data_3PRJ # _model_server_result.job_id W-4n0u8z256gj1A8jr34Ag _model_server_result.datetime_utc '2025-07-21 13:08:47' _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 3prj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 3PRJ # _exptl.entry_id 3PRJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 536.276 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE" _entity.pdbx_number_of_molecules 6 _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 3PRJ _cell.length_a 111.79 _cell.length_b 160.64 _cell.length_c 205.86 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PRJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R N N # _chem_comp.formula 'C14 H22 N2 O16 P2' _chem_comp.formula_weight 536.276 _chem_comp.id UDX _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms UDP-ALPHA-D-XYLOPYRANOSE # 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' UDX sing 435 n n C1' O5' UDX sing 436 n n C1' O3B UDX sing 437 n n C1' H1' UDX sing 438 n n C2' O2' UDX sing 439 n n C2' C3' UDX sing 440 n n C2' "H2'1" UDX sing 441 n n O2' "HO'2" UDX sing 442 n n C3' O3' UDX sing 443 n n C3' C4' UDX sing 444 n n C3' "H3'1" UDX sing 445 n n O3' "HO'3" UDX sing 446 n n C4' O4' UDX sing 447 n n C4' C5' UDX sing 448 n n C4' "H4'1" UDX sing 449 n n O4' "HO'4" UDX sing 450 n n C5' O5' UDX sing 451 n n C5' "H5'1" UDX sing 452 n n C5' "H5'2" UDX sing 453 n n PB O1B UDX doub 454 n n PB O2B UDX sing 455 n n PB O3B UDX sing 456 n n PB O3A UDX sing 457 n n O2B HOB2 UDX sing 458 n n O3A PA UDX sing 459 n n PA O1A UDX doub 460 n n PA O2A UDX sing 461 n n PA O5D UDX sing 462 n n O2A HOA2 UDX sing 463 n n O5D C5D UDX sing 464 n n C5D C4D UDX sing 465 n n C5D H5A1 UDX sing 466 n n C5D H5A2 UDX sing 467 n n C4D O4D UDX sing 468 n n C4D C3D UDX sing 469 n n C4D H4A1 UDX sing 470 n n O4D C1D UDX sing 471 n n C3D O3D UDX sing 472 n n C3D C2D UDX sing 473 n n C3D H3A1 UDX sing 474 n n O3D HOA3 UDX sing 475 n n C2D O2D UDX sing 476 n n C2D C1D UDX sing 477 n n C2D H2A1 UDX sing 478 n n O2D HOC2 UDX sing 479 n n C1D N1 UDX sing 480 n n C1D "H1'1" UDX sing 481 n n N1 C6 UDX sing 482 n n N1 C2 UDX sing 483 n n C6 C5 UDX doub 484 n n C6 H61 UDX sing 485 n n C2 O2 UDX doub 486 n n C2 N3 UDX sing 487 n n N3 C4 UDX sing 488 n n N3 HN3 UDX sing 489 n n C4 O4 UDX doub 490 n n C4 C5 UDX sing 491 n n C5 H51 UDX sing 492 n n # _atom_sites.entry_id 3PRJ _atom_sites.fract_transf_matrix[1][1] 0.008945 _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] 0.006225 _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] 0.004858 _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 G 2 NAI A 1 500 500 NAI NAI . H 3 UDX A 1 501 501 UDX UDX . I 2 NAI B 1 500 500 NAI NAI . J 3 UDX B 1 501 501 UDX UDX . K 2 NAI C 1 500 500 NAI NAI . L 3 UDX C 1 501 501 UDX UDX . M 2 NAI D 1 500 500 NAI NAI . N 3 UDX D 1 501 501 UDX UDX . O 2 NAI E 1 500 500 NAI NAI . P 3 UDX E 1 501 501 UDX UDX . Q 2 NAI F 1 500 500 NAI NAI . R 3 UDX F 1 501 501 UDX UDX . S 4 HOH A 1 495 495 HOH HOH . S 4 HOH A 2 496 496 HOH HOH . S 4 HOH A 3 497 497 HOH HOH . S 4 HOH A 4 498 498 HOH HOH . S 4 HOH A 5 499 499 HOH HOH . S 4 HOH A 6 502 502 HOH HOH . S 4 HOH A 7 503 503 HOH HOH . S 4 HOH A 8 504 504 HOH HOH . S 4 HOH A 9 505 505 HOH HOH . S 4 HOH A 10 506 506 HOH HOH . S 4 HOH A 11 507 507 HOH HOH . S 4 HOH A 12 508 508 HOH HOH . S 4 HOH A 13 509 509 HOH HOH . S 4 HOH A 14 510 510 HOH HOH . S 4 HOH A 15 511 511 HOH HOH . S 4 HOH A 16 512 512 HOH HOH . S 4 HOH A 17 513 513 HOH HOH . S 4 HOH A 18 514 514 HOH HOH . S 4 HOH A 19 515 515 HOH HOH . S 4 HOH A 20 516 516 HOH HOH . S 4 HOH A 21 517 517 HOH HOH . S 4 HOH A 22 518 518 HOH HOH . S 4 HOH A 23 519 519 HOH HOH . S 4 HOH A 24 520 520 HOH HOH . S 4 HOH A 25 521 521 HOH HOH . S 4 HOH A 26 522 522 HOH HOH . S 4 HOH A 27 523 523 HOH HOH . S 4 HOH A 28 524 524 HOH HOH . S 4 HOH A 29 525 525 HOH HOH . S 4 HOH A 30 526 526 HOH HOH . S 4 HOH A 31 527 527 HOH HOH . S 4 HOH A 32 528 528 HOH HOH . S 4 HOH A 33 529 529 HOH HOH . S 4 HOH A 34 530 530 HOH HOH . S 4 HOH A 35 531 531 HOH HOH . S 4 HOH A 36 532 532 HOH HOH . T 4 HOH B 1 495 495 HOH HOH . T 4 HOH B 2 496 496 HOH HOH . T 4 HOH B 3 497 497 HOH HOH . T 4 HOH B 4 498 498 HOH HOH . T 4 HOH B 5 499 499 HOH HOH . T 4 HOH B 6 502 502 HOH HOH . T 4 HOH B 7 503 503 HOH HOH . T 4 HOH B 8 504 504 HOH HOH . T 4 HOH B 9 505 505 HOH HOH . T 4 HOH B 10 506 506 HOH HOH . T 4 HOH B 11 507 507 HOH HOH . T 4 HOH B 12 508 508 HOH HOH . T 4 HOH B 13 509 509 HOH HOH . T 4 HOH B 14 510 510 HOH HOH . T 4 HOH B 15 511 511 HOH HOH . T 4 HOH B 16 512 512 HOH HOH . T 4 HOH B 17 513 513 HOH HOH . T 4 HOH B 18 514 514 HOH HOH . T 4 HOH B 19 515 515 HOH HOH . T 4 HOH B 20 516 516 HOH HOH . T 4 HOH B 21 517 517 HOH HOH . T 4 HOH B 22 518 518 HOH HOH . T 4 HOH B 23 519 519 HOH HOH . T 4 HOH B 24 520 520 HOH HOH . T 4 HOH B 25 521 521 HOH HOH . T 4 HOH B 26 522 522 HOH HOH . T 4 HOH B 27 523 523 HOH HOH . T 4 HOH B 28 524 524 HOH HOH . T 4 HOH B 29 525 525 HOH HOH . T 4 HOH B 30 526 526 HOH HOH . T 4 HOH B 31 527 527 HOH HOH . T 4 HOH B 32 528 528 HOH HOH . U 4 HOH C 1 495 495 HOH HOH . U 4 HOH C 2 496 496 HOH HOH . U 4 HOH C 3 497 497 HOH HOH . U 4 HOH C 4 498 498 HOH HOH . U 4 HOH C 5 499 499 HOH HOH . U 4 HOH C 6 502 502 HOH HOH . U 4 HOH C 7 503 503 HOH HOH . U 4 HOH C 8 504 504 HOH HOH . U 4 HOH C 9 505 505 HOH HOH . U 4 HOH C 10 506 506 HOH HOH . U 4 HOH C 11 507 507 HOH HOH . U 4 HOH C 12 508 508 HOH HOH . U 4 HOH C 13 509 509 HOH HOH . V 4 HOH D 1 495 495 HOH HOH . V 4 HOH D 2 496 496 HOH HOH . V 4 HOH D 3 497 497 HOH HOH . V 4 HOH D 4 498 498 HOH HOH . V 4 HOH D 5 499 499 HOH HOH . V 4 HOH D 6 502 502 HOH HOH . V 4 HOH D 7 503 503 HOH HOH . V 4 HOH D 8 504 504 HOH HOH . V 4 HOH D 9 505 505 HOH HOH . V 4 HOH D 10 506 506 HOH HOH . V 4 HOH D 11 507 507 HOH HOH . V 4 HOH D 12 508 508 HOH HOH . V 4 HOH D 13 509 509 HOH HOH . V 4 HOH D 14 510 510 HOH HOH . V 4 HOH D 15 511 511 HOH HOH . V 4 HOH D 16 512 512 HOH HOH . V 4 HOH D 17 513 513 HOH HOH . V 4 HOH D 18 514 514 HOH HOH . V 4 HOH D 19 515 515 HOH HOH . V 4 HOH D 20 516 516 HOH HOH . V 4 HOH D 21 517 517 HOH HOH . V 4 HOH D 22 518 518 HOH HOH . V 4 HOH D 23 519 519 HOH HOH . W 4 HOH E 1 495 495 HOH HOH . W 4 HOH E 2 496 496 HOH HOH . W 4 HOH E 3 497 497 HOH HOH . W 4 HOH E 4 498 498 HOH HOH . W 4 HOH E 5 499 499 HOH HOH . W 4 HOH E 6 502 502 HOH HOH . W 4 HOH E 7 503 503 HOH HOH . W 4 HOH E 8 504 504 HOH HOH . W 4 HOH E 9 505 505 HOH HOH . W 4 HOH E 10 506 506 HOH HOH . W 4 HOH E 11 507 507 HOH HOH . W 4 HOH E 12 508 508 HOH HOH . W 4 HOH E 13 509 509 HOH HOH . W 4 HOH E 14 510 510 HOH HOH . W 4 HOH E 15 511 511 HOH HOH . W 4 HOH E 16 512 512 HOH HOH . W 4 HOH E 17 513 513 HOH HOH . W 4 HOH E 18 514 514 HOH HOH . W 4 HOH E 19 515 515 HOH HOH . W 4 HOH E 20 516 516 HOH HOH . W 4 HOH E 21 517 517 HOH HOH . W 4 HOH E 22 518 518 HOH HOH . W 4 HOH E 23 519 519 HOH HOH . W 4 HOH E 24 520 520 HOH HOH . W 4 HOH E 25 521 521 HOH HOH . W 4 HOH E 26 522 522 HOH HOH . W 4 HOH E 27 523 523 HOH HOH . W 4 HOH E 28 524 524 HOH HOH . X 4 HOH F 1 495 495 HOH HOH . X 4 HOH F 2 496 496 HOH HOH . X 4 HOH F 3 497 497 HOH HOH . X 4 HOH F 4 498 498 HOH HOH . X 4 HOH F 5 499 499 HOH HOH . X 4 HOH F 6 502 502 HOH HOH . X 4 HOH F 7 503 503 HOH HOH . X 4 HOH F 8 504 504 HOH HOH . X 4 HOH F 9 505 505 HOH HOH . X 4 HOH F 10 506 506 HOH HOH . X 4 HOH F 11 507 507 HOH HOH . X 4 HOH F 12 508 508 HOH HOH . X 4 HOH F 13 509 509 HOH HOH . X 4 HOH F 14 510 510 HOH HOH . X 4 HOH F 15 511 511 HOH HOH . X 4 HOH F 16 512 512 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' UDX . . . H 3 -11.06 16.305 53.853 1 36.01 ? C1' UDX 501 A 1 HETATM 2 C C2' UDX . . . H 3 -12.045 17.373 53.347 1 37.3 ? C2' UDX 501 A 1 HETATM 3 O O2' UDX . . . H 3 -13.012 17.704 54.359 1 39.14 ? O2' UDX 501 A 1 HETATM 4 C C3' UDX . . . H 3 -12.74 16.882 52.101 1 36.83 ? C3' UDX 501 A 1 HETATM 5 O O3' UDX . . . H 3 -13.467 17.944 51.52 1 37.3 ? O3' UDX 501 A 1 HETATM 6 C C4' UDX . . . H 3 -11.669 16.401 51.157 1 36.79 ? C4' UDX 501 A 1 HETATM 7 O O4' UDX . . . H 3 -12.269 16.048 49.933 1 37.03 ? O4' UDX 501 A 1 HETATM 8 C C5' UDX . . . H 3 -11.025 15.165 51.782 1 37.07 ? C5' UDX 501 A 1 HETATM 9 O O5' UDX . . . H 3 -10.249 15.688 52.856 1 36.51 ? O5' UDX 501 A 1 HETATM 10 P PB UDX . . . H 3 -10.807 14.207 55.109 1 37.26 ? PB UDX 501 A 1 HETATM 11 O O1B UDX . . . H 3 -9.335 14.333 54.913 1 39.92 ? O1B UDX 501 A 1 HETATM 12 O O2B UDX . . . H 3 -11.194 12.779 54.552 1 38.23 ? O2B UDX 501 A 1 HETATM 13 O O3B UDX . . . H 3 -11.721 15.231 54.388 1 34.99 ? O3B UDX 501 A 1 HETATM 14 O O3A UDX . . . H 3 -11.229 14.339 56.648 1 36.96 ? O3A UDX 501 A 1 HETATM 15 P PA UDX . . . H 3 -11.225 15.825 57.384 1 37.15 ? PA UDX 501 A 1 HETATM 16 O O1A UDX . . . H 3 -12.442 16.145 58.158 1 38.08 ? O1A UDX 501 A 1 HETATM 17 O O2A UDX . . . H 3 -10.974 17.026 56.401 1 33.63 ? O2A UDX 501 A 1 HETATM 18 O O5D UDX . . . H 3 -9.933 15.769 58.319 1 37.41 ? O5D UDX 501 A 1 HETATM 19 C C5D UDX . . . H 3 -8.618 15.638 57.723 1 38.42 ? C5D UDX 501 A 1 HETATM 20 C C4D UDX . . . H 3 -7.546 15.865 58.782 1 38.93 ? C4D UDX 501 A 1 HETATM 21 O O4D UDX . . . H 3 -7.635 17.217 59.339 1 37.35 ? O4D UDX 501 A 1 HETATM 22 C C3D UDX . . . H 3 -7.865 14.913 59.926 1 39.16 ? C3D UDX 501 A 1 HETATM 23 O O3D UDX . . . H 3 -6.635 14.443 60.454 1 39.35 ? O3D UDX 501 A 1 HETATM 24 C C2D UDX . . . H 3 -8.585 15.82 60.925 1 38.75 ? C2D UDX 501 A 1 HETATM 25 O O2D UDX . . . H 3 -8.466 15.318 62.258 1 39.75 ? O2D UDX 501 A 1 HETATM 26 C C1D UDX . . . H 3 -7.804 17.112 60.758 1 36.74 ? C1D UDX 501 A 1 HETATM 27 N N1 UDX . . . H 3 -8.581 18.253 61.302 1 35.66 ? N1 UDX 501 A 1 HETATM 28 C C6 UDX . . . H 3 -9.765 18.735 60.68 1 36.71 ? C6 UDX 501 A 1 HETATM 29 C C2 UDX . . . H 3 -8.114 18.878 62.472 1 35.91 ? C2 UDX 501 A 1 HETATM 30 O O2 UDX . . . H 3 -7.099 18.507 63.036 1 34.07 ? O2 UDX 501 A 1 HETATM 31 N N3 UDX . . . H 3 -8.792 19.944 63.043 1 39.01 ? N3 UDX 501 A 1 HETATM 32 C C4 UDX . . . H 3 -9.96 20.422 62.427 1 41.5 ? C4 UDX 501 A 1 HETATM 33 O O4 UDX . . . H 3 -10.513 21.38 62.973 1 43.24 ? O4 UDX 501 A 1 HETATM 34 C C5 UDX . . . H 3 -10.452 19.823 61.237 1 39.11 ? C5 UDX 501 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #