data_5VYS # _model_server_result.job_id hXRknEjmQSMhMZi-bQdfPg _model_server_result.datetime_utc '2024-11-29 01:22:11' _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 5vys # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5VYS # _exptl.entry_id 5VYS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 445.429 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid' _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 5VYS _cell.length_a 65.927 _cell.length_b 65.927 _cell.length_c 234.7 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VYS _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # 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 F N N # _chem_comp.formula 'C19 H23 N7 O6' _chem_comp.formula_weight 445.429 _chem_comp.id 1YJ _chem_comp.mon_nstd_flag . _chem_comp.name 'N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C7 N8 1YJ sing 1 n n C7 C6 1YJ sing 2 n n N8 C8A 1YJ sing 3 n n C6 N5 1YJ sing 4 n n C6 C9 1YJ sing 5 n n N10 C9 1YJ sing 6 n n N10 C4' 1YJ sing 7 n n C3' C4' 1YJ doub 8 n y C3' C2' 1YJ sing 9 n y C8A C4A 1YJ doub 10 n n C8A N1 1YJ sing 11 n n N5 C4A 1YJ sing 12 n n C4' C5' 1YJ sing 13 n y C4A C4 1YJ sing 14 n n N1 C2 1YJ doub 15 n n C2' C1' 1YJ doub 16 n y C2 N3 1YJ sing 17 n n C2 N2 1YJ sing 18 n n C4 N3 1YJ sing 19 n n C4 O4 1YJ doub 20 n n C5' C6' 1YJ doub 21 n y C1' C6' 1YJ sing 22 n y C1' C11 1YJ sing 23 n n O11 C11 1YJ doub 24 n n C11 N 1YJ sing 25 n n N CA 1YJ sing 26 n n CA C 1YJ sing 27 n n CA CB 1YJ sing 28 n n C OX1 1YJ doub 29 n n C OX2 1YJ sing 30 n n CG CB 1YJ sing 31 n n CG CD 1YJ sing 32 n n OE1 CD 1YJ doub 33 n n CD OE2 1YJ sing 34 n n C7 H3 1YJ sing 35 n n C7 H4 1YJ sing 36 n n C6 H5 1YJ sing 37 n n N5 H6 1YJ sing 38 n n C9 H8 1YJ sing 39 n n C3' H9 1YJ sing 40 n n C2' H10 1YJ sing 41 n n C6' H11 1YJ sing 42 n n C5' H12 1YJ sing 43 n n N H13 1YJ sing 44 n n CA H14 1YJ sing 45 n n OX2 H15 1YJ sing 46 n n CB H16 1YJ sing 47 n n CB H17 1YJ sing 48 n n CG H18 1YJ sing 49 n n CG H19 1YJ sing 50 n n OE2 H20 1YJ sing 51 n n N2 H21 1YJ sing 52 n n N2 H22 1YJ sing 53 n n N3 H23 1YJ sing 54 n n N8 H1 1YJ sing 55 n n C9 H2 1YJ sing 56 n n N10 H7 1YJ sing 57 n n # _atom_sites.entry_id 5VYS _atom_sites.fract_transf_matrix[1][1] 0.015168 _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] 0.015168 _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] 0.004261 _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 1YJ A 1 301 301 1YJ 1YJ . D 3 EDO A 1 302 1 EDO EDO . E 4 GDP A 1 303 1 GDP GDP . F 2 1YJ B 1 301 301 1YJ 1YJ . G 4 GDP B 1 302 2 GDP GDP . H 5 GMP B 1 303 3 GMP GDP . I 6 HOH A 1 401 491 HOH HOH . I 6 HOH A 2 402 107 HOH HOH . I 6 HOH A 3 403 36 HOH HOH . I 6 HOH A 4 404 116 HOH HOH . I 6 HOH A 5 405 336 HOH HOH . I 6 HOH A 6 406 424 HOH HOH . I 6 HOH A 7 407 9 HOH HOH . I 6 HOH A 8 408 181 HOH HOH . I 6 HOH A 9 409 493 HOH HOH . I 6 HOH A 10 410 174 HOH HOH . I 6 HOH A 11 411 102 HOH HOH . I 6 HOH A 12 412 113 HOH HOH . I 6 HOH A 13 413 481 HOH HOH . I 6 HOH A 14 414 182 HOH HOH . I 6 HOH A 15 415 452 HOH HOH . I 6 HOH A 16 416 5 HOH HOH . I 6 HOH A 17 417 177 HOH HOH . I 6 HOH A 18 418 229 HOH HOH . I 6 HOH A 19 419 23 HOH HOH . I 6 HOH A 20 420 259 HOH HOH . I 6 HOH A 21 421 211 HOH HOH . I 6 HOH A 22 422 212 HOH HOH . I 6 HOH A 23 423 148 HOH HOH . I 6 HOH A 24 424 300 HOH HOH . I 6 HOH A 25 425 339 HOH HOH . I 6 HOH A 26 426 105 HOH HOH . I 6 HOH A 27 427 122 HOH HOH . I 6 HOH A 28 428 464 HOH HOH . I 6 HOH A 29 429 408 HOH HOH . I 6 HOH A 30 430 170 HOH HOH . I 6 HOH A 31 431 461 HOH HOH . I 6 HOH A 32 432 152 HOH HOH . I 6 HOH A 33 433 46 HOH HOH . I 6 HOH A 34 434 126 HOH HOH . I 6 HOH A 35 435 111 HOH HOH . I 6 HOH A 36 436 477 HOH HOH . I 6 HOH A 37 437 224 HOH HOH . I 6 HOH A 38 438 166 HOH HOH . I 6 HOH A 39 439 157 HOH HOH . I 6 HOH A 40 440 256 HOH HOH . I 6 HOH A 41 441 118 HOH HOH . I 6 HOH A 42 442 28 HOH HOH . I 6 HOH A 43 443 119 HOH HOH . I 6 HOH A 44 444 8 HOH HOH . I 6 HOH A 45 445 445 HOH HOH . I 6 HOH A 46 446 14 HOH HOH . I 6 HOH A 47 447 147 HOH HOH . I 6 HOH A 48 448 394 HOH HOH . I 6 HOH A 49 449 162 HOH HOH . I 6 HOH A 50 450 130 HOH HOH . I 6 HOH A 51 451 112 HOH HOH . I 6 HOH A 52 452 15 HOH HOH . I 6 HOH A 53 453 353 HOH HOH . I 6 HOH A 54 454 176 HOH HOH . I 6 HOH A 55 455 16 HOH HOH . I 6 HOH A 56 456 450 HOH HOH . I 6 HOH A 57 457 377 HOH HOH . I 6 HOH A 58 458 280 HOH HOH . I 6 HOH A 59 459 43 HOH HOH . I 6 HOH A 60 460 124 HOH HOH . I 6 HOH A 61 461 199 HOH HOH . I 6 HOH A 62 462 108 HOH HOH . I 6 HOH A 63 463 1 HOH HOH . I 6 HOH A 64 464 230 HOH HOH . I 6 HOH A 65 465 399 HOH HOH . I 6 HOH A 66 466 3 HOH HOH . I 6 HOH A 67 467 227 HOH HOH . I 6 HOH A 68 468 291 HOH HOH . I 6 HOH A 69 469 449 HOH HOH . I 6 HOH A 70 470 490 HOH HOH . I 6 HOH A 71 471 110 HOH HOH . I 6 HOH A 72 472 446 HOH HOH . I 6 HOH A 73 473 276 HOH HOH . I 6 HOH A 74 474 172 HOH HOH . I 6 HOH A 75 475 42 HOH HOH . I 6 HOH A 76 476 26 HOH HOH . I 6 HOH A 77 477 158 HOH HOH . I 6 HOH A 78 478 298 HOH HOH . I 6 HOH A 79 479 99 HOH HOH . I 6 HOH A 80 480 453 HOH HOH . I 6 HOH A 81 481 35 HOH HOH . I 6 HOH A 82 482 25 HOH HOH . I 6 HOH A 83 483 97 HOH HOH . I 6 HOH A 84 484 106 HOH HOH . I 6 HOH A 85 485 21 HOH HOH . I 6 HOH A 86 486 12 HOH HOH . I 6 HOH A 87 487 498 HOH HOH . I 6 HOH A 88 488 234 HOH HOH . I 6 HOH A 89 489 150 HOH HOH . I 6 HOH A 90 490 218 HOH HOH . I 6 HOH A 91 491 17 HOH HOH . I 6 HOH A 92 492 231 HOH HOH . I 6 HOH A 93 493 104 HOH HOH . I 6 HOH A 94 494 164 HOH HOH . I 6 HOH A 95 495 33 HOH HOH . I 6 HOH A 96 496 454 HOH HOH . I 6 HOH A 97 497 257 HOH HOH . I 6 HOH A 98 498 295 HOH HOH . I 6 HOH A 99 499 159 HOH HOH . I 6 HOH A 100 500 210 HOH HOH . I 6 HOH A 101 501 153 HOH HOH . I 6 HOH A 102 502 24 HOH HOH . I 6 HOH A 103 503 232 HOH HOH . I 6 HOH A 104 504 233 HOH HOH . I 6 HOH A 105 505 32 HOH HOH . I 6 HOH A 106 506 448 HOH HOH . I 6 HOH A 107 507 494 HOH HOH . I 6 HOH A 108 508 296 HOH HOH . I 6 HOH A 109 509 462 HOH HOH . I 6 HOH A 110 510 217 HOH HOH . I 6 HOH A 111 511 495 HOH HOH . I 6 HOH A 112 512 381 HOH HOH . I 6 HOH A 113 513 418 HOH HOH . I 6 HOH A 114 514 415 HOH HOH . I 6 HOH A 115 515 497 HOH HOH . I 6 HOH A 116 516 422 HOH HOH . I 6 HOH A 117 517 478 HOH HOH . I 6 HOH A 118 518 297 HOH HOH . I 6 HOH A 119 519 447 HOH HOH . J 6 HOH B 1 401 55 HOH HOH . J 6 HOH B 2 402 483 HOH HOH . J 6 HOH B 3 403 460 HOH HOH . J 6 HOH B 4 404 416 HOH HOH . J 6 HOH B 5 405 285 HOH HOH . J 6 HOH B 6 406 474 HOH HOH . J 6 HOH B 7 407 374 HOH HOH . J 6 HOH B 8 408 83 HOH HOH . J 6 HOH B 9 409 68 HOH HOH . J 6 HOH B 10 410 70 HOH HOH . J 6 HOH B 11 411 128 HOH HOH . J 6 HOH B 12 412 482 HOH HOH . J 6 HOH B 13 413 76 HOH HOH . J 6 HOH B 14 414 49 HOH HOH . J 6 HOH B 15 415 129 HOH HOH . J 6 HOH B 16 416 370 HOH HOH . J 6 HOH B 17 417 441 HOH HOH . J 6 HOH B 18 418 362 HOH HOH . J 6 HOH B 19 419 18 HOH HOH . J 6 HOH B 20 420 62 HOH HOH . J 6 HOH B 21 421 144 HOH HOH . J 6 HOH B 22 422 346 HOH HOH . J 6 HOH B 23 423 57 HOH HOH . J 6 HOH B 24 424 420 HOH HOH . J 6 HOH B 25 425 48 HOH HOH . J 6 HOH B 26 426 270 HOH HOH . J 6 HOH B 27 427 331 HOH HOH . J 6 HOH B 28 428 50 HOH HOH . J 6 HOH B 29 429 444 HOH HOH . J 6 HOH B 30 430 455 HOH HOH . J 6 HOH B 31 431 442 HOH HOH . J 6 HOH B 32 432 499 HOH HOH . J 6 HOH B 33 433 239 HOH HOH . J 6 HOH B 34 434 86 HOH HOH . J 6 HOH B 35 435 137 HOH HOH . J 6 HOH B 36 436 20 HOH HOH . J 6 HOH B 37 437 66 HOH HOH . J 6 HOH B 38 438 463 HOH HOH . J 6 HOH B 39 439 80 HOH HOH . J 6 HOH B 40 440 434 HOH HOH . J 6 HOH B 41 441 85 HOH HOH . J 6 HOH B 42 442 131 HOH HOH . J 6 HOH B 43 443 456 HOH HOH . J 6 HOH B 44 444 138 HOH HOH . J 6 HOH B 45 445 433 HOH HOH . J 6 HOH B 46 446 487 HOH HOH . J 6 HOH B 47 447 265 HOH HOH . J 6 HOH B 48 448 127 HOH HOH . J 6 HOH B 49 449 173 HOH HOH . J 6 HOH B 50 450 74 HOH HOH . J 6 HOH B 51 451 37 HOH HOH . J 6 HOH B 52 452 109 HOH HOH . J 6 HOH B 53 453 100 HOH HOH . J 6 HOH B 54 454 342 HOH HOH . J 6 HOH B 55 455 54 HOH HOH . J 6 HOH B 56 456 430 HOH HOH . J 6 HOH B 57 457 6 HOH HOH . J 6 HOH B 58 458 432 HOH HOH . J 6 HOH B 59 459 82 HOH HOH . J 6 HOH B 60 460 286 HOH HOH . J 6 HOH B 61 461 101 HOH HOH . J 6 HOH B 62 462 73 HOH HOH . J 6 HOH B 63 463 160 HOH HOH . J 6 HOH B 64 464 65 HOH HOH . J 6 HOH B 65 465 409 HOH HOH . J 6 HOH B 66 466 40 HOH HOH . J 6 HOH B 67 467 133 HOH HOH . J 6 HOH B 68 468 56 HOH HOH . J 6 HOH B 69 469 69 HOH HOH . J 6 HOH B 70 470 473 HOH HOH . J 6 HOH B 71 471 471 HOH HOH . J 6 HOH B 72 472 184 HOH HOH . J 6 HOH B 73 473 488 HOH HOH . J 6 HOH B 74 474 436 HOH HOH . J 6 HOH B 75 475 38 HOH HOH . J 6 HOH B 76 476 317 HOH HOH . J 6 HOH B 77 477 192 HOH HOH . J 6 HOH B 78 478 61 HOH HOH . J 6 HOH B 79 479 443 HOH HOH . J 6 HOH B 80 480 469 HOH HOH . J 6 HOH B 81 481 351 HOH HOH . J 6 HOH B 82 482 88 HOH HOH . J 6 HOH B 83 483 53 HOH HOH . J 6 HOH B 84 484 175 HOH HOH . J 6 HOH B 85 485 466 HOH HOH . J 6 HOH B 86 486 451 HOH HOH . J 6 HOH B 87 487 293 HOH HOH . J 6 HOH B 88 488 288 HOH HOH . J 6 HOH B 89 489 412 HOH HOH . J 6 HOH B 90 490 238 HOH HOH . J 6 HOH B 91 491 79 HOH HOH . J 6 HOH B 92 492 496 HOH HOH . J 6 HOH B 93 493 345 HOH HOH . J 6 HOH B 94 494 371 HOH HOH . J 6 HOH B 95 495 316 HOH HOH . J 6 HOH B 96 496 52 HOH HOH . J 6 HOH B 97 497 440 HOH HOH . J 6 HOH B 98 498 81 HOH HOH . J 6 HOH B 99 499 4 HOH HOH . J 6 HOH B 100 500 458 HOH HOH . J 6 HOH B 101 501 437 HOH HOH . J 6 HOH B 102 502 467 HOH HOH . J 6 HOH B 103 503 151 HOH HOH . J 6 HOH B 104 504 142 HOH HOH . J 6 HOH B 105 505 228 HOH HOH . J 6 HOH B 106 506 343 HOH HOH . J 6 HOH B 107 507 39 HOH HOH . J 6 HOH B 108 508 375 HOH HOH . J 6 HOH B 109 509 51 HOH HOH . J 6 HOH B 110 510 431 HOH HOH . J 6 HOH B 111 511 87 HOH HOH . J 6 HOH B 112 512 486 HOH HOH . J 6 HOH B 113 513 167 HOH HOH . J 6 HOH B 114 514 479 HOH HOH . J 6 HOH B 115 515 489 HOH HOH . J 6 HOH B 116 516 426 HOH HOH . J 6 HOH B 117 517 429 HOH HOH . J 6 HOH B 118 518 332 HOH HOH . J 6 HOH B 119 519 262 HOH HOH . J 6 HOH B 120 520 306 HOH HOH . J 6 HOH B 121 521 484 HOH HOH . J 6 HOH B 122 522 459 HOH HOH . J 6 HOH B 123 523 279 HOH HOH . J 6 HOH B 124 524 411 HOH HOH . J 6 HOH B 125 525 492 HOH HOH . J 6 HOH B 126 526 475 HOH HOH . J 6 HOH B 127 527 485 HOH HOH . J 6 HOH B 128 528 472 HOH HOH . J 6 HOH B 129 529 77 HOH HOH . J 6 HOH B 130 530 423 HOH HOH . J 6 HOH B 131 531 435 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 N N3 1YJ . . . C 2 2.972 15.458 9.986 1 32.59 ? N3 1YJ 301 A 1 HETATM 2 C C2 1YJ . . . C 2 1.764 15.838 9.512 1 32.69 ? C2 1YJ 301 A 1 HETATM 3 N N1 1YJ . . . C 2 0.809 16.358 10.341 1 35.24 ? N1 1YJ 301 A 1 HETATM 4 C C8A 1YJ . . . C 2 0.976 16.526 11.661 1 34.86 ? C8A 1YJ 301 A 1 HETATM 5 C C4A 1YJ . . . C 2 2.252 16.122 12.269 1 35.58 ? C4A 1YJ 301 A 1 HETATM 6 C C4 1YJ . . . C 2 3.265 15.566 11.305 1 36.59 ? C4 1YJ 301 A 1 HETATM 7 N N8 1YJ . . . C 2 0.006 17.015 12.435 1 35.9 ? N8 1YJ 301 A 1 HETATM 8 C C7 1YJ . . . C 2 0.157 17.17 13.775 1 38.55 ? C7 1YJ 301 A 1 HETATM 9 C C6 1YJ . . . C 2 1.38 16.793 14.537 1 37.24 ? C6 1YJ 301 A 1 HETATM 10 N N5 1YJ . . . C 2 2.439 16.28 13.667 1 35.33 ? N5 1YJ 301 A 1 HETATM 11 O O4 1YJ . . . C 2 4.4 15.209 11.699 1 42.23 ? O4 1YJ 301 A 1 HETATM 12 N N2 1YJ . . . C 2 1.55 15.701 8.178 1 31.24 ? N2 1YJ 301 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 12 #