data_3VVC # _model_server_result.job_id HY-VPHvxqlF5AlmV_rjXYw _model_server_result.datetime_utc '2024-11-05 00:32:05' _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 3vvc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 3VVC # _exptl.entry_id 3VVC _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 90 _cell.angle_gamma 120 _cell.entry_id 3VVC _cell.length_a 160.54 _cell.length_b 160.54 _cell.length_c 80.05 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VVC _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 5_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 6 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 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 3VVC _atom_sites.fract_transf_matrix[1][1] 0.006229 _atom_sites.fract_transf_matrix[1][2] 0.003596 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007193 _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] 0.012492 _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 1 401 401 NAP NAP . C 3 SO4 A 1 402 402 SO4 SO4 . D 3 SO4 A 1 403 403 SO4 SO4 . E 3 SO4 A 1 404 404 SO4 SO4 . F 3 SO4 A 1 405 405 SO4 SO4 . G 3 SO4 A 1 406 406 SO4 SO4 . H 4 HOH A 1 501 501 HOH HOH . H 4 HOH A 2 502 502 HOH HOH . H 4 HOH A 3 503 503 HOH HOH . H 4 HOH A 4 504 504 HOH HOH . H 4 HOH A 5 505 505 HOH HOH . H 4 HOH A 6 506 506 HOH HOH . H 4 HOH A 7 507 507 HOH HOH . H 4 HOH A 8 508 508 HOH HOH . H 4 HOH A 9 509 509 HOH HOH . H 4 HOH A 10 510 510 HOH HOH . H 4 HOH A 11 511 511 HOH HOH . H 4 HOH A 12 512 512 HOH HOH . H 4 HOH A 13 513 513 HOH HOH . H 4 HOH A 14 514 514 HOH HOH . H 4 HOH A 15 515 515 HOH HOH . H 4 HOH A 16 516 516 HOH HOH . H 4 HOH A 17 517 517 HOH HOH . H 4 HOH A 18 518 518 HOH HOH . H 4 HOH A 19 519 519 HOH HOH . H 4 HOH A 20 520 520 HOH HOH . H 4 HOH A 21 521 521 HOH HOH . H 4 HOH A 22 522 522 HOH HOH . H 4 HOH A 23 523 523 HOH HOH . H 4 HOH A 24 524 524 HOH HOH . H 4 HOH A 25 525 525 HOH HOH . H 4 HOH A 26 526 526 HOH HOH . H 4 HOH A 27 527 527 HOH HOH . H 4 HOH A 28 528 528 HOH HOH . H 4 HOH A 29 529 529 HOH HOH . H 4 HOH A 30 530 530 HOH HOH . H 4 HOH A 31 531 531 HOH HOH . H 4 HOH A 32 532 532 HOH HOH . H 4 HOH A 33 533 533 HOH HOH . H 4 HOH A 34 534 534 HOH HOH . H 4 HOH A 35 535 535 HOH HOH . H 4 HOH A 36 536 536 HOH HOH . H 4 HOH A 37 537 537 HOH HOH . H 4 HOH A 38 538 538 HOH HOH . H 4 HOH A 39 539 539 HOH HOH . H 4 HOH A 40 540 540 HOH HOH . H 4 HOH A 41 541 541 HOH HOH . H 4 HOH A 42 542 542 HOH HOH . H 4 HOH A 43 543 543 HOH HOH . H 4 HOH A 44 544 544 HOH HOH . H 4 HOH A 45 545 545 HOH HOH . H 4 HOH A 46 546 546 HOH HOH . H 4 HOH A 47 547 547 HOH HOH . H 4 HOH A 48 548 548 HOH HOH . H 4 HOH A 49 549 549 HOH HOH . H 4 HOH A 50 550 550 HOH HOH . H 4 HOH A 51 551 551 HOH HOH . H 4 HOH A 52 552 552 HOH HOH . H 4 HOH A 53 553 553 HOH HOH . H 4 HOH A 54 554 554 HOH HOH . H 4 HOH A 55 555 555 HOH HOH . H 4 HOH A 56 556 556 HOH HOH . H 4 HOH A 57 557 557 HOH HOH . H 4 HOH A 58 558 558 HOH HOH . H 4 HOH A 59 559 559 HOH HOH . H 4 HOH A 60 560 560 HOH HOH . H 4 HOH A 61 561 561 HOH HOH . H 4 HOH A 62 562 562 HOH HOH . H 4 HOH A 63 563 563 HOH HOH . H 4 HOH A 64 564 564 HOH HOH . H 4 HOH A 65 565 565 HOH HOH . H 4 HOH A 66 566 566 HOH HOH . H 4 HOH A 67 567 567 HOH HOH . H 4 HOH A 68 568 568 HOH HOH . H 4 HOH A 69 569 569 HOH HOH . H 4 HOH A 70 570 570 HOH HOH . H 4 HOH A 71 571 571 HOH HOH . H 4 HOH A 72 572 572 HOH HOH . H 4 HOH A 73 573 573 HOH HOH . H 4 HOH A 74 574 574 HOH HOH . H 4 HOH A 75 575 575 HOH HOH . H 4 HOH A 76 576 576 HOH HOH . H 4 HOH A 77 577 577 HOH HOH . H 4 HOH A 78 578 578 HOH HOH . H 4 HOH A 79 579 579 HOH HOH . H 4 HOH A 80 580 580 HOH HOH . H 4 HOH A 81 581 581 HOH HOH . H 4 HOH A 82 582 582 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 6.443 -27.616 -4.869 1 95.09 ? PA NAP 401 A 1 HETATM 2 O O1A NAP . . . B 2 7.468 -28.751 -4.959 1 96.12 ? O1A NAP 401 A 1 HETATM 3 O O2A NAP . . . B 2 5.836 -27.118 -3.569 1 78.61 ? O2A NAP 401 A 1 HETATM 4 O O5B NAP . . . B 2 6.962 -26.316 -5.63 1 83.99 ? O5B NAP 401 A 1 HETATM 5 C C5B NAP . . . B 2 6.076 -25.201 -5.662 1 78.25 ? C5B NAP 401 A 1 HETATM 6 C C4B NAP . . . B 2 6.959 -23.982 -5.716 1 70.15 ? C4B NAP 401 A 1 HETATM 7 O O4B NAP . . . B 2 6.226 -22.832 -5.324 1 70.42 ? O4B NAP 401 A 1 HETATM 8 C C3B NAP . . . B 2 8.162 -24.038 -4.773 1 68.59 ? C3B NAP 401 A 1 HETATM 9 O O3B NAP . . . B 2 9.261 -24.708 -5.444 1 70.9 ? O3B NAP 401 A 1 HETATM 10 C C2B NAP . . . B 2 8.345 -22.569 -4.344 1 53.04 ? C2B NAP 401 A 1 HETATM 11 O O2B NAP . . . B 2 9.462 -21.929 -4.843 1 39.87 ? O2B NAP 401 A 1 HETATM 12 C C1B NAP . . . B 2 7.229 -21.858 -5.056 1 60.27 ? C1B NAP 401 A 1 HETATM 13 N N9A NAP . . . B 2 6.534 -20.842 -4.273 1 64.53 ? N9A NAP 401 A 1 HETATM 14 C C8A NAP . . . B 2 5.827 -20.926 -3.118 1 57.58 ? C8A NAP 401 A 1 HETATM 15 N N7A NAP . . . B 2 5.285 -19.691 -2.797 1 54.55 ? N7A NAP 401 A 1 HETATM 16 C C5A NAP . . . B 2 5.636 -18.825 -3.763 1 58.37 ? C5A NAP 401 A 1 HETATM 17 C C6A NAP . . . B 2 5.434 -17.383 -4.068 1 54.23 ? C6A NAP 401 A 1 HETATM 18 N N6A NAP . . . B 2 4.722 -16.537 -3.242 1 45.63 ? N6A NAP 401 A 1 HETATM 19 N N1A NAP . . . B 2 5.999 -16.956 -5.231 1 41.65 ? N1A NAP 401 A 1 HETATM 20 C C2A NAP . . . B 2 6.732 -17.723 -6.058 1 56.24 ? C2A NAP 401 A 1 HETATM 21 N N3A NAP . . . B 2 6.978 -19.038 -5.874 1 59.55 ? N3A NAP 401 A 1 HETATM 22 C C4A NAP . . . B 2 6.462 -19.607 -4.747 1 67 ? C4A NAP 401 A 1 HETATM 23 O O3 NAP . . . B 2 5.181 -27.958 -5.803 1 95.33 ? O3 NAP 401 A 1 HETATM 24 P PN NAP . . . B 2 5.199 -28.945 -7.075 1 98.25 ? PN NAP 401 A 1 HETATM 25 O O1N NAP . . . B 2 4.611 -30.189 -6.438 1 87.22 ? O1N NAP 401 A 1 HETATM 26 O O2N NAP . . . B 2 6.561 -28.975 -7.798 1 82.02 ? O2N NAP 401 A 1 HETATM 27 O O5D NAP . . . B 2 4.027 -28.208 -7.929 1 79.01 ? O5D NAP 401 A 1 HETATM 28 C C5D NAP . . . B 2 2.831 -27.922 -7.168 1 88.86 ? C5D NAP 401 A 1 HETATM 29 C C4D NAP . . . B 2 1.622 -27.199 -7.79 1 75.57 ? C4D NAP 401 A 1 HETATM 30 O O4D NAP . . . B 2 0.72 -28.17 -8.353 1 85.14 ? O4D NAP 401 A 1 HETATM 31 C C3D NAP . . . B 2 0.842 -26.428 -6.705 1 74.99 ? C3D NAP 401 A 1 HETATM 32 O O3D NAP . . . B 2 0.32 -25.172 -7.194 1 61.68 ? O3D NAP 401 A 1 HETATM 33 C C2D NAP . . . B 2 -0.272 -27.395 -6.325 1 80.46 ? C2D NAP 401 A 1 HETATM 34 O O2D NAP . . . B 2 -1.514 -26.752 -6.024 1 71.61 ? O2D NAP 401 A 1 HETATM 35 C C1D NAP . . . B 2 -0.423 -28.368 -7.506 1 80.83 ? C1D NAP 401 A 1 HETATM 36 N N1N NAP . . . B 2 -0.509 -29.764 -7.024 1 80.03 ? N1N NAP 401 A 1 HETATM 37 C C2N NAP . . . B 2 0.59 -30.475 -6.709 1 77.62 ? C2N NAP 401 A 1 HETATM 38 C C3N NAP . . . B 2 0.433 -31.793 -6.252 1 89.18 ? C3N NAP 401 A 1 HETATM 39 C C7N NAP . . . B 2 1.635 -32.599 -5.891 1 83.23 ? C7N NAP 401 A 1 HETATM 40 O O7N NAP . . . B 2 2.586 -32.022 -5.402 1 91.11 ? O7N NAP 401 A 1 HETATM 41 N N7N NAP . . . B 2 1.616 -33.912 -6.103 1 77.32 ? N7N NAP 401 A 1 HETATM 42 C C4N NAP . . . B 2 -0.833 -32.378 -6.103 1 82.93 ? C4N NAP 401 A 1 HETATM 43 C C5N NAP . . . B 2 -1.945 -31.628 -6.418 1 71.69 ? C5N NAP 401 A 1 HETATM 44 C C6N NAP . . . B 2 -1.736 -30.325 -6.89 1 79.46 ? C6N NAP 401 A 1 HETATM 45 P P2B NAP . . . B 2 10.465 -21.046 -3.828 1 62.31 ? P2B NAP 401 A 1 HETATM 46 O O1X NAP . . . B 2 10.608 -21.659 -2.408 1 47.16 ? O1X NAP 401 A 1 HETATM 47 O O2X NAP . . . B 2 11.794 -21.088 -4.622 1 48.4 ? O2X NAP 401 A 1 HETATM 48 O O3X NAP . . . B 2 9.823 -19.622 -3.768 1 46.26 ? O3X NAP 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #