data_3SWI # _model_server_result.job_id 1UsNO0IJnIj7SJg_ozZjTw _model_server_result.datetime_utc '2024-11-02 11:36:05' _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 3swi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":426}' # _entry.id 3SWI # _exptl.entry_id 3SWI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 607.354 _entity.id 5 _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 _cell.angle_gamma 90 _cell.entry_id 3SWI _cell.length_a 137.4 _cell.length_b 137.4 _cell.length_c 137.4 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SWI _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C ARG 66 A ARG 66 1_555 A N IAS 67 A IAS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 A CG IAS 67 A IAS 67 1_555 A N GLY 68 A GLY 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale3 A C GLY 114 A GLY 114 1_555 A N QPA 115 A QPA 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C QPA 115 A QPA 115 1_555 A N ALA 116 A ALA 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 A O13 QPA 115 A QPA 115 1_555 G MG MG . A MG 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.779 ? metalc ? metalc2 A O9 QPA 115 A QPA 115 1_555 G MG MG . A MG 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc3 G MG MG . A MG 425 1_555 H O1A UD2 . A UD2 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc4 G MG MG . A MG 425 1_555 J O HOH . A HOH 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc5 G MG MG . A MG 425 1_555 J O HOH . A HOH 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc6 G MG MG . A MG 425 1_555 J O HOH . A HOH 537 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? # _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 431 n n C4 N3 UD2 sing 432 n n C4 C5 UD2 sing 433 n n N3 C2 UD2 sing 434 n n C5 C6 UD2 doub 435 n n C2 O2 UD2 doub 436 n n C2 N1 UD2 sing 437 n n C6 N1 UD2 sing 438 n n N1 C1B UD2 sing 439 n n O2' C2B UD2 sing 440 n n C1B C2B UD2 sing 441 n n C1B O4B UD2 sing 442 n n C2B C3B UD2 sing 443 n n O2A PA UD2 doub 444 n n O4B C4B UD2 sing 445 n n O6' C6' UD2 sing 446 n n O5B PA UD2 sing 447 n n O5B C5B UD2 sing 448 n n C3B C4B UD2 sing 449 n n C3B O3B UD2 sing 450 n n PA O3A UD2 sing 451 n n PA O1A UD2 sing 452 n n C4B C5B UD2 sing 453 n n O3A PB UD2 sing 454 n n C6' C5' UD2 sing 455 n n O2B PB UD2 doub 456 n n C5' O5' UD2 sing 457 n n C5' C4' UD2 sing 458 n n PB O1B UD2 sing 459 n n PB O1' UD2 sing 460 n n O5' C1' UD2 sing 461 n n C4' O4' UD2 sing 462 n n C4' C3' UD2 sing 463 n n O1' C1' UD2 sing 464 n n C1' C2' UD2 sing 465 n n C3' C2' UD2 sing 466 n n C3' O3' UD2 sing 467 n n C2' N2' UD2 sing 468 n n N2' C7' UD2 sing 469 n n C7' O7' UD2 doub 470 n n C7' C8' UD2 sing 471 n n C1' H1' UD2 sing 472 n n C2' H2' UD2 sing 473 n n C3' H3' UD2 sing 474 n n C4' H4' UD2 sing 475 n n C5' H5' UD2 sing 476 n n C6' "H6'1" UD2 sing 477 n n C6' "H6'2" UD2 sing 478 n n C8' "H8'1" UD2 sing 479 n n C8' "H8'2" UD2 sing 480 n n C8' "H8'3" UD2 sing 481 n n N2' HN2' UD2 sing 482 n n O3' HO3' UD2 sing 483 n n O4' HO4' UD2 sing 484 n n O6' HO6' UD2 sing 485 n n N3 HN3 UD2 sing 486 n n C5 H5 UD2 sing 487 n n C6 H6 UD2 sing 488 n n C1B H1B UD2 sing 489 n n C2B H2B UD2 sing 490 n n O2' HO2' UD2 sing 491 n n C3B H3B UD2 sing 492 n n C4B H4B UD2 sing 493 n n O3B HO3A UD2 sing 494 n n C5B "H5'1" UD2 sing 495 n n C5B "H5'2" UD2 sing 496 n n O1A HOA2 UD2 sing 497 n n O1B HOB2 UD2 sing 498 n n # _atom_sites.entry_id 3SWI _atom_sites.fract_transf_matrix[1][1] 0.007278 _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] 0.007278 _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] 0.007278 _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 MOE A 1 420 1 MOE MOE . C 2 MOE A 1 421 2 MOE MOE . D 3 PG0 A 1 422 1 PG0 PG0 . E 3 PG0 A 1 423 2 PG0 PG0 . F 3 PG0 A 1 424 3 PG0 PG0 . G 4 MG A 1 425 1 MG MG2 . H 5 UD2 A 1 426 1 UD2 UD2 . I 6 UPN A 1 427 1 UPN UPN . J 7 HOH A 1 428 1 HOH HOH . J 7 HOH A 2 429 2 HOH HOH . J 7 HOH A 3 430 3 HOH HOH . J 7 HOH A 4 431 4 HOH HOH . J 7 HOH A 5 432 5 HOH HOH . J 7 HOH A 6 433 6 HOH HOH . J 7 HOH A 7 434 7 HOH HOH . J 7 HOH A 8 435 8 HOH HOH . J 7 HOH A 9 436 9 HOH HOH . J 7 HOH A 10 437 10 HOH HOH . J 7 HOH A 11 438 11 HOH HOH . J 7 HOH A 12 439 12 HOH HOH . J 7 HOH A 13 440 13 HOH HOH . J 7 HOH A 14 441 14 HOH HOH . J 7 HOH A 15 442 15 HOH HOH . J 7 HOH A 16 443 16 HOH HOH . J 7 HOH A 17 444 17 HOH HOH . J 7 HOH A 18 445 18 HOH HOH . J 7 HOH A 19 446 19 HOH HOH . J 7 HOH A 20 447 20 HOH HOH . J 7 HOH A 21 448 21 HOH HOH . J 7 HOH A 22 449 22 HOH HOH . J 7 HOH A 23 450 23 HOH HOH . J 7 HOH A 24 451 24 HOH HOH . J 7 HOH A 25 452 25 HOH HOH . J 7 HOH A 26 453 26 HOH HOH . J 7 HOH A 27 454 27 HOH HOH . J 7 HOH A 28 455 28 HOH HOH . J 7 HOH A 29 456 29 HOH HOH . J 7 HOH A 30 457 30 HOH HOH . J 7 HOH A 31 458 31 HOH HOH . J 7 HOH A 32 459 32 HOH HOH . J 7 HOH A 33 460 33 HOH HOH . J 7 HOH A 34 461 34 HOH HOH . J 7 HOH A 35 462 35 HOH HOH . J 7 HOH A 36 463 36 HOH HOH . J 7 HOH A 37 464 37 HOH HOH . J 7 HOH A 38 465 38 HOH HOH . J 7 HOH A 39 466 39 HOH HOH . J 7 HOH A 40 467 40 HOH HOH . J 7 HOH A 41 468 41 HOH HOH . J 7 HOH A 42 469 42 HOH HOH . J 7 HOH A 43 470 43 HOH HOH . J 7 HOH A 44 471 44 HOH HOH . J 7 HOH A 45 472 45 HOH HOH . J 7 HOH A 46 473 46 HOH HOH . J 7 HOH A 47 474 47 HOH HOH . J 7 HOH A 48 475 48 HOH HOH . J 7 HOH A 49 476 49 HOH HOH . J 7 HOH A 50 477 50 HOH HOH . J 7 HOH A 51 478 51 HOH HOH . J 7 HOH A 52 479 52 HOH HOH . J 7 HOH A 53 480 53 HOH HOH . J 7 HOH A 54 481 54 HOH HOH . J 7 HOH A 55 482 55 HOH HOH . J 7 HOH A 56 483 56 HOH HOH . J 7 HOH A 57 484 57 HOH HOH . J 7 HOH A 58 485 58 HOH HOH . J 7 HOH A 59 486 59 HOH HOH . J 7 HOH A 60 487 60 HOH HOH . J 7 HOH A 61 488 61 HOH HOH . J 7 HOH A 62 489 62 HOH HOH . J 7 HOH A 63 490 63 HOH HOH . J 7 HOH A 64 491 64 HOH HOH . J 7 HOH A 65 492 65 HOH HOH . J 7 HOH A 66 493 66 HOH HOH . J 7 HOH A 67 494 67 HOH HOH . J 7 HOH A 68 495 68 HOH HOH . J 7 HOH A 69 496 69 HOH HOH . J 7 HOH A 70 497 70 HOH HOH . J 7 HOH A 71 498 71 HOH HOH . J 7 HOH A 72 499 72 HOH HOH . J 7 HOH A 73 500 73 HOH HOH . J 7 HOH A 74 501 74 HOH HOH . J 7 HOH A 75 502 75 HOH HOH . J 7 HOH A 76 503 76 HOH HOH . J 7 HOH A 77 504 77 HOH HOH . J 7 HOH A 78 505 78 HOH HOH . J 7 HOH A 79 506 79 HOH HOH . J 7 HOH A 80 507 80 HOH HOH . J 7 HOH A 81 508 81 HOH HOH . J 7 HOH A 82 509 82 HOH HOH . J 7 HOH A 83 510 83 HOH HOH . J 7 HOH A 84 511 84 HOH HOH . J 7 HOH A 85 512 85 HOH HOH . J 7 HOH A 86 513 86 HOH HOH . J 7 HOH A 87 514 87 HOH HOH . J 7 HOH A 88 515 88 HOH HOH . J 7 HOH A 89 516 89 HOH HOH . J 7 HOH A 90 517 90 HOH HOH . J 7 HOH A 91 518 91 HOH HOH . J 7 HOH A 92 519 92 HOH HOH . J 7 HOH A 93 520 93 HOH HOH . J 7 HOH A 94 521 94 HOH HOH . J 7 HOH A 95 522 95 HOH HOH . J 7 HOH A 96 523 96 HOH HOH . J 7 HOH A 97 524 97 HOH HOH . J 7 HOH A 98 525 98 HOH HOH . J 7 HOH A 99 526 99 HOH HOH . J 7 HOH A 100 527 100 HOH HOH . J 7 HOH A 101 528 101 HOH HOH . J 7 HOH A 102 529 102 HOH HOH . J 7 HOH A 103 530 103 HOH HOH . J 7 HOH A 104 531 104 HOH HOH . J 7 HOH A 105 532 105 HOH HOH . J 7 HOH A 106 533 106 HOH HOH . J 7 HOH A 107 534 107 HOH HOH . J 7 HOH A 108 535 108 HOH HOH . J 7 HOH A 109 536 109 HOH HOH . J 7 HOH A 110 537 110 HOH HOH . J 7 HOH A 111 538 111 HOH HOH . J 7 HOH A 112 539 112 HOH HOH . J 7 HOH A 113 540 113 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 . . . H 5 141.429 69.836 176.415 1 34.63 ? C1' UD2 426 A 1 HETATM 2 C C2' UD2 . . . H 5 141.339 69.113 175.025 1 35.22 ? C2' UD2 426 A 1 HETATM 3 C C3' UD2 . . . H 5 142.741 68.452 174.678 1 34.39 ? C3' UD2 426 A 1 HETATM 4 C C4' UD2 . . . H 5 143.853 69.529 174.634 1 35.81 ? C4' UD2 426 A 1 HETATM 5 C C5' UD2 . . . H 5 143.855 70.248 176.071 1 36.58 ? C5' UD2 426 A 1 HETATM 6 C C6' UD2 . . . H 5 144.869 71.386 176.31 1 37.41 ? C6' UD2 426 A 1 HETATM 7 C C7' UD2 . . . H 5 139.335 67.839 174.043 1 37.58 ? C7' UD2 426 A 1 HETATM 8 C C8' UD2 . . . H 5 139.562 68.364 172.631 1 37.13 ? C8' UD2 426 A 1 HETATM 9 N N2' UD2 . . . H 5 140.219 68.113 175.092 1 36.24 ? N2' UD2 426 A 1 HETATM 10 O O1' UD2 . . . H 5 141.608 68.829 177.387 1 35.03 ? O1' UD2 426 A 1 HETATM 11 O O3' UD2 . . . H 5 142.723 67.802 173.424 1 32.18 ? O3' UD2 426 A 1 HETATM 12 O O4' UD2 . . . H 5 143.541 70.452 173.582 1 34.32 ? O4' UD2 426 A 1 HETATM 13 O O5' UD2 . . . H 5 142.509 70.774 176.374 1 36.84 ? O5' UD2 426 A 1 HETATM 14 O O6' UD2 . . . H 5 144.594 72.019 177.547 1 36.35 ? O6' UD2 426 A 1 HETATM 15 O O7' UD2 . . . H 5 138.371 67.156 174.278 1 37.2 ? O7' UD2 426 A 1 HETATM 16 N N1 UD2 . . . H 5 140.146 74.732 183.272 1 35.54 ? N1 UD2 426 A 1 HETATM 17 C C2 UD2 . . . H 5 139.758 76.008 183.765 1 35.52 ? C2 UD2 426 A 1 HETATM 18 N N3 UD2 . . . H 5 140.538 77.11 183.345 1 35.41 ? N3 UD2 426 A 1 HETATM 19 C C4 UD2 . . . H 5 141.669 77.054 182.475 1 36.16 ? C4 UD2 426 A 1 HETATM 20 C C5 UD2 . . . H 5 142.038 75.699 181.982 1 37.46 ? C5 UD2 426 A 1 HETATM 21 C C6 UD2 . . . H 5 141.284 74.624 182.389 1 36.62 ? C6 UD2 426 A 1 HETATM 22 O O2 UD2 . . . H 5 138.808 76.181 184.516 1 36.74 ? O2 UD2 426 A 1 HETATM 23 O O4 UD2 . . . H 5 142.261 78.078 182.186 1 34.81 ? O4 UD2 426 A 1 HETATM 24 C C1B UD2 . . . H 5 139.351 73.505 183.695 1 38.64 ? C1B UD2 426 A 1 HETATM 25 C C2B UD2 . . . H 5 138.424 72.982 182.584 1 38.43 ? C2B UD2 426 A 1 HETATM 26 O O2' UD2 . . . H 5 137.107 73.509 182.712 1 42.24 ? O2' UD2 426 A 1 HETATM 27 C C3B UD2 . . . H 5 138.439 71.468 182.895 1 37.21 ? C3B UD2 426 A 1 HETATM 28 C C4B UD2 . . . H 5 139.837 71.25 183.574 1 37.31 ? C4B UD2 426 A 1 HETATM 29 O O4B UD2 . . . H 5 140.279 72.502 184.019 1 40.86 ? O4B UD2 426 A 1 HETATM 30 O O3B UD2 . . . H 5 137.444 71.113 183.859 1 32.82 ? O3B UD2 426 A 1 HETATM 31 C C5B UD2 . . . H 5 140.929 70.713 182.6 1 35.75 ? C5B UD2 426 A 1 HETATM 32 O O5B UD2 . . . H 5 140.925 71.564 181.457 1 36.03 ? O5B UD2 426 A 1 HETATM 33 P PA UD2 . . . H 5 141.913 71.423 180.123 1 36.27 ? PA UD2 426 A 1 HETATM 34 O O1A UD2 . . . H 5 143.26 71.082 180.537 1 36.46 ? O1A UD2 426 A 1 HETATM 35 O O2A UD2 . . . H 5 141.648 72.439 179.093 1 38.58 ? O2A UD2 426 A 1 HETATM 36 O O3A UD2 . . . H 5 141.108 70.079 179.752 1 34.95 ? O3A UD2 426 A 1 HETATM 37 P PB UD2 . . . H 5 140.791 68.862 178.821 1 33.13 ? PB UD2 426 A 1 HETATM 38 O O1B UD2 . . . H 5 139.375 69.057 178.473 1 35.75 ? O1B UD2 426 A 1 HETATM 39 O O2B UD2 . . . H 5 141.136 67.693 179.591 1 33.19 ? O2B UD2 426 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 420 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 39 #