data_9JN3 # _model_server_result.job_id OMQ4yyx8_E4JoUb1gbC9gA _model_server_result.datetime_utc '2025-07-16 09:29:08' _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 9jn3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 9JN3 # _exptl.entry_id 9JN3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 101.12 _cell.angle_gamma 90 _cell.entry_id 9JN3 _cell.length_a 43.302 _cell.length_b 95.114 _cell.length_c 70.988 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JN3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 # 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 metalc ? metalc1 A OD1 ASP 91 A ASP 91 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc2 A OD2 ASP 91 A ASP 91 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc3 C O2A UPG . A UPG 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc4 C O1B UPG . A UPG 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc5 E MG MG . A MG 403 1_555 I O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc6 E MG MG . A MG 403 1_555 I O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc7 B OD1 ASP 91 B ASP 91 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc8 B OD2 ASP 91 B ASP 91 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc9 F O2A UPG . B UPG 401 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc10 F O1B UPG . B UPG 401 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc11 H MG MG . B MG 403 1_555 J O HOH . B HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc12 H MG MG . B MG 403 1_555 J O HOH . B HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 N1 C2 UPG sing 392 n n N1 C6 UPG sing 393 n n N1 C1C UPG sing 394 n n C2 N3 UPG sing 395 n n C2 O2 UPG doub 396 n n N3 C4 UPG sing 397 n n N3 HN3 UPG sing 398 n n C4 C5 UPG sing 399 n n C4 O4 UPG doub 400 n n C5 C6 UPG doub 401 n n C5 H5 UPG sing 402 n n C6 H6 UPG sing 403 n n C1C C2C UPG sing 404 n n C1C O4C UPG sing 405 n n C1C H1C UPG sing 406 n n C2C O2C UPG sing 407 n n C2C C3C UPG sing 408 n n C2C H2C UPG sing 409 n n O2C HO2C UPG sing 410 n n C3C C4C UPG sing 411 n n C3C O3C UPG sing 412 n n C3C H3C UPG sing 413 n n C4C O4C UPG sing 414 n n C4C C5C UPG sing 415 n n C4C H4C UPG sing 416 n n O3C HO3C UPG sing 417 n n C5C O5C UPG sing 418 n n C5C H5C1 UPG sing 419 n n C5C H5C2 UPG sing 420 n n O5C PA UPG sing 421 n n PA O1A UPG doub 422 n n PA O2A UPG sing 423 n n PA O3A UPG sing 424 n n O2A HOA2 UPG sing 425 n n O3A PB UPG sing 426 n n PB O1B UPG doub 427 n n PB O2B UPG sing 428 n n PB O3B UPG sing 429 n n O2B HOB2 UPG sing 430 n n O3B C1' UPG sing 431 n n C1' C2' UPG sing 432 n n C1' O5' UPG sing 433 n n C1' H1' UPG sing 434 n n C2' C3' UPG sing 435 n n C2' O2' UPG sing 436 n n C2' H2' UPG sing 437 n n C3' C4' UPG sing 438 n n C3' O3' UPG sing 439 n n C3' H3' UPG sing 440 n n C4' C5' UPG sing 441 n n C4' O4' UPG sing 442 n n C4' H4' UPG sing 443 n n C5' C6' UPG sing 444 n n C5' O5' UPG sing 445 n n C5' H5' UPG sing 446 n n C6' O6' UPG sing 447 n n C6' "H6'1" UPG sing 448 n n C6' "H6'2" UPG sing 449 n n O2' HO2' UPG sing 450 n n O3' HO3' UPG sing 451 n n O4' HO4' UPG sing 452 n n O6' HO6' UPG sing 453 n n # _atom_sites.entry_id 9JN3 _atom_sites.fract_transf_matrix[1][1] 0.023094 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004538 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010514 _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] 0.014356 _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 UPG A 1 401 401 UPG DRG . D 3 RAB A 1 402 501 RAB Ara . E 4 MG A 1 403 2 MG MG . F 2 UPG B 1 401 401 UPG DRG . G 3 RAB B 1 402 501 RAB Ara . H 4 MG B 1 403 1 MG MG . I 5 HOH A 1 501 129 HOH HOH . I 5 HOH A 2 502 114 HOH HOH . I 5 HOH A 3 503 128 HOH HOH . I 5 HOH A 4 504 22 HOH HOH . I 5 HOH A 5 505 65 HOH HOH . I 5 HOH A 6 506 54 HOH HOH . I 5 HOH A 7 507 44 HOH HOH . I 5 HOH A 8 508 68 HOH HOH . I 5 HOH A 9 509 111 HOH HOH . I 5 HOH A 10 510 46 HOH HOH . I 5 HOH A 11 511 24 HOH HOH . I 5 HOH A 12 512 132 HOH HOH . I 5 HOH A 13 513 82 HOH HOH . I 5 HOH A 14 514 59 HOH HOH . I 5 HOH A 15 515 43 HOH HOH . I 5 HOH A 16 516 13 HOH HOH . I 5 HOH A 17 517 126 HOH HOH . I 5 HOH A 18 518 40 HOH HOH . I 5 HOH A 19 519 103 HOH HOH . I 5 HOH A 20 520 20 HOH HOH . I 5 HOH A 21 521 77 HOH HOH . I 5 HOH A 22 522 57 HOH HOH . I 5 HOH A 23 523 48 HOH HOH . I 5 HOH A 24 524 67 HOH HOH . I 5 HOH A 25 525 3 HOH HOH . I 5 HOH A 26 526 12 HOH HOH . I 5 HOH A 27 527 35 HOH HOH . I 5 HOH A 28 528 42 HOH HOH . I 5 HOH A 29 529 10 HOH HOH . I 5 HOH A 30 530 11 HOH HOH . I 5 HOH A 31 531 94 HOH HOH . I 5 HOH A 32 532 38 HOH HOH . I 5 HOH A 33 533 99 HOH HOH . I 5 HOH A 34 534 97 HOH HOH . I 5 HOH A 35 535 98 HOH HOH . I 5 HOH A 36 536 31 HOH HOH . I 5 HOH A 37 537 47 HOH HOH . I 5 HOH A 38 538 101 HOH HOH . I 5 HOH A 39 539 8 HOH HOH . I 5 HOH A 40 540 133 HOH HOH . I 5 HOH A 41 541 29 HOH HOH . I 5 HOH A 42 542 137 HOH HOH . I 5 HOH A 43 543 23 HOH HOH . I 5 HOH A 44 544 53 HOH HOH . I 5 HOH A 45 545 34 HOH HOH . I 5 HOH A 46 546 89 HOH HOH . I 5 HOH A 47 547 100 HOH HOH . I 5 HOH A 48 548 93 HOH HOH . I 5 HOH A 49 549 30 HOH HOH . I 5 HOH A 50 550 21 HOH HOH . I 5 HOH A 51 551 25 HOH HOH . I 5 HOH A 52 552 49 HOH HOH . I 5 HOH A 53 553 102 HOH HOH . I 5 HOH A 54 554 96 HOH HOH . I 5 HOH A 55 555 62 HOH HOH . I 5 HOH A 56 556 139 HOH HOH . I 5 HOH A 57 557 134 HOH HOH . I 5 HOH A 58 558 79 HOH HOH . I 5 HOH A 59 559 105 HOH HOH . I 5 HOH A 60 560 135 HOH HOH . I 5 HOH A 61 561 87 HOH HOH . I 5 HOH A 62 562 136 HOH HOH . I 5 HOH A 63 563 80 HOH HOH . I 5 HOH A 64 564 63 HOH HOH . I 5 HOH A 65 565 130 HOH HOH . J 5 HOH B 1 501 84 HOH HOH . J 5 HOH B 2 502 55 HOH HOH . J 5 HOH B 3 503 119 HOH HOH . J 5 HOH B 4 504 74 HOH HOH . J 5 HOH B 5 505 4 HOH HOH . J 5 HOH B 6 506 112 HOH HOH . J 5 HOH B 7 507 104 HOH HOH . J 5 HOH B 8 508 14 HOH HOH . J 5 HOH B 9 509 75 HOH HOH . J 5 HOH B 10 510 70 HOH HOH . J 5 HOH B 11 511 71 HOH HOH . J 5 HOH B 12 512 107 HOH HOH . J 5 HOH B 13 513 45 HOH HOH . J 5 HOH B 14 514 52 HOH HOH . J 5 HOH B 15 515 122 HOH HOH . J 5 HOH B 16 516 9 HOH HOH . J 5 HOH B 17 517 64 HOH HOH . J 5 HOH B 18 518 33 HOH HOH . J 5 HOH B 19 519 118 HOH HOH . J 5 HOH B 20 520 36 HOH HOH . J 5 HOH B 21 521 41 HOH HOH . J 5 HOH B 22 522 39 HOH HOH . J 5 HOH B 23 523 28 HOH HOH . J 5 HOH B 24 524 76 HOH HOH . J 5 HOH B 25 525 16 HOH HOH . J 5 HOH B 26 526 6 HOH HOH . J 5 HOH B 27 527 26 HOH HOH . J 5 HOH B 28 528 83 HOH HOH . J 5 HOH B 29 529 85 HOH HOH . J 5 HOH B 30 530 72 HOH HOH . J 5 HOH B 31 531 61 HOH HOH . J 5 HOH B 32 532 19 HOH HOH . J 5 HOH B 33 533 5 HOH HOH . J 5 HOH B 34 534 88 HOH HOH . J 5 HOH B 35 535 66 HOH HOH . J 5 HOH B 36 536 116 HOH HOH . J 5 HOH B 37 537 18 HOH HOH . J 5 HOH B 38 538 81 HOH HOH . J 5 HOH B 39 539 51 HOH HOH . J 5 HOH B 40 540 7 HOH HOH . J 5 HOH B 41 541 37 HOH HOH . J 5 HOH B 42 542 91 HOH HOH . J 5 HOH B 43 543 27 HOH HOH . J 5 HOH B 44 544 60 HOH HOH . J 5 HOH B 45 545 86 HOH HOH . J 5 HOH B 46 546 1 HOH HOH . J 5 HOH B 47 547 50 HOH HOH . J 5 HOH B 48 548 73 HOH HOH . J 5 HOH B 49 549 90 HOH HOH . J 5 HOH B 50 550 17 HOH HOH . J 5 HOH B 51 551 2 HOH HOH . J 5 HOH B 52 552 32 HOH HOH . J 5 HOH B 53 553 125 HOH HOH . J 5 HOH B 54 554 120 HOH HOH . J 5 HOH B 55 555 78 HOH HOH . J 5 HOH B 56 556 58 HOH HOH . J 5 HOH B 57 557 92 HOH HOH . J 5 HOH B 58 558 121 HOH HOH . J 5 HOH B 59 559 110 HOH HOH . J 5 HOH B 60 560 56 HOH HOH . J 5 HOH B 61 561 138 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 N1 UPG . . . C 2 28.316 0.874 11.978 1 41.9 ? N1 UPG 401 A 1 HETATM 2 C C2 UPG . . . C 2 29.008 0.938 13.185 1 42.15 ? C2 UPG 401 A 1 HETATM 3 N N3 UPG . . . C 2 30.03 0.029 13.317 1 39.47 ? N3 UPG 401 A 1 HETATM 4 C C4 UPG . . . C 2 30.413 -0.93 12.4 1 41.52 ? C4 UPG 401 A 1 HETATM 5 C C5 UPG . . . C 2 29.64 -0.951 11.188 1 34.31 ? C5 UPG 401 A 1 HETATM 6 C C6 UPG . . . C 2 28.64 -0.071 11.025 1 38.59 ? C6 UPG 401 A 1 HETATM 7 O O2 UPG . . . C 2 28.764 1.749 14.06 1 40.24 ? O2 UPG 401 A 1 HETATM 8 O O4 UPG . . . C 2 31.348 -1.685 12.678 1 45.1 ? O4 UPG 401 A 1 HETATM 9 C C1C UPG . . . C 2 27.166 1.785 11.762 1 38.42 ? C1C UPG 401 A 1 HETATM 10 C C2C UPG . . . C 2 27.009 2.32 10.344 1 40.77 ? C2C UPG 401 A 1 HETATM 11 O O2C UPG . . . C 2 27.846 3.445 10.14 1 43.98 ? O2C UPG 401 A 1 HETATM 12 C C3C UPG . . . C 2 25.517 2.667 10.357 1 36.01 ? C3C UPG 401 A 1 HETATM 13 C C4C UPG . . . C 2 24.947 1.42 11.035 1 40 ? C4C UPG 401 A 1 HETATM 14 O O4C UPG . . . C 2 25.984 1.025 11.966 1 43.62 ? O4C UPG 401 A 1 HETATM 15 O O3C UPG . . . C 2 25.291 3.813 11.162 1 37.79 ? O3C UPG 401 A 1 HETATM 16 C C5C UPG . . . C 2 24.568 0.282 10.113 1 41.92 ? C5C UPG 401 A 1 HETATM 17 O O5C UPG . . . C 2 25.717 -0.149 9.316 1 50.27 ? O5C UPG 401 A 1 HETATM 18 P PA UPG . . . C 2 25.44 -0.505 7.779 1 43.86 ? PA UPG 401 A 1 HETATM 19 O O1A UPG . . . C 2 26.622 -1.175 7.185 1 55.38 -1 O1A UPG 401 A 1 HETATM 20 O O2A UPG . . . C 2 24.774 0.655 7.132 1 41.27 ? O2A UPG 401 A 1 HETATM 21 O O3A UPG . . . C 2 24.276 -1.56 8.022 1 54.8 ? O3A UPG 401 A 1 HETATM 22 P PB UPG . . . C 2 23.244 -2.211 6.998 1 50.73 ? PB UPG 401 A 1 HETATM 23 O O1B UPG . . . C 2 22.579 -1.073 6.322 1 49.21 ? O1B UPG 401 A 1 HETATM 24 O O2B UPG . . . C 2 23.92 -3.251 6.185 1 64.75 -1 O2B UPG 401 A 1 HETATM 25 O O3B UPG . . . C 2 22.279 -2.91 8.051 1 58.22 ? O3B UPG 401 A 1 HETATM 26 C C1' UPG . . . C 2 22.868 -3.671 9.068 1 67 ? C1' UPG 401 A 1 HETATM 27 C C2' UPG . . . C 2 22.38 -5.128 9.09 1 63.59 ? C2' UPG 401 A 1 HETATM 28 C C3' UPG . . . C 2 20.956 -5.331 9.602 1 64.25 ? C3' UPG 401 A 1 HETATM 29 C C4' UPG . . . C 2 20.386 -4.202 10.463 1 57.59 ? C4' UPG 401 A 1 HETATM 30 C C5' UPG . . . C 2 21.041 -2.854 10.173 1 62.62 ? C5' UPG 401 A 1 HETATM 31 C C6' UPG . . . C 2 20.675 -1.688 11.054 1 54.65 ? C6' UPG 401 A 1 HETATM 32 O O2' UPG . . . C 2 22.448 -5.677 7.778 1 65.34 ? O2' UPG 401 A 1 HETATM 33 O O3' UPG . . . C 2 21.011 -6.541 10.365 1 63.44 ? O3' UPG 401 A 1 HETATM 34 O O4' UPG . . . C 2 19.023 -4.026 10.086 1 58.32 ? O4' UPG 401 A 1 HETATM 35 O O5' UPG . . . C 2 22.47 -2.981 10.247 1 63.7 ? O5' UPG 401 A 1 HETATM 36 O O6' UPG . . . C 2 21.347 -0.583 10.46 1 52.65 ? O6' UPG 401 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 36 #