5B NAP . . . J 3 71.127 91.016 20.925 1 40.39 ? O5B NAP 2353 C 1 
HETATM 5 C C5B NAP . . . J 3 72.546 91.05 20.883 1 100.87 ? C5B NAP 2353 C 1 
HETATM 6 C C4B NAP . . . J 3 73.026 90.385 19.625 1 97.78 ? C4B NAP 2353 C 1 
HETATM 7 O O4B NAP . . . J 3 72.443 91.014 18.466 1 40.39 ? O4B NAP 2353 C 1 
HETATM 8 C C3B NAP . . . J 3 74.499 90.478 19.479 1 96.13 ? C3B NAP 2353 C 1 
HETATM 9 O O3B NAP . . . J 3 75.064 89.364 18.765 1 40.39 ? O3B NAP 2353 C 1 
HETATM 10 C C2B NAP . . . J 3 74.57 91.765 18.656 1 96.21 ? C2B NAP 2353 C 1 
HETATM 11 O O2B NAP . . . J 3 75.823 92.111 18.022 1 40.39 ? O2B NAP 2353 C 1 
HETATM 12 C C1B NAP . . . J 3 73.523 91.456 17.644 1 95.99 ? C1B NAP 2353 C 1 
HETATM 13 N N9A NAP . . . J 3 73.078 92.609 16.809 1 97.19 ? N9A NAP 2353 C 1 
HETATM 14 C C8A NAP . . . J 3 72.703 93.912 17.16 1 96.4 ? C8A NAP 2353 C 1 
HETATM 15 N N7A NAP . . . J 3 72.381 94.632 16.122 1 96.6 ? N7A NAP 2353 C 1 
HETATM 16 C C5A NAP . . . J 3 72.549 93.778 15.057 1 96.36 ? C5A NAP 2353 C 1 
HETATM 17 C C6A NAP . . . J 3 72.372 93.938 13.676 1 97.46 ? C6A NAP 2353 C 1 
HETATM 18 N N6A NAP . . . J 3 71.97 95.084 13.172 1 97.55 ? N6A NAP 2353 C 1 
HETATM 19 N N1A NAP . . . J 3 72.628 92.862 12.851 1 97.45 ? N1A NAP 2353 C 1 
HETATM 20 C C2A NAP . . . J 3 73.041 91.679 13.365 1 96.82 ? C2A NAP 2353 C 1 
HETATM 21 N N3A NAP . . . J 3 73.236 91.444 14.663 1 96.43 ? N3A NAP 2353 C 1 
HETATM 22 C C4A NAP . . . J 3 72.966 92.555 15.457 1 95.97 ? C4A NAP 2353 C 1 
HETATM 23 O O3 NAP . . . J 3 70.518 90.449 23.329 1 99.99 ? O3 NAP 2353 C 1 
HETATM 24 P PN NAP . . . J 3 69.553 89.902 24.532 1 97.07 ? PN NAP 2353 C 1 
HETATM 25 O O1N NAP . . . J 3 70.396 89.647 25.69 1 97.07 ? O1N NAP 2353 C 1 
HETATM 26 O O2N NAP . . . J 3 68.575 91.018 24.672 1 88.35 ? O2N NAP 2353 C 1 
HETATM 27 O O5D NAP . . . J 3 68.616 88.652 24.101 1 40.39 ? O5D NAP 2353 C 1 
HETATM 28 C C5D NAP . . . J 3 67.996 88.504 22.778 1 40.39 ? C5D NAP 2353 C 1 
HETATM 29 C C4D NAP . . . J 3 66.504 88.979 22.668 1 40.39 ? C4D NAP 2353 C 1 
HETATM 30 O O4D NAP . . . J 3 65.617 87.875 22.303 1 40.39 ? O4D NAP 2353 C 1 
HETATM 31 C C3D NAP . . . J 3 65.839 89.333 23.99 1 40.39 ? C3D NAP 2353 C 1 
HETATM 32 O O3D NAP . . . J 3 66.312 90.441 24.699 1 40.39 ? O3D NAP 2353 C 1 
HETATM 33 C C2D NAP . . . J 3 64.46 89.584 23.518 1 40.39 ? C2D NAP 2353 C 1 
HETATM 34 O O2D NAP . . . J 3 64.318 90.689 22.638 1 40.39 ? O2D NAP 2353 C 1 
HETATM 35 C C1D NAP . . . J 3 64.247 88.197 22.81 1 40.39 ? C1D NAP 2353 C 1 
HETATM 36 N N1N NAP . . . J 3 63.753 87.286 23.892 1 86.28 ? N1N NAP 2353 C 1 
HETATM 37 C C2N NAP . . . J 3 62.419 87.541 24.38 1 86.61 ? C2N NAP 2353 C 1 
HETATM 38 C C3N NAP . . . J 3 61.936 86.677 25.441 1 88.75 ? C3N NAP 2353 C 1 
HETATM 39 C C7N NAP . . . J 3 60.603 86.796 26.059 1 89.98 ? C7N NAP 2353 C 1 
HETATM 40 O O7N NAP . . . J 3 60.223 86.037 26.969 1 90.31 ? O7N NAP 2353 C 1 
HETATM 41 N N7N NAP . . . J 3 59.74 87.732 25.666 1 91.82 ? N7N NAP 2353 C 1 
HETATM 42 C C4N NAP . . . J 3 62.777 85.683 25.905 1 87.6 ? C4N NAP 2353 C 1 
HETATM 43 C C5N NAP . . . J 3 64.018 85.467 25.433 1 87.13 ? C5N NAP 2353 C 1 
HETATM 44 C C6N NAP . . . J 3 64.513 86.255 24.434 1 85.86 ? C6N NAP 2353 C 1 
HETATM 45 P P2B NAP . . . J 3 77.03 92.791 18.89 1 40.39 ? P2B NAP 2353 C 1 
HETATM 46 O O1X NAP . . . J 3 77.972 91.696 19.322 1 40.39 ? O1X NAP 2353 C 1 
HETATM 47 O O2X NAP . . . J 3 77.575 93.735 17.885 1 40.39 ? O2X NAP 2353 C 1 
HETATM 48 O O3X NAP . . . J 3 76.342 93.514 20.019 1 40.39 ? O3X NAP 2353 C 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           48 
#