data_3SRZ # _model_server_result.job_id W-iMJIpJwKOKl3RO936TmQ _model_server_result.datetime_utc '2024-11-04 23:06:15' _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 3srz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":556}' # _entry.id 3SRZ # _exptl.entry_id 3SRZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 3SRZ _cell.length_a 141.779 _cell.length_b 141.779 _cell.length_c 63.351 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SRZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _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 metalc ? metalc1 A OD2 ASP 287 A ASP 287 1_555 B MN MN . A MN 1542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc2 A OE1 GLU 514 A GLU 514 1_555 B MN MN . A MN 1542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc3 C O1A UPG . A UPG 556 1_555 B MN MN . A MN 1542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc4 C O1B UPG . A UPG 556 1_555 B MN MN . A MN 1542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc5 D O HOH . A HOH 589 1_555 B MN MN . A MN 1542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc6 D O HOH . A HOH 614 1_555 B MN MN . A MN 1542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? # _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 345 n n N1 C6 UPG sing 346 n n N1 C1C UPG sing 347 n n C2 N3 UPG sing 348 n n C2 O2 UPG doub 349 n n N3 C4 UPG sing 350 n n N3 HN3 UPG sing 351 n n C4 C5 UPG sing 352 n n C4 O4 UPG doub 353 n n C5 C6 UPG doub 354 n n C5 H5 UPG sing 355 n n C6 H6 UPG sing 356 n n C1C C2C UPG sing 357 n n C1C O4C UPG sing 358 n n C1C H1C UPG sing 359 n n C2C O2C UPG sing 360 n n C2C C3C UPG sing 361 n n C2C H2C UPG sing 362 n n O2C HO2C UPG sing 363 n n C3C C4C UPG sing 364 n n C3C O3C UPG sing 365 n n C3C H3C UPG sing 366 n n C4C O4C UPG sing 367 n n C4C C5C UPG sing 368 n n C4C H4C UPG sing 369 n n O3C HO3C UPG sing 370 n n C5C O5C UPG sing 371 n n C5C H5C1 UPG sing 372 n n C5C H5C2 UPG sing 373 n n O5C PA UPG sing 374 n n PA O1A UPG doub 375 n n PA O2A UPG sing 376 n n PA O3A UPG sing 377 n n O2A HOA2 UPG sing 378 n n O3A PB UPG sing 379 n n PB O1B UPG doub 380 n n PB O2B UPG sing 381 n n PB O3B UPG sing 382 n n O2B HOB2 UPG sing 383 n n O3B C1' UPG sing 384 n n C1' C2' UPG sing 385 n n C1' O5' UPG sing 386 n n C1' H1' UPG sing 387 n n C2' C3' UPG sing 388 n n C2' O2' UPG sing 389 n n C2' H2' UPG sing 390 n n C3' C4' UPG sing 391 n n C3' O3' UPG sing 392 n n C3' H3' UPG sing 393 n n C4' C5' UPG sing 394 n n C4' O4' UPG sing 395 n n C4' H4' UPG sing 396 n n C5' C6' UPG sing 397 n n C5' O5' UPG sing 398 n n C5' H5' UPG sing 399 n n C6' O6' UPG sing 400 n n C6' "H6'1" UPG sing 401 n n C6' "H6'2" UPG sing 402 n n O2' HO2' UPG sing 403 n n O3' HO3' UPG sing 404 n n O4' HO4' UPG sing 405 n n O6' HO6' UPG sing 406 n n # _atom_sites.entry_id 3SRZ _atom_sites.fract_transf_matrix[1][1] 0.007053 _atom_sites.fract_transf_matrix[1][2] 0.004072 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008144 _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] 0.015785 _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 MN A 1 1542 1542 MN MN . C 3 UPG A 1 556 1 UPG UPG . D 4 HOH A 1 557 1 HOH HOH . D 4 HOH A 2 558 2 HOH HOH . D 4 HOH A 3 559 3 HOH HOH . D 4 HOH A 4 560 4 HOH HOH . D 4 HOH A 5 561 5 HOH HOH . D 4 HOH A 6 562 6 HOH HOH . D 4 HOH A 7 563 7 HOH HOH . D 4 HOH A 8 564 8 HOH HOH . D 4 HOH A 9 565 9 HOH HOH . D 4 HOH A 10 566 10 HOH HOH . D 4 HOH A 11 567 11 HOH HOH . D 4 HOH A 12 568 12 HOH HOH . D 4 HOH A 13 569 13 HOH HOH . D 4 HOH A 14 570 14 HOH HOH . D 4 HOH A 15 571 15 HOH HOH . D 4 HOH A 16 572 16 HOH HOH . D 4 HOH A 17 573 17 HOH HOH . D 4 HOH A 18 574 18 HOH HOH . D 4 HOH A 19 575 19 HOH HOH . D 4 HOH A 20 576 20 HOH HOH . D 4 HOH A 21 577 21 HOH HOH . D 4 HOH A 22 578 22 HOH HOH . D 4 HOH A 23 579 23 HOH HOH . D 4 HOH A 24 580 24 HOH HOH . D 4 HOH A 25 581 25 HOH HOH . D 4 HOH A 26 582 26 HOH HOH . D 4 HOH A 27 583 27 HOH HOH . D 4 HOH A 28 584 28 HOH HOH . D 4 HOH A 29 585 29 HOH HOH . D 4 HOH A 30 586 30 HOH HOH . D 4 HOH A 31 587 31 HOH HOH . D 4 HOH A 32 588 32 HOH HOH . D 4 HOH A 33 589 33 HOH HOH . D 4 HOH A 34 590 34 HOH HOH . D 4 HOH A 35 591 35 HOH HOH . D 4 HOH A 36 592 36 HOH HOH . D 4 HOH A 37 593 37 HOH HOH . D 4 HOH A 38 594 38 HOH HOH . D 4 HOH A 39 595 39 HOH HOH . D 4 HOH A 40 596 40 HOH HOH . D 4 HOH A 41 597 41 HOH HOH . D 4 HOH A 42 598 42 HOH HOH . D 4 HOH A 43 599 43 HOH HOH . D 4 HOH A 44 600 44 HOH HOH . D 4 HOH A 45 601 45 HOH HOH . D 4 HOH A 46 602 46 HOH HOH . D 4 HOH A 47 603 47 HOH HOH . D 4 HOH A 48 604 48 HOH HOH . D 4 HOH A 49 605 49 HOH HOH . D 4 HOH A 50 606 50 HOH HOH . D 4 HOH A 51 607 51 HOH HOH . D 4 HOH A 52 608 52 HOH HOH . D 4 HOH A 53 609 53 HOH HOH . D 4 HOH A 54 610 54 HOH HOH . D 4 HOH A 55 611 55 HOH HOH . D 4 HOH A 56 612 56 HOH HOH . D 4 HOH A 57 613 57 HOH HOH . D 4 HOH A 58 614 58 HOH HOH . D 4 HOH A 59 615 59 HOH HOH . D 4 HOH A 60 616 60 HOH HOH . D 4 HOH A 61 617 61 HOH HOH . D 4 HOH A 62 618 62 HOH HOH . D 4 HOH A 63 619 63 HOH HOH . D 4 HOH A 64 620 64 HOH HOH . D 4 HOH A 65 621 65 HOH HOH . D 4 HOH A 66 622 66 HOH HOH . D 4 HOH A 67 623 67 HOH HOH . D 4 HOH A 68 624 68 HOH HOH . D 4 HOH A 69 625 69 HOH HOH . D 4 HOH A 70 626 70 HOH HOH . D 4 HOH A 71 627 71 HOH HOH . D 4 HOH A 72 628 72 HOH HOH . D 4 HOH A 73 629 73 HOH HOH . D 4 HOH A 74 630 74 HOH HOH . D 4 HOH A 75 631 75 HOH HOH . D 4 HOH A 76 632 76 HOH HOH . D 4 HOH A 77 633 77 HOH HOH . D 4 HOH A 78 634 78 HOH HOH . D 4 HOH A 79 635 79 HOH HOH . D 4 HOH A 80 636 80 HOH HOH . D 4 HOH A 81 637 81 HOH HOH . D 4 HOH A 82 638 82 HOH HOH . D 4 HOH A 83 639 83 HOH HOH . D 4 HOH A 84 640 84 HOH HOH . D 4 HOH A 85 641 85 HOH HOH . D 4 HOH A 86 642 86 HOH HOH . D 4 HOH A 87 643 87 HOH HOH . D 4 HOH A 88 644 88 HOH HOH . D 4 HOH A 89 645 89 HOH HOH . D 4 HOH A 90 646 90 HOH HOH . D 4 HOH A 91 647 91 HOH HOH . D 4 HOH A 92 648 92 HOH HOH . D 4 HOH A 93 649 93 HOH HOH . D 4 HOH A 94 650 94 HOH HOH . D 4 HOH A 95 651 95 HOH HOH . D 4 HOH A 96 652 96 HOH HOH . D 4 HOH A 97 653 97 HOH HOH . D 4 HOH A 98 654 98 HOH HOH . D 4 HOH A 99 655 99 HOH HOH . D 4 HOH A 100 656 100 HOH HOH . D 4 HOH A 101 657 101 HOH HOH . D 4 HOH A 102 658 102 HOH HOH . D 4 HOH A 103 659 103 HOH HOH . D 4 HOH A 104 660 104 HOH HOH . D 4 HOH A 105 661 105 HOH HOH . D 4 HOH A 106 662 106 HOH HOH . D 4 HOH A 107 663 107 HOH HOH . D 4 HOH A 108 664 108 HOH HOH . D 4 HOH A 109 665 109 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 3 -31.229 -40.618 -9.978 1 26.88 ? N1 UPG 556 A 1 HETATM 2 C C2 UPG . . . C 3 -30.941 -39.97 -8.761 1 28.53 ? C2 UPG 556 A 1 HETATM 3 N N3 UPG . . . C 3 -29.748 -40.121 -8.16 1 30.02 ? N3 UPG 556 A 1 HETATM 4 C C4 UPG . . . C 3 -28.808 -40.888 -8.727 1 37.67 ? C4 UPG 556 A 1 HETATM 5 C C5 UPG . . . C 3 -29.07 -41.537 -9.94 1 32.67 ? C5 UPG 556 A 1 HETATM 6 C C6 UPG . . . C 3 -30.306 -41.39 -10.564 1 22.82 ? C6 UPG 556 A 1 HETATM 7 O O2 UPG . . . C 3 -31.827 -39.256 -8.249 1 25.47 ? O2 UPG 556 A 1 HETATM 8 O O4 UPG . . . C 3 -27.695 -41.018 -8.164 1 40.09 ? O4 UPG 556 A 1 HETATM 9 C C1C UPG . . . C 3 -32.548 -40.404 -10.57 1 30.37 ? C1C UPG 556 A 1 HETATM 10 C C2C UPG . . . C 3 -32.598 -38.969 -11.057 1 26.81 ? C2C UPG 556 A 1 HETATM 11 O O2C UPG . . . C 3 -33.838 -38.374 -10.634 1 17.19 ? O2C UPG 556 A 1 HETATM 12 C C3C UPG . . . C 3 -32.439 -39.153 -12.573 1 31.63 ? C3C UPG 556 A 1 HETATM 13 C C4C UPG . . . C 3 -33.136 -40.47 -12.837 1 35.18 ? C4C UPG 556 A 1 HETATM 14 O O4C UPG . . . C 3 -32.747 -41.256 -11.709 1 39.28 ? O4C UPG 556 A 1 HETATM 15 O O3C UPG . . . C 3 -32.977 -38.11 -13.391 1 29.21 ? O3C UPG 556 A 1 HETATM 16 C C5C UPG . . . C 3 -32.709 -41.101 -14.155 1 37.25 ? C5C UPG 556 A 1 HETATM 17 O O5C UPG . . . C 3 -31.385 -41.624 -14.073 1 33.25 ? O5C UPG 556 A 1 HETATM 18 P PA UPG . . . C 3 -30.534 -41.767 -15.424 1 43.36 ? PA UPG 556 A 1 HETATM 19 O O1A UPG . . . C 3 -30.968 -40.717 -16.42 1 41.56 ? O1A UPG 556 A 1 HETATM 20 O O2A UPG . . . C 3 -29.084 -41.59 -15.069 1 52.32 ? O2A UPG 556 A 1 HETATM 21 O O3A UPG . . . C 3 -30.772 -43.285 -15.914 1 33.38 ? O3A UPG 556 A 1 HETATM 22 P PB UPG . . . C 3 -31.616 -43.785 -17.202 1 42.39 ? PB UPG 556 A 1 HETATM 23 O O1B UPG . . . C 3 -31.811 -42.701 -18.236 1 42.02 ? O1B UPG 556 A 1 HETATM 24 O O2B UPG . . . C 3 -30.984 -45.006 -17.826 1 41.37 ? O2B UPG 556 A 1 HETATM 25 O O3B UPG . . . C 3 -33.024 -44.19 -16.534 1 55.39 ? O3B UPG 556 A 1 HETATM 26 C C1' UPG . . . C 3 -34.118 -44.764 -17.246 1 52.65 ? C1' UPG 556 A 1 HETATM 27 C C2' UPG . . . C 3 -35.211 -43.716 -17.336 1 49.42 ? C2' UPG 556 A 1 HETATM 28 C C3' UPG . . . C 3 -35.449 -43.167 -15.933 1 38.78 ? C3' UPG 556 A 1 HETATM 29 C C4' UPG . . . C 3 -35.901 -44.298 -15.016 1 44.14 ? C4' UPG 556 A 1 HETATM 30 C C5' UPG . . . C 3 -34.922 -45.466 -15.098 1 51.85 ? C5' UPG 556 A 1 HETATM 31 C C6' UPG . . . C 3 -35.503 -46.648 -14.331 1 48.15 ? C6' UPG 556 A 1 HETATM 32 O O2' UPG . . . C 3 -34.82 -42.657 -18.212 1 54.17 ? O2' UPG 556 A 1 HETATM 33 O O3' UPG . . . C 3 -36.456 -42.169 -15.993 1 25.6 ? O3' UPG 556 A 1 HETATM 34 O O4' UPG . . . C 3 -35.999 -43.854 -13.659 1 35.48 ? O4' UPG 556 A 1 HETATM 35 O O5' UPG . . . C 3 -34.649 -45.835 -16.463 1 58.36 ? O5' UPG 556 A 1 HETATM 36 O O6' UPG . . . C 3 -36.84 -46.916 -14.775 1 39.23 ? O6' UPG 556 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #