data_3D8V # _model_server_result.job_id W3O9lOKJCa9Ypp7ZpBr5eA _model_server_result.datetime_utc '2024-11-14 20:46:08' _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 3d8v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":496}' # _entry.id 3D8V # _exptl.entry_id 3D8V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 607.354 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE _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 3D8V _cell.length_a 114.238 _cell.length_b 114.238 _cell.length_c 361.796 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D8V _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 57.119 -98.93301 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 114.238 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 'C17 H27 N3 O17 P2' _chem_comp.formula_weight 607.354 _chem_comp.id UD1 _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE _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 C1' C2' UD1 sing 358 n n C1' O1' UD1 sing 359 n n C1' O5' UD1 sing 360 n n C1' H1' UD1 sing 361 n n C2' C3' UD1 sing 362 n n C2' N2' UD1 sing 363 n n C2' H2' UD1 sing 364 n n C3' C4' UD1 sing 365 n n C3' O3' UD1 sing 366 n n C3' H3' UD1 sing 367 n n C4' C5' UD1 sing 368 n n C4' O4' UD1 sing 369 n n C4' H4' UD1 sing 370 n n C5' C6' UD1 sing 371 n n C5' O5' UD1 sing 372 n n C5' H5' UD1 sing 373 n n C6' O6' UD1 sing 374 n n C6' "H6'1" UD1 sing 375 n n C6' "H6'2" UD1 sing 376 n n C7' C8' UD1 sing 377 n n C7' N2' UD1 sing 378 n n C7' O7' UD1 doub 379 n n C8' "H8'1" UD1 sing 380 n n C8' "H8'2" UD1 sing 381 n n C8' "H8'3" UD1 sing 382 n n N2' HN2' UD1 sing 383 n n O1' PB UD1 sing 384 n n O3' HO3' UD1 sing 385 n n O4' HO4' UD1 sing 386 n n O6' HO6' UD1 sing 387 n n N1 C2 UD1 sing 388 n n N1 C6 UD1 sing 389 n n N1 C1B UD1 sing 390 n n C2 N3 UD1 sing 391 n n C2 O2 UD1 doub 392 n n N3 C4 UD1 sing 393 n n N3 HN3 UD1 sing 394 n n C4 C5 UD1 sing 395 n n C4 O4 UD1 doub 396 n n C5 C6 UD1 doub 397 n n C5 H5 UD1 sing 398 n n C6 H6 UD1 sing 399 n n C1B C2B UD1 sing 400 n n C1B O4B UD1 sing 401 n n C1B H1B UD1 sing 402 n n C2B O2' UD1 sing 403 n n C2B C3B UD1 sing 404 n n C2B H2B UD1 sing 405 n n O2' HO2' UD1 sing 406 n n C3B C4B UD1 sing 407 n n C3B O3B UD1 sing 408 n n C3B H3B UD1 sing 409 n n C4B O4B UD1 sing 410 n n C4B C5B UD1 sing 411 n n C4B H4B UD1 sing 412 n n O3B HO3A UD1 sing 413 n n C5B O5B UD1 sing 414 n n C5B "H5'1" UD1 sing 415 n n C5B "H5'2" UD1 sing 416 n n O5B PA UD1 sing 417 n n PA O1A UD1 doub 418 n n PA O2A UD1 sing 419 n n PA O3A UD1 sing 420 n n O2A HOA2 UD1 sing 421 n n O3A PB UD1 sing 422 n n PB O1B UD1 doub 423 n n PB O2B UD1 sing 424 n n O2B HOB2 UD1 sing 425 n n # _atom_sites.entry_id 3D8V _atom_sites.fract_transf_matrix[1][1] 0.008754 _atom_sites.fract_transf_matrix[1][2] 0.005054 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010108 _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] 0.002764 _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 UD1 A 1 496 496 UD1 UD1 . C 3 HOH A 1 497 1 HOH HOH . C 3 HOH A 2 498 2 HOH HOH . C 3 HOH A 3 499 3 HOH HOH . C 3 HOH A 4 500 4 HOH HOH . C 3 HOH A 5 501 1 HOH HOH . C 3 HOH A 6 502 2 HOH HOH . C 3 HOH A 7 503 5 HOH HOH . C 3 HOH A 8 504 7 HOH HOH . C 3 HOH A 9 505 8 HOH HOH . C 3 HOH A 10 506 10 HOH HOH . C 3 HOH A 11 507 12 HOH HOH . C 3 HOH A 12 508 13 HOH HOH . C 3 HOH A 13 509 14 HOH HOH . C 3 HOH A 14 510 17 HOH HOH . C 3 HOH A 15 511 18 HOH HOH . C 3 HOH A 16 512 20 HOH HOH . C 3 HOH A 17 513 21 HOH HOH . C 3 HOH A 18 514 23 HOH HOH . C 3 HOH A 19 515 24 HOH HOH . C 3 HOH A 20 516 25 HOH HOH . C 3 HOH A 21 517 26 HOH HOH . C 3 HOH A 22 518 27 HOH HOH . C 3 HOH A 23 519 28 HOH HOH . C 3 HOH A 24 520 30 HOH HOH . C 3 HOH A 25 521 33 HOH HOH . C 3 HOH A 26 522 34 HOH HOH . C 3 HOH A 27 523 35 HOH HOH . C 3 HOH A 28 524 36 HOH HOH . C 3 HOH A 29 525 38 HOH HOH . C 3 HOH A 30 526 41 HOH HOH . C 3 HOH A 31 527 43 HOH HOH . C 3 HOH A 32 528 44 HOH HOH . C 3 HOH A 33 529 47 HOH HOH . C 3 HOH A 34 530 48 HOH HOH . C 3 HOH A 35 531 49 HOH HOH . C 3 HOH A 36 532 50 HOH HOH . C 3 HOH A 37 533 52 HOH HOH . C 3 HOH A 38 534 55 HOH HOH . C 3 HOH A 39 535 56 HOH HOH . C 3 HOH A 40 536 57 HOH HOH . C 3 HOH A 41 537 58 HOH HOH . C 3 HOH A 42 538 59 HOH HOH . C 3 HOH A 43 539 60 HOH HOH . C 3 HOH A 44 540 62 HOH HOH . C 3 HOH A 45 541 63 HOH HOH . C 3 HOH A 46 542 64 HOH HOH . C 3 HOH A 47 543 66 HOH HOH . C 3 HOH A 48 544 67 HOH HOH . C 3 HOH A 49 545 71 HOH HOH . C 3 HOH A 50 546 72 HOH HOH . C 3 HOH A 51 547 73 HOH HOH . C 3 HOH A 52 548 74 HOH HOH . C 3 HOH A 53 549 76 HOH HOH . C 3 HOH A 54 550 79 HOH HOH . C 3 HOH A 55 551 81 HOH HOH . C 3 HOH A 56 552 82 HOH HOH . C 3 HOH A 57 553 83 HOH HOH . C 3 HOH A 58 554 86 HOH HOH . C 3 HOH A 59 555 88 HOH HOH . C 3 HOH A 60 556 89 HOH HOH . C 3 HOH A 61 557 93 HOH HOH . C 3 HOH A 62 558 94 HOH HOH . C 3 HOH A 63 559 95 HOH HOH . C 3 HOH A 64 560 97 HOH HOH . C 3 HOH A 65 561 98 HOH HOH . C 3 HOH A 66 562 99 HOH HOH . C 3 HOH A 67 563 100 HOH HOH . C 3 HOH A 68 564 103 HOH HOH . C 3 HOH A 69 565 105 HOH HOH . C 3 HOH A 70 566 109 HOH HOH . C 3 HOH A 71 567 110 HOH HOH . C 3 HOH A 72 568 111 HOH HOH . C 3 HOH A 73 569 115 HOH HOH . C 3 HOH A 74 570 124 HOH HOH . C 3 HOH A 75 571 125 HOH HOH . C 3 HOH A 76 572 126 HOH HOH . C 3 HOH A 77 573 127 HOH HOH . C 3 HOH A 78 574 128 HOH HOH . C 3 HOH A 79 575 129 HOH HOH . C 3 HOH A 80 576 130 HOH HOH . C 3 HOH A 81 577 131 HOH HOH . C 3 HOH A 82 578 132 HOH HOH . C 3 HOH A 83 579 133 HOH HOH . C 3 HOH A 84 580 134 HOH HOH . C 3 HOH A 85 581 135 HOH HOH . C 3 HOH A 86 582 136 HOH HOH . C 3 HOH A 87 583 137 HOH HOH . C 3 HOH A 88 584 138 HOH HOH . C 3 HOH A 89 585 139 HOH HOH . C 3 HOH A 90 586 140 HOH HOH . C 3 HOH A 91 587 141 HOH HOH . C 3 HOH A 92 588 142 HOH HOH . C 3 HOH A 93 589 144 HOH HOH . C 3 HOH A 94 590 146 HOH HOH . C 3 HOH A 95 591 149 HOH HOH . C 3 HOH A 96 592 150 HOH HOH . C 3 HOH A 97 593 151 HOH HOH . C 3 HOH A 98 594 152 HOH HOH . C 3 HOH A 99 595 153 HOH HOH . C 3 HOH A 100 596 154 HOH HOH . C 3 HOH A 101 597 156 HOH HOH . C 3 HOH A 102 598 159 HOH HOH . C 3 HOH A 103 599 160 HOH HOH . C 3 HOH A 104 600 161 HOH HOH . C 3 HOH A 105 601 162 HOH HOH . C 3 HOH A 106 602 163 HOH HOH . C 3 HOH A 107 603 164 HOH HOH . C 3 HOH A 108 604 165 HOH HOH . C 3 HOH A 109 605 166 HOH HOH . C 3 HOH A 110 606 167 HOH HOH . C 3 HOH A 111 607 168 HOH HOH . C 3 HOH A 112 608 169 HOH HOH . C 3 HOH A 113 609 170 HOH HOH . C 3 HOH A 114 610 171 HOH HOH . C 3 HOH A 115 611 173 HOH HOH . C 3 HOH A 116 612 174 HOH HOH . C 3 HOH A 117 613 175 HOH HOH . C 3 HOH A 118 614 176 HOH HOH . C 3 HOH A 119 615 177 HOH HOH . C 3 HOH A 120 616 179 HOH HOH . C 3 HOH A 121 617 180 HOH HOH . C 3 HOH A 122 618 181 HOH HOH . C 3 HOH A 123 619 182 HOH HOH . C 3 HOH A 124 620 183 HOH HOH . C 3 HOH A 125 621 185 HOH HOH . C 3 HOH A 126 622 186 HOH HOH . C 3 HOH A 127 623 187 HOH HOH . C 3 HOH A 128 624 188 HOH HOH . C 3 HOH A 129 625 191 HOH HOH . C 3 HOH A 130 626 192 HOH HOH . C 3 HOH A 131 627 193 HOH HOH . C 3 HOH A 132 628 194 HOH HOH . C 3 HOH A 133 629 196 HOH HOH . C 3 HOH A 134 630 200 HOH HOH . C 3 HOH A 135 631 201 HOH HOH . C 3 HOH A 136 632 202 HOH HOH . C 3 HOH A 137 633 203 HOH HOH . C 3 HOH A 138 634 204 HOH HOH . C 3 HOH A 139 635 205 HOH HOH . C 3 HOH A 140 636 206 HOH HOH . C 3 HOH A 141 637 208 HOH HOH . C 3 HOH A 142 638 209 HOH HOH . C 3 HOH A 143 639 212 HOH HOH . C 3 HOH A 144 640 213 HOH HOH . C 3 HOH A 145 641 214 HOH HOH . C 3 HOH A 146 642 215 HOH HOH . C 3 HOH A 147 643 217 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 C C1' UD1 . . . B 2 30.092 -32.217 39.75 1 58.7 ? C1' UD1 496 A 1 HETATM 2 C C2' UD1 . . . B 2 29.849 -32.322 41.251 1 53.74 ? C2' UD1 496 A 1 HETATM 3 C C3' UD1 . . . B 2 31.16 -32.096 41.986 1 53.95 ? C3' UD1 496 A 1 HETATM 4 C C4' UD1 . . . B 2 32.188 -33.101 41.484 1 57.54 ? C4' UD1 496 A 1 HETATM 5 C C5' UD1 . . . B 2 32.339 -33.02 39.961 1 47.62 ? C5' UD1 496 A 1 HETATM 6 C C6' UD1 . . . B 2 33.299 -34.086 39.429 1 44.35 ? C6' UD1 496 A 1 HETATM 7 C C7' UD1 . . . B 2 27.602 -31.589 41.767 1 49.65 ? C7' UD1 496 A 1 HETATM 8 C C8' UD1 . . . B 2 27.208 -32.922 41.238 1 32.66 ? C8' UD1 496 A 1 HETATM 9 N N2' UD1 . . . B 2 28.896 -31.312 41.648 1 59.05 ? N2' UD1 496 A 1 HETATM 10 O O1' UD1 . . . B 2 30.631 -30.926 39.492 1 50.3 ? O1' UD1 496 A 1 HETATM 11 O O3' UD1 . . . B 2 30.986 -32.244 43.398 1 55.17 ? O3' UD1 496 A 1 HETATM 12 O O4' UD1 . . . B 2 33.426 -32.839 42.149 1 51.47 ? O4' UD1 496 A 1 HETATM 13 O O5' UD1 . . . B 2 31.051 -33.199 39.356 1 51.06 ? O5' UD1 496 A 1 HETATM 14 O O6' UD1 . . . B 2 33.705 -33.765 38.089 1 65.01 ? O6' UD1 496 A 1 HETATM 15 O O7' UD1 . . . B 2 26.795 -30.822 42.274 1 57.21 ? O7' UD1 496 A 1 HETATM 16 N N1 UD1 . . . B 2 24.821 -32.864 34.395 1 50.13 ? N1 UD1 496 A 1 HETATM 17 C C2 UD1 . . . B 2 23.56 -33.162 33.841 1 56.67 ? C2 UD1 496 A 1 HETATM 18 N N3 UD1 . . . B 2 22.521 -32.351 34.071 1 51.31 ? N3 UD1 496 A 1 HETATM 19 C C4 UD1 . . . B 2 22.656 -31.259 34.835 1 50.71 ? C4 UD1 496 A 1 HETATM 20 C C5 UD1 . . . B 2 23.892 -30.948 35.401 1 54.53 ? C5 UD1 496 A 1 HETATM 21 C C6 UD1 . . . B 2 24.985 -31.783 35.163 1 59.99 ? C6 UD1 496 A 1 HETATM 22 O O2 UD1 . . . B 2 23.431 -34.19 33.129 1 52.02 ? O2 UD1 496 A 1 HETATM 23 O O4 UD1 . . . B 2 21.664 -30.524 35.045 1 59.58 ? O4 UD1 496 A 1 HETATM 24 C C1B UD1 . . . B 2 25.916 -33.781 34.107 1 49.8 ? C1B UD1 496 A 1 HETATM 25 C C2B UD1 . . . B 2 27.033 -33.139 33.299 1 50.99 ? C2B UD1 496 A 1 HETATM 26 O O2' UD1 . . . B 2 26.833 -33.288 31.888 1 51.92 ? O2' UD1 496 A 1 HETATM 27 C C3B UD1 . . . B 2 28.235 -33.94 33.748 1 52.69 ? C3B UD1 496 A 1 HETATM 28 C C4B UD1 . . . B 2 27.908 -34.357 35.175 1 55.69 ? C4B UD1 496 A 1 HETATM 29 O O4B UD1 . . . B 2 26.491 -34.252 35.325 1 57.92 ? O4B UD1 496 A 1 HETATM 30 O O3B UD1 . . . B 2 28.354 -35.097 32.913 1 52.22 ? O3B UD1 496 A 1 HETATM 31 C C5B UD1 . . . B 2 28.506 -33.361 36.145 1 37.11 ? C5B UD1 496 A 1 HETATM 32 O O5B UD1 . . . B 2 28.117 -32.114 35.579 1 56.79 ? O5B UD1 496 A 1 HETATM 33 P PA UD1 . . . B 2 29.054 -30.849 35.807 1 56.37 ? PA UD1 496 A 1 HETATM 34 O O1A UD1 . . . B 2 28.279 -29.568 35.588 1 48.47 ? O1A UD1 496 A 1 HETATM 35 O O2A UD1 . . . B 2 30.274 -31.207 34.997 1 54.06 ? O2A UD1 496 A 1 HETATM 36 O O3A UD1 . . . B 2 29.358 -31.048 37.369 1 68.15 ? O3A UD1 496 A 1 HETATM 37 P PB UD1 . . . B 2 30.532 -30.216 38.058 1 68.43 ? PB UD1 496 A 1 HETATM 38 O O1B UD1 . . . B 2 30.059 -28.796 38.27 1 63.86 ? O1B UD1 496 A 1 HETATM 39 O O2B UD1 . . . B 2 31.836 -30.51 37.326 1 59.38 ? O2B UD1 496 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #