data_6KVI # _model_server_result.job_id o8nJNVH2p5ygXibbo9Ftjw _model_server_result.datetime_utc '2025-07-27 05:04:50' _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 6kvi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6KVI # _exptl.entry_id 6KVI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 6KVI _cell.length_a 98.058 _cell.length_b 98.058 _cell.length_c 91.618 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KVI _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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 B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # 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 UDP sing 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 6KVI _atom_sites.fract_transf_matrix[1][1] 0.010198 _atom_sites.fract_transf_matrix[1][2] 0.005888 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011776 _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] 0.010915 _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 UDP A 1 501 1 UDP UDP . C 3 HOH A 1 601 71 HOH HOH . C 3 HOH A 2 602 82 HOH HOH . C 3 HOH A 3 603 51 HOH HOH . C 3 HOH A 4 604 75 HOH HOH . C 3 HOH A 5 605 65 HOH HOH . C 3 HOH A 6 606 93 HOH HOH . C 3 HOH A 7 607 46 HOH HOH . C 3 HOH A 8 608 17 HOH HOH . C 3 HOH A 9 609 69 HOH HOH . C 3 HOH A 10 610 73 HOH HOH . C 3 HOH A 11 611 4 HOH HOH . C 3 HOH A 12 612 53 HOH HOH . C 3 HOH A 13 613 70 HOH HOH . C 3 HOH A 14 614 3 HOH HOH . C 3 HOH A 15 615 81 HOH HOH . C 3 HOH A 16 616 44 HOH HOH . C 3 HOH A 17 617 34 HOH HOH . C 3 HOH A 18 618 6 HOH HOH . C 3 HOH A 19 619 32 HOH HOH . C 3 HOH A 20 620 92 HOH HOH . C 3 HOH A 21 621 90 HOH HOH . C 3 HOH A 22 622 56 HOH HOH . C 3 HOH A 23 623 66 HOH HOH . C 3 HOH A 24 624 38 HOH HOH . C 3 HOH A 25 625 23 HOH HOH . C 3 HOH A 26 626 52 HOH HOH . C 3 HOH A 27 627 29 HOH HOH . C 3 HOH A 28 628 84 HOH HOH . C 3 HOH A 29 629 57 HOH HOH . C 3 HOH A 30 630 43 HOH HOH . C 3 HOH A 31 631 8 HOH HOH . C 3 HOH A 32 632 91 HOH HOH . C 3 HOH A 33 633 14 HOH HOH . C 3 HOH A 34 634 45 HOH HOH . C 3 HOH A 35 635 20 HOH HOH . C 3 HOH A 36 636 5 HOH HOH . C 3 HOH A 37 637 54 HOH HOH . C 3 HOH A 38 638 47 HOH HOH . C 3 HOH A 39 639 15 HOH HOH . C 3 HOH A 40 640 16 HOH HOH . C 3 HOH A 41 641 7 HOH HOH . C 3 HOH A 42 642 87 HOH HOH . C 3 HOH A 43 643 9 HOH HOH . C 3 HOH A 44 644 41 HOH HOH . C 3 HOH A 45 645 19 HOH HOH . C 3 HOH A 46 646 12 HOH HOH . C 3 HOH A 47 647 2 HOH HOH . C 3 HOH A 48 648 83 HOH HOH . C 3 HOH A 49 649 39 HOH HOH . C 3 HOH A 50 650 64 HOH HOH . C 3 HOH A 51 651 63 HOH HOH . C 3 HOH A 52 652 33 HOH HOH . C 3 HOH A 53 653 30 HOH HOH . C 3 HOH A 54 654 18 HOH HOH . C 3 HOH A 55 655 36 HOH HOH . C 3 HOH A 56 656 28 HOH HOH . C 3 HOH A 57 657 37 HOH HOH . C 3 HOH A 58 658 31 HOH HOH . C 3 HOH A 59 659 22 HOH HOH . C 3 HOH A 60 660 42 HOH HOH . C 3 HOH A 61 661 10 HOH HOH . C 3 HOH A 62 662 21 HOH HOH . C 3 HOH A 63 663 1 HOH HOH . C 3 HOH A 64 664 26 HOH HOH . C 3 HOH A 65 665 35 HOH HOH . C 3 HOH A 66 666 89 HOH HOH . C 3 HOH A 67 667 11 HOH HOH . C 3 HOH A 68 668 13 HOH HOH . C 3 HOH A 69 669 59 HOH HOH . C 3 HOH A 70 670 27 HOH HOH . C 3 HOH A 71 671 78 HOH HOH . C 3 HOH A 72 672 79 HOH HOH . C 3 HOH A 73 673 76 HOH HOH . C 3 HOH A 74 674 86 HOH HOH . C 3 HOH A 75 675 60 HOH HOH . C 3 HOH A 76 676 58 HOH HOH . C 3 HOH A 77 677 77 HOH HOH . C 3 HOH A 78 678 74 HOH HOH . C 3 HOH A 79 679 68 HOH HOH . C 3 HOH A 80 680 25 HOH HOH . C 3 HOH A 81 681 88 HOH HOH . C 3 HOH A 82 682 80 HOH HOH . C 3 HOH A 83 683 40 HOH HOH . C 3 HOH A 84 684 85 HOH HOH . C 3 HOH A 85 685 49 HOH HOH . C 3 HOH A 86 686 50 HOH HOH . C 3 HOH A 87 687 24 HOH HOH . C 3 HOH A 88 688 67 HOH HOH . C 3 HOH A 89 689 48 HOH HOH . C 3 HOH A 90 690 72 HOH HOH . C 3 HOH A 91 691 62 HOH HOH . C 3 HOH A 92 692 55 HOH HOH . C 3 HOH A 93 693 61 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 UDP . . . B 2 32.871 69.81 12.571 1 30.37 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 33.493 70.354 11.461 1 28.28 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 34.795 70.789 11.566 1 27.16 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 35.448 70.68 12.779 1 30.67 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 34.798 70.128 13.897 1 24.86 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 33.52 69.635 13.766 1 24.93 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 32.879 70.423 10.387 1 24.84 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 36.614 71.086 12.864 1 31.65 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 31.483 69.356 12.427 1 27.52 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 31.394 67.844 12.5 1 25.93 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 31.626 67.213 11.263 1 28.11 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 29.979 67.671 12.984 1 29.09 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 29.637 68.966 13.739 1 32.7 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 30.694 69.874 13.476 1 31.37 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 29.143 67.458 11.869 1 29.29 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 29.522 68.815 15.258 1 30.98 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 28.362 68.115 15.617 1 32.02 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 28.362 67.129 16.899 1 31.89 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 29.291 66.029 16.661 1 35.85 -1 O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 27.005 66.654 17.213 1 25.36 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 29.043 68.004 18.047 1 37.08 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 28.415 69.189 18.946 1 32.5 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 29.124 70.399 18.539 1 32.5 -1 O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 28.712 68.821 20.339 1 39.19 -1 O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 26.965 69.34 18.749 1 29.7 ? O3B UDP 501 A 1 HETATM 26 H HN3 UDP . . . B 2 35.227 71.33 10.79 1 32.6 ? HN3 UDP 501 A 1 HETATM 27 H H5 UDP . . . B 2 35.342 69.993 14.831 1 29.84 ? H5 UDP 501 A 1 HETATM 28 H H6 UDP . . . B 2 32.959 69.334 14.651 1 29.91 ? H6 UDP 501 A 1 HETATM 29 H H1' UDP . . . B 2 31.084 69.684 11.467 1 33.03 ? H1' UDP 501 A 1 HETATM 30 H H2' UDP . . . B 2 32.085 67.476 13.258 1 31.12 ? H2' UDP 501 A 1 HETATM 31 H HO2' UDP . . . B 2 30.802 66.778 10.959 1 33.73 ? HO2' UDP 501 A 1 HETATM 32 H H3' UDP . . . B 2 29.93 66.826 13.669 1 34.91 ? H3' UDP 501 A 1 HETATM 33 H H4' UDP . . . B 2 28.7 69.364 13.352 1 39.24 ? H4' UDP 501 A 1 HETATM 34 H HO3' UDP . . . B 2 28.498 68.193 11.798 1 35.15 ? HO3' UDP 501 A 1 HETATM 35 H "H5'1" UDP . . . B 2 30.396 68.284 15.635 1 37.18 ? "H5'1" UDP 501 A 1 HETATM 36 H "H5'2" UDP . . . B 2 29.506 69.802 15.72 1 37.18 ? "H5'2" UDP 501 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 357 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #