data_8B63 # _model_server_result.job_id xLkAbE31ChyGy2eGfmlxVQ _model_server_result.datetime_utc '2024-11-13 22:24:02' _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 8b63 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8B63 # _exptl.entry_id 8B63 _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-ACETYLGALACTOSAMINE _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 90.22 _cell.angle_gamma 90 _cell.entry_id 8B63 _cell.length_a 41.762 _cell.length_b 109.963 _cell.length_c 94.326 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8B63 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _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 UD2 _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' # 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 O4 C4 UD2 doub 364 n n C4 N3 UD2 sing 365 n n C4 C5 UD2 sing 366 n n N3 C2 UD2 sing 367 n n C5 C6 UD2 doub 368 n n C2 O2 UD2 doub 369 n n C2 N1 UD2 sing 370 n n C6 N1 UD2 sing 371 n n N1 C1B UD2 sing 372 n n O2' C2B UD2 sing 373 n n C1B C2B UD2 sing 374 n n C1B O4B UD2 sing 375 n n C2B C3B UD2 sing 376 n n O2A PA UD2 doub 377 n n O4B C4B UD2 sing 378 n n O6' C6' UD2 sing 379 n n O5B PA UD2 sing 380 n n O5B C5B UD2 sing 381 n n C3B C4B UD2 sing 382 n n C3B O3B UD2 sing 383 n n PA O3A UD2 sing 384 n n PA O1A UD2 sing 385 n n C4B C5B UD2 sing 386 n n O3A PB UD2 sing 387 n n C6' C5' UD2 sing 388 n n O2B PB UD2 doub 389 n n C5' O5' UD2 sing 390 n n C5' C4' UD2 sing 391 n n PB O1B UD2 sing 392 n n PB O1' UD2 sing 393 n n O5' C1' UD2 sing 394 n n C4' O4' UD2 sing 395 n n C4' C3' UD2 sing 396 n n O1' C1' UD2 sing 397 n n C1' C2' UD2 sing 398 n n C3' C2' UD2 sing 399 n n C3' O3' UD2 sing 400 n n C2' N2' UD2 sing 401 n n N2' C7' UD2 sing 402 n n C7' O7' UD2 doub 403 n n C7' C8' UD2 sing 404 n n C1' H1' UD2 sing 405 n n C2' H2' UD2 sing 406 n n C3' H3' UD2 sing 407 n n C4' H4' UD2 sing 408 n n C5' H5' UD2 sing 409 n n C6' "H6'1" UD2 sing 410 n n C6' "H6'2" UD2 sing 411 n n C8' "H8'1" UD2 sing 412 n n C8' "H8'2" UD2 sing 413 n n C8' "H8'3" UD2 sing 414 n n N2' HN2' UD2 sing 415 n n O3' HO3' UD2 sing 416 n n O4' HO4' UD2 sing 417 n n O6' HO6' UD2 sing 418 n n N3 HN3 UD2 sing 419 n n C5 H5 UD2 sing 420 n n C6 H6 UD2 sing 421 n n C1B H1B UD2 sing 422 n n C2B H2B UD2 sing 423 n n O2' HO2' UD2 sing 424 n n C3B H3B UD2 sing 425 n n C4B H4B UD2 sing 426 n n O3B HO3A UD2 sing 427 n n C5B "H5'1" UD2 sing 428 n n C5B "H5'2" UD2 sing 429 n n O1A HOA2 UD2 sing 430 n n O1B HOB2 UD2 sing 431 n n # _atom_sites.entry_id 8B63 _atom_sites.fract_transf_matrix[1][1] 0.023945 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000093 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009094 _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] 0.010602 _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 UD2 A 1 401 1 UD2 UD2 . D 3 ACT A 1 402 1 ACT ACT . E 4 UDP B 1 401 1 UDP UDP . F 5 HOH A 1 501 16 HOH HOH . F 5 HOH A 2 502 60 HOH HOH . F 5 HOH A 3 503 4 HOH HOH . F 5 HOH A 4 504 50 HOH HOH . F 5 HOH A 5 505 49 HOH HOH . F 5 HOH A 6 506 66 HOH HOH . F 5 HOH A 7 507 3 HOH HOH . F 5 HOH A 8 508 35 HOH HOH . F 5 HOH A 9 509 64 HOH HOH . F 5 HOH A 10 510 62 HOH HOH . F 5 HOH A 11 511 39 HOH HOH . F 5 HOH A 12 512 18 HOH HOH . F 5 HOH A 13 513 1 HOH HOH . F 5 HOH A 14 514 2 HOH HOH . F 5 HOH A 15 515 22 HOH HOH . F 5 HOH A 16 516 57 HOH HOH . F 5 HOH A 17 517 10 HOH HOH . F 5 HOH A 18 518 34 HOH HOH . F 5 HOH A 19 519 33 HOH HOH . F 5 HOH A 20 520 14 HOH HOH . F 5 HOH A 21 521 20 HOH HOH . F 5 HOH A 22 522 21 HOH HOH . F 5 HOH A 23 523 38 HOH HOH . F 5 HOH A 24 524 9 HOH HOH . F 5 HOH A 25 525 8 HOH HOH . F 5 HOH A 26 526 36 HOH HOH . F 5 HOH A 27 527 65 HOH HOH . F 5 HOH A 28 528 51 HOH HOH . F 5 HOH A 29 529 46 HOH HOH . F 5 HOH A 30 530 56 HOH HOH . F 5 HOH A 31 531 63 HOH HOH . F 5 HOH A 32 532 6 HOH HOH . F 5 HOH A 33 533 7 HOH HOH . F 5 HOH A 34 534 48 HOH HOH . F 5 HOH A 35 535 19 HOH HOH . F 5 HOH A 36 536 31 HOH HOH . F 5 HOH A 37 537 12 HOH HOH . F 5 HOH A 38 538 15 HOH HOH . F 5 HOH A 39 539 11 HOH HOH . F 5 HOH A 40 540 40 HOH HOH . F 5 HOH A 41 541 61 HOH HOH . F 5 HOH A 42 542 59 HOH HOH . F 5 HOH A 43 543 68 HOH HOH . F 5 HOH A 44 544 52 HOH HOH . F 5 HOH A 45 545 13 HOH HOH . F 5 HOH A 46 546 54 HOH HOH . F 5 HOH A 47 547 67 HOH HOH . F 5 HOH A 48 548 32 HOH HOH . F 5 HOH A 49 549 47 HOH HOH . F 5 HOH A 50 550 17 HOH HOH . F 5 HOH A 51 551 55 HOH HOH . F 5 HOH A 52 552 58 HOH HOH . G 5 HOH B 1 501 71 HOH HOH . G 5 HOH B 2 502 30 HOH HOH . G 5 HOH B 3 503 27 HOH HOH . G 5 HOH B 4 504 75 HOH HOH . G 5 HOH B 5 505 81 HOH HOH . G 5 HOH B 6 506 44 HOH HOH . G 5 HOH B 7 507 53 HOH HOH . G 5 HOH B 8 508 74 HOH HOH . G 5 HOH B 9 509 43 HOH HOH . G 5 HOH B 10 510 83 HOH HOH . G 5 HOH B 11 511 95 HOH HOH . G 5 HOH B 12 512 90 HOH HOH . G 5 HOH B 13 513 93 HOH HOH . G 5 HOH B 14 514 24 HOH HOH . G 5 HOH B 15 515 28 HOH HOH . G 5 HOH B 16 516 72 HOH HOH . G 5 HOH B 17 517 94 HOH HOH . G 5 HOH B 18 518 45 HOH HOH . G 5 HOH B 19 519 79 HOH HOH . G 5 HOH B 20 520 26 HOH HOH . G 5 HOH B 21 521 41 HOH HOH . G 5 HOH B 22 522 69 HOH HOH . G 5 HOH B 23 523 86 HOH HOH . G 5 HOH B 24 524 78 HOH HOH . G 5 HOH B 25 525 82 HOH HOH . G 5 HOH B 26 526 89 HOH HOH . G 5 HOH B 27 527 91 HOH HOH . G 5 HOH B 28 528 77 HOH HOH . G 5 HOH B 29 529 23 HOH HOH . G 5 HOH B 30 530 85 HOH HOH . G 5 HOH B 31 531 25 HOH HOH . G 5 HOH B 32 532 80 HOH HOH . G 5 HOH B 33 533 88 HOH HOH . G 5 HOH B 34 534 42 HOH HOH . G 5 HOH B 35 535 73 HOH HOH . G 5 HOH B 36 536 76 HOH HOH . G 5 HOH B 37 537 92 HOH HOH . G 5 HOH B 38 538 84 HOH HOH . G 5 HOH B 39 539 96 HOH HOH . G 5 HOH B 40 540 70 HOH HOH . G 5 HOH B 41 541 29 HOH HOH . G 5 HOH B 42 542 87 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' UD2 . . . C 2 4.897 4.282 35.536 1 58.24 ? C1' UD2 401 A 1 HETATM 2 C C2' UD2 . . . C 2 4.084 3.294 36.393 1 59.5 ? C2' UD2 401 A 1 HETATM 3 C C3' UD2 . . . C 2 2.607 3.509 36.055 1 50.52 ? C3' UD2 401 A 1 HETATM 4 C C4' UD2 . . . C 2 2.181 4.974 36.243 1 49.28 ? C4' UD2 401 A 1 HETATM 5 C C5' UD2 . . . C 2 3.052 5.793 35.301 1 41.22 ? C5' UD2 401 A 1 HETATM 6 C C6' UD2 . . . C 2 2.727 7.283 35.222 1 43.15 ? C6' UD2 401 A 1 HETATM 7 C C7' UD2 . . . C 2 4.493 0.916 37.199 1 55.48 ? C7' UD2 401 A 1 HETATM 8 C C8' UD2 . . . C 2 5.02 -0.4 36.714 1 49.26 ? C8' UD2 401 A 1 HETATM 9 N N2' UD2 . . . C 2 4.522 1.904 36.281 1 65.54 ? N2' UD2 401 A 1 HETATM 10 O O1' UD2 . . . C 2 4.782 3.939 34.167 1 42.38 ? O1' UD2 401 A 1 HETATM 11 O O3' UD2 . . . C 2 1.817 2.599 36.798 1 38.63 ? O3' UD2 401 A 1 HETATM 12 O O4' UD2 . . . C 2 2.277 5.475 37.587 1 40.34 ? O4' UD2 401 A 1 HETATM 13 O O5' UD2 . . . C 2 4.415 5.613 35.737 1 60.05 ? O5' UD2 401 A 1 HETATM 14 O O6' UD2 . . . C 2 3.396 8.111 36.172 1 31.12 ? O6' UD2 401 A 1 HETATM 15 O O7' UD2 . . . C 2 4.042 1.056 38.342 1 52.55 ? O7' UD2 401 A 1 HETATM 16 N N1 UD2 . . . C 2 6.974 4.541 26.183 1 25.64 ? N1 UD2 401 A 1 HETATM 17 C C2 UD2 . . . C 2 7.599 5.109 25.083 1 29.11 ? C2 UD2 401 A 1 HETATM 18 N N3 UD2 . . . C 2 8.491 4.276 24.449 1 27.01 ? N3 UD2 401 A 1 HETATM 19 C C4 UD2 . . . C 2 8.762 2.958 24.762 1 28.68 ? C4 UD2 401 A 1 HETATM 20 C C5 UD2 . . . C 2 8.045 2.43 25.887 1 27.21 ? C5 UD2 401 A 1 HETATM 21 C C6 UD2 . . . C 2 7.191 3.23 26.547 1 29.27 ? C6 UD2 401 A 1 HETATM 22 O O2 UD2 . . . C 2 7.412 6.278 24.732 1 27.17 ? O2 UD2 401 A 1 HETATM 23 O O4 UD2 . . . C 2 9.563 2.339 24.069 1 34.14 ? O4 UD2 401 A 1 HETATM 24 C C1B UD2 . . . C 2 5.964 5.366 26.838 1 27.76 ? C1B UD2 401 A 1 HETATM 25 C C2B UD2 . . . C 2 4.55 4.811 26.664 1 28.54 ? C2B UD2 401 A 1 HETATM 26 O O2' UD2 . . . C 2 4.039 5.079 25.377 1 30.8 ? O2' UD2 401 A 1 HETATM 27 C C3B UD2 . . . C 2 3.879 5.567 27.813 1 29.2 ? C3B UD2 401 A 1 HETATM 28 C C4B UD2 . . . C 2 4.932 5.382 28.929 1 27.15 ? C4B UD2 401 A 1 HETATM 29 O O4B UD2 . . . C 2 6.192 5.364 28.219 1 28.48 ? O4B UD2 401 A 1 HETATM 30 O O3B UD2 . . . C 2 3.659 6.925 27.445 1 28.84 ? O3B UD2 401 A 1 HETATM 31 C C5B UD2 . . . C 2 4.872 4.099 29.713 1 28.28 ? C5B UD2 401 A 1 HETATM 32 O O5B UD2 . . . C 2 4.099 4.313 30.892 1 29.11 ? O5B UD2 401 A 1 HETATM 33 P PA UD2 . . . C 2 3.169 3.181 31.571 1 28.32 ? PA UD2 401 A 1 HETATM 34 O O1A UD2 . . . C 2 2.299 3.92 32.541 1 23.13 ? O1A UD2 401 A 1 HETATM 35 O O2A UD2 . . . C 2 2.574 2.232 30.586 1 28.57 ? O2A UD2 401 A 1 HETATM 36 O O3A UD2 . . . C 2 4.288 2.328 32.338 1 33.03 ? O3A UD2 401 A 1 HETATM 37 P PB UD2 . . . C 2 5.49 2.75 33.328 1 43.29 ? PB UD2 401 A 1 HETATM 38 O O1B UD2 . . . C 2 5.854 1.572 34.154 1 37.88 ? O1B UD2 401 A 1 HETATM 39 O O2B UD2 . . . C 2 6.618 3.328 32.526 1 49.96 ? O2B UD2 401 A 1 # _model_server_stats.io_time_ms 109 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #