data_7YB1
#
_model_server_result.job_id            lYdQQi4-WwGsm4JHNaOVRQ 
_model_server_result.datetime_utc      '2024-11-28 16:01:30' 
_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          7yb1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":301}' 
#
_entry.id    7YB1 
#
_exptl.entry_id    7YB1 
_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    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            7YB1 
_cell.length_a            124.624 
_cell.length_b            124.624 
_cell.length_c            134.213 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7YB1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
B,C,D,F,G,H,J,K,L 1 1 
A,E,I 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' 5_455 -x-1/2,y+1/2,-z+1/4 -1 0 0 0 1 0 0 0 -1 -62.312 62.312 33.55325 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N 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                     7YB1 
_atom_sites.fract_transf_matrix[1][1]    0.008024 
_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]    0.008024 
_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]    0.007451 
_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 NAP D 1 301 3 NAP NAP . 
F 2 NAP A 1 301 4 NAP NAP . 
G 2 NAP B 1 301 1 NAP NAP . 
H 2 NAP C 1 301 2 NAP NAP . 
I 3 HOH D 1 401 7 HOH HOH . 
I 3 HOH D 2 402 9 HOH HOH . 
I 3 HOH D 3 403 11 HOH HOH . 
J 3 HOH A 1 401 15 HOH HOH . 
J 3 HOH A 2 402 3 HOH HOH . 
J 3 HOH A 3 403 1 HOH HOH . 
J 3 HOH A 4 404 10 HOH HOH . 
J 3 HOH A 5 405 8 HOH HOH . 
J 3 HOH A 6 406 16 HOH HOH . 
J 3 HOH A 7 407 17 HOH HOH . 
J 3 HOH A 8 408 13 HOH HOH . 
J 3 HOH A 9 409 5 HOH HOH . 
K 3 HOH B 1 401 4 HOH HOH . 
K 3 HOH B 2 402 2 HOH HOH . 
K 3 HOH B 3 403 6 HOH HOH . 
L 3 HOH C 1 401 12 HOH HOH . 
L 3 HOH C 2 402 18 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 . . . F 2 -28.804 62.666 21.194 1 10.36 ? PA NAP 301 A 1 
HETATM 2 O O1A NAP . . . F 2 -27.868 62.29 20.171 1 10.45 ? O1A NAP 301 A 1 
HETATM 3 O O2A NAP . . . F 2 -30.15 62.661 20.77 1 10.75 ? O2A NAP 301 A 1 
HETATM 4 O O5B NAP . . . F 2 -28.757 61.709 22.353 1 10.8 ? O5B NAP 301 A 1 
HETATM 5 C C5B NAP . . . F 2 -29.681 60.659 22.491 1 11.54 ? C5B NAP 301 A 1 
HETATM 6 C C4B NAP . . . F 2 -29.537 60.08 23.855 1 12.38 ? C4B NAP 301 A 1 
HETATM 7 O O4B NAP . . . F 2 -30.788 59.867 24.415 1 12.81 ? O4B NAP 301 A 1 
HETATM 8 C C3B NAP . . . F 2 -28.991 58.735 23.75 1 12.72 ? C3B NAP 301 A 1 
HETATM 9 O O3B NAP . . . F 2 -28.113 58.76 24.822 1 12.71 ? O3B NAP 301 A 1 
HETATM 10 C C2B NAP . . . F 2 -30.159 57.868 24.048 1 13.05 ? C2B NAP 301 A 1 
HETATM 11 O O2B NAP . . . F 2 -29.817 56.552 24.365 1 13.77 ? O2B NAP 301 A 1 
HETATM 12 C C1B NAP . . . F 2 -30.786 58.67 25.116 1 12.94 ? C1B NAP 301 A 1 
HETATM 13 N N9A NAP . . . F 2 -32.12 58.177 25.303 1 13.18 ? N9A NAP 301 A 1 
HETATM 14 C C8A NAP . . . F 2 -33.08 58.227 24.43 1 13.62 ? C8A NAP 301 A 1 
HETATM 15 N N7A NAP . . . F 2 -34.179 57.681 24.914 1 13.77 ? N7A NAP 301 A 1 
HETATM 16 C C5A NAP . . . F 2 -33.919 57.246 26.138 1 13.58 ? C5A NAP 301 A 1 
HETATM 17 C C6A NAP . . . F 2 -34.628 56.566 27.216 1 13.17 ? C6A NAP 301 A 1 
HETATM 18 N N6A NAP . . . F 2 -35.896 56.188 27.159 1 12.62 ? N6A NAP 301 A 1 
HETATM 19 N N1A NAP . . . F 2 -33.952 56.319 28.296 1 13.38 ? N1A NAP 301 A 1 
HETATM 20 C C2A NAP . . . F 2 -32.702 56.669 28.472 1 13.53 ? C2A NAP 301 A 1 
HETATM 21 N N3A NAP . . . F 2 -31.997 57.283 27.546 1 13.69 ? N3A NAP 301 A 1 
HETATM 22 C C4A NAP . . . F 2 -32.545 57.588 26.374 1 13.53 ? C4A NAP 301 A 1 
HETATM 23 O O3 NAP . . . F 2 -28.759 64.086 21.729 1 10.44 ? O3 NAP 301 A 1 
HETATM 24 P PN NAP . . . F 2 -27.762 64.671 22.702 1 10.71 ? PN NAP 301 A 1 
HETATM 25 O O1N NAP . . . F 2 -27.342 63.534 23.428 1 10.87 ? O1N NAP 301 A 1 
HETATM 26 O O2N NAP . . . F 2 -26.928 65.542 21.881 1 10.68 ? O2N NAP 301 A 1 
HETATM 27 O O5D NAP . . . F 2 -28.569 65.553 23.69 1 11.23 ? O5D NAP 301 A 1 
HETATM 28 C C5D NAP . . . F 2 -28.588 65.265 25.065 1 11.34 ? C5D NAP 301 A 1 
HETATM 29 C C4D NAP . . . F 2 -29.191 66.335 25.928 1 11.37 ? C4D NAP 301 A 1 
HETATM 30 O O4D NAP . . . F 2 -28.78 67.561 25.462 1 11.18 ? O4D NAP 301 A 1 
HETATM 31 C C3D NAP . . . F 2 -30.657 66.35 25.787 1 11.67 ? C3D NAP 301 A 1 
HETATM 32 O O3D NAP . . . F 2 -31.106 66.542 27.088 1 12.01 ? O3D NAP 301 A 1 
HETATM 33 C C2D NAP . . . F 2 -30.968 67.556 24.988 1 11.65 ? C2D NAP 301 A 1 
HETATM 34 O O2D NAP . . . F 2 -32.213 68.175 25.284 1 11.71 ? O2D NAP 301 A 1 
HETATM 35 C C1D NAP . . . F 2 -29.854 68.435 25.36 1 11.48 ? C1D NAP 301 A 1 
HETATM 36 N N1N NAP . . . F 2 -29.669 69.361 24.289 1 11.64 ? N1N NAP 301 A 1 
HETATM 37 C C2N NAP . . . F 2 -28.961 69.037 23.228 1 11.56 ? C2N NAP 301 A 1 
HETATM 38 C C3N NAP . . . F 2 -28.767 69.906 22.223 1 11.5 ? C3N NAP 301 A 1 
HETATM 39 C C7N NAP . . . F 2 -28.035 69.442 21.066 1 11.35 ? C7N NAP 301 A 1 
HETATM 40 O O7N NAP . . . F 2 -28.005 70.126 20.125 1 11.48 ? O7N NAP 301 A 1 
HETATM 41 N N7N NAP . . . F 2 -27.544 68.253 21.046 1 11.41 ? N7N NAP 301 A 1 
HETATM 42 C C4N NAP . . . F 2 -29.34 71.141 22.304 1 11.58 ? C4N NAP 301 A 1 
HETATM 43 C C5N NAP . . . F 2 -30.075 71.481 23.412 1 11.5 ? C5N NAP 301 A 1 
HETATM 44 C C6N NAP . . . F 2 -30.231 70.538 24.393 1 11.66 ? C6N NAP 301 A 1 
HETATM 45 P P2B NAP . . . F 2 -30.407 55.432 23.484 1 14.14 ? P2B NAP 301 A 1 
HETATM 46 O O1X NAP . . . F 2 -31.557 55.949 22.766 1 13.22 ? O1X NAP 301 A 1 
HETATM 47 O O2X NAP . . . F 2 -29.316 55.135 22.638 1 14.33 ? O2X NAP 301 A 1 
HETATM 48 O O3X NAP . . . F 2 -30.644 54.397 24.443 1 14.32 ? O3X NAP 301 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           48 
#