data_5V2J # _model_server_result.job_id 3KPAa_NYMo08UBbTmun0uQ _model_server_result.datetime_utc '2024-10-18 16:32:07' _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 5v2j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":503}' # _entry.id 5V2J # _exptl.entry_id 5V2J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 90 _cell.angle_gamma 90 _cell.entry_id 5V2J _cell.length_a 65.224 _cell.length_b 87.41 _cell.length_c 162.826 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V2J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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,E,F,G,K 1 1 B,D,H,I,J,L 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 ? 4 F N N ? 4 I N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 BGC _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C BGC 1 C 1 BGC D 2 LB2 2 n C BGC 2 C 2 BGC D 2 LB2 2 n D BGC 1 D 1 BGC D 4 LB2 2 n D BGC 2 D 2 BGC D 4 LB2 # 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 OH TYR 177 A TYR 177 1_555 E C1 BGC . A BGC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.364 ? covale ? covale2 A OH TYR 180 A TYR 180 1_555 C C1 BGC . C BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale3 B OH TYR 177 B TYR 177 1_555 H C1 BGC . B BGC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale4 B OH TYR 180 B TYR 180 1_555 D C1 BGC . D BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale5 C O3 BGC . C BGC 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 sing covale ? covale6 D O3 BGC . D BGC 1 1_555 D C1 BGC . D BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 sing # _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 397 n n N1 C6 UDP sing 398 n n N1 C1' UDP sing 399 n n C2 N3 UDP sing 400 n n C2 O2 UDP doub 401 n n N3 C4 UDP sing 402 n n N3 HN3 UDP sing 403 n n C4 C5 UDP sing 404 n n C4 O4 UDP doub 405 n n C5 C6 UDP doub 406 n n C5 H5 UDP sing 407 n n C6 H6 UDP sing 408 n n C1' C2' UDP sing 409 n n C1' O4' UDP sing 410 n n C1' H1' UDP sing 411 n n C2' O2' UDP sing 412 n n C2' C3' UDP sing 413 n n C2' H2' UDP sing 414 n n O2' HO2' UDP sing 415 n n C3' C4' UDP sing 416 n n C3' O3' UDP sing 417 n n C3' H3' UDP sing 418 n n C4' O4' UDP sing 419 n n C4' C5' UDP sing 420 n n C4' H4' UDP sing 421 n n O3' HO3' UDP sing 422 n n C5' O5' UDP sing 423 n n C5' "H5'1" UDP sing 424 n n C5' "H5'2" UDP sing 425 n n O5' PA UDP sing 426 n n PA O1A UDP doub 427 n n PA O2A UDP sing 428 n n PA O3A UDP sing 429 n n O2A HOA2 UDP sing 430 n n O3A PB UDP sing 431 n n PB O1B UDP doub 432 n n PB O2B UDP sing 433 n n PB O3B UDP sing 434 n n O2B HOB2 UDP sing 435 n n O3B HOB3 UDP sing 436 n n # _atom_sites.entry_id 5V2J _atom_sites.fract_transf_matrix[1][1] 0.015332 _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] 0.01144 _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] 0.006142 _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 E 3 BGC A 1 501 1 BGC BGC . F 4 UDP A 1 503 5 UDP UDP . G 5 7WV A 1 504 7 7WV OBA . H 3 BGC B 1 501 3 BGC BGC . I 4 UDP B 1 503 6 UDP UDP . J 5 7WV B 1 504 8 7WV OBA . K 6 HOH A 1 601 28 HOH HOH . K 6 HOH A 2 602 157 HOH HOH . K 6 HOH A 3 603 74 HOH HOH . K 6 HOH A 4 604 100 HOH HOH . K 6 HOH A 5 605 125 HOH HOH . K 6 HOH A 6 606 147 HOH HOH . K 6 HOH A 7 607 70 HOH HOH . K 6 HOH A 8 608 53 HOH HOH . K 6 HOH A 9 609 1 HOH HOH . K 6 HOH A 10 610 6 HOH HOH . K 6 HOH A 11 611 104 HOH HOH . K 6 HOH A 12 612 54 HOH HOH . K 6 HOH A 13 613 87 HOH HOH . K 6 HOH A 14 614 44 HOH HOH . K 6 HOH A 15 615 94 HOH HOH . K 6 HOH A 16 616 89 HOH HOH . K 6 HOH A 17 617 95 HOH HOH . K 6 HOH A 18 618 80 HOH HOH . K 6 HOH A 19 619 123 HOH HOH . K 6 HOH A 20 620 45 HOH HOH . K 6 HOH A 21 621 12 HOH HOH . K 6 HOH A 22 622 23 HOH HOH . K 6 HOH A 23 623 133 HOH HOH . K 6 HOH A 24 624 5 HOH HOH . K 6 HOH A 25 625 130 HOH HOH . K 6 HOH A 26 626 27 HOH HOH . K 6 HOH A 27 627 64 HOH HOH . K 6 HOH A 28 628 156 HOH HOH . K 6 HOH A 29 629 144 HOH HOH . K 6 HOH A 30 630 58 HOH HOH . K 6 HOH A 31 631 158 HOH HOH . K 6 HOH A 32 632 3 HOH HOH . K 6 HOH A 33 633 2 HOH HOH . K 6 HOH A 34 634 139 HOH HOH . K 6 HOH A 35 635 68 HOH HOH . K 6 HOH A 36 636 78 HOH HOH . K 6 HOH A 37 637 99 HOH HOH . K 6 HOH A 38 638 88 HOH HOH . K 6 HOH A 39 639 119 HOH HOH . K 6 HOH A 40 640 29 HOH HOH . K 6 HOH A 41 641 82 HOH HOH . K 6 HOH A 42 642 8 HOH HOH . K 6 HOH A 43 643 31 HOH HOH . K 6 HOH A 44 644 165 HOH HOH . K 6 HOH A 45 645 143 HOH HOH . K 6 HOH A 46 646 72 HOH HOH . K 6 HOH A 47 647 167 HOH HOH . K 6 HOH A 48 648 43 HOH HOH . K 6 HOH A 49 649 22 HOH HOH . K 6 HOH A 50 650 15 HOH HOH . K 6 HOH A 51 651 126 HOH HOH . K 6 HOH A 52 652 55 HOH HOH . K 6 HOH A 53 653 135 HOH HOH . K 6 HOH A 54 654 34 HOH HOH . K 6 HOH A 55 655 16 HOH HOH . K 6 HOH A 56 656 24 HOH HOH . K 6 HOH A 57 657 118 HOH HOH . K 6 HOH A 58 658 121 HOH HOH . K 6 HOH A 59 659 30 HOH HOH . K 6 HOH A 60 660 79 HOH HOH . K 6 HOH A 61 661 49 HOH HOH . K 6 HOH A 62 662 113 HOH HOH . K 6 HOH A 63 663 40 HOH HOH . K 6 HOH A 64 664 50 HOH HOH . K 6 HOH A 65 665 145 HOH HOH . K 6 HOH A 66 666 25 HOH HOH . K 6 HOH A 67 667 138 HOH HOH . K 6 HOH A 68 668 48 HOH HOH . K 6 HOH A 69 669 76 HOH HOH . K 6 HOH A 70 670 106 HOH HOH . K 6 HOH A 71 671 164 HOH HOH . K 6 HOH A 72 672 63 HOH HOH . K 6 HOH A 73 673 97 HOH HOH . K 6 HOH A 74 674 137 HOH HOH . K 6 HOH A 75 675 160 HOH HOH . K 6 HOH A 76 676 102 HOH HOH . K 6 HOH A 77 677 65 HOH HOH . K 6 HOH A 78 678 91 HOH HOH . K 6 HOH A 79 679 150 HOH HOH . K 6 HOH A 80 680 96 HOH HOH . K 6 HOH A 81 681 85 HOH HOH . K 6 HOH A 82 682 146 HOH HOH . K 6 HOH A 83 683 41 HOH HOH . K 6 HOH A 84 684 162 HOH HOH . K 6 HOH A 85 685 42 HOH HOH . K 6 HOH A 86 686 111 HOH HOH . K 6 HOH A 87 687 39 HOH HOH . K 6 HOH A 88 688 114 HOH HOH . K 6 HOH A 89 689 140 HOH HOH . K 6 HOH A 90 690 92 HOH HOH . K 6 HOH A 91 691 103 HOH HOH . K 6 HOH A 92 692 151 HOH HOH . K 6 HOH A 93 693 86 HOH HOH . K 6 HOH A 94 694 154 HOH HOH . K 6 HOH A 95 695 67 HOH HOH . K 6 HOH A 96 696 17 HOH HOH . K 6 HOH A 97 697 170 HOH HOH . K 6 HOH A 98 698 33 HOH HOH . K 6 HOH A 99 699 84 HOH HOH . K 6 HOH A 100 700 109 HOH HOH . K 6 HOH A 101 701 142 HOH HOH . K 6 HOH A 102 702 108 HOH HOH . K 6 HOH A 103 703 38 HOH HOH . K 6 HOH A 104 704 98 HOH HOH . K 6 HOH A 105 705 116 HOH HOH . K 6 HOH A 106 706 152 HOH HOH . K 6 HOH A 107 707 105 HOH HOH . K 6 HOH A 108 708 171 HOH HOH . K 6 HOH A 109 709 155 HOH HOH . K 6 HOH A 110 710 56 HOH HOH . L 6 HOH B 1 601 18 HOH HOH . L 6 HOH B 2 602 13 HOH HOH . L 6 HOH B 3 603 60 HOH HOH . L 6 HOH B 4 604 129 HOH HOH . L 6 HOH B 5 605 20 HOH HOH . L 6 HOH B 6 606 163 HOH HOH . L 6 HOH B 7 607 75 HOH HOH . L 6 HOH B 8 608 19 HOH HOH . L 6 HOH B 9 609 4 HOH HOH . L 6 HOH B 10 610 136 HOH HOH . L 6 HOH B 11 611 132 HOH HOH . L 6 HOH B 12 612 36 HOH HOH . L 6 HOH B 13 613 101 HOH HOH . L 6 HOH B 14 614 81 HOH HOH . L 6 HOH B 15 615 71 HOH HOH . L 6 HOH B 16 616 14 HOH HOH . L 6 HOH B 17 617 11 HOH HOH . L 6 HOH B 18 618 66 HOH HOH . L 6 HOH B 19 619 7 HOH HOH . L 6 HOH B 20 620 127 HOH HOH . L 6 HOH B 21 621 62 HOH HOH . L 6 HOH B 22 622 141 HOH HOH . L 6 HOH B 23 623 26 HOH HOH . L 6 HOH B 24 624 37 HOH HOH . L 6 HOH B 25 625 120 HOH HOH . L 6 HOH B 26 626 21 HOH HOH . L 6 HOH B 27 627 32 HOH HOH . L 6 HOH B 28 628 52 HOH HOH . L 6 HOH B 29 629 124 HOH HOH . L 6 HOH B 30 630 93 HOH HOH . L 6 HOH B 31 631 83 HOH HOH . L 6 HOH B 32 632 69 HOH HOH . L 6 HOH B 33 633 47 HOH HOH . L 6 HOH B 34 634 51 HOH HOH . L 6 HOH B 35 635 9 HOH HOH . L 6 HOH B 36 636 149 HOH HOH . L 6 HOH B 37 637 131 HOH HOH . L 6 HOH B 38 638 46 HOH HOH . L 6 HOH B 39 639 10 HOH HOH . L 6 HOH B 40 640 122 HOH HOH . L 6 HOH B 41 641 57 HOH HOH . L 6 HOH B 42 642 59 HOH HOH . L 6 HOH B 43 643 90 HOH HOH . L 6 HOH B 44 644 73 HOH HOH . L 6 HOH B 45 645 112 HOH HOH . L 6 HOH B 46 646 161 HOH HOH . L 6 HOH B 47 647 169 HOH HOH . L 6 HOH B 48 648 61 HOH HOH . L 6 HOH B 49 649 35 HOH HOH . L 6 HOH B 50 650 159 HOH HOH . L 6 HOH B 51 651 134 HOH HOH . L 6 HOH B 52 652 107 HOH HOH . L 6 HOH B 53 653 110 HOH HOH . L 6 HOH B 54 654 166 HOH HOH . L 6 HOH B 55 655 77 HOH HOH . L 6 HOH B 56 656 117 HOH HOH . L 6 HOH B 57 657 148 HOH HOH . L 6 HOH B 58 658 168 HOH HOH . L 6 HOH B 59 659 128 HOH HOH . L 6 HOH B 60 660 115 HOH HOH . L 6 HOH B 61 661 153 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 . . . F 4 -11.399 0.7 -7.285 1 29.38 ? N1 UDP 503 A 1 HETATM 2 C C2 UDP . . . F 4 -10.986 0.116 -8.539 1 35.57 ? C2 UDP 503 A 1 HETATM 3 N N3 UDP . . . F 4 -9.559 0.069 -8.824 1 34.42 ? N3 UDP 503 A 1 HETATM 4 C C4 UDP . . . F 4 -8.543 0.571 -7.951 1 35.89 ? C4 UDP 503 A 1 HETATM 5 C C5 UDP . . . F 4 -8.971 1.162 -6.659 1 27.56 ? C5 UDP 503 A 1 HETATM 6 C C6 UDP . . . F 4 -10.434 1.224 -6.331 1 30.05 ? C6 UDP 503 A 1 HETATM 7 O O2 UDP . . . F 4 -11.774 -0.3 -9.306 1 30.01 ? O2 UDP 503 A 1 HETATM 8 O O4 UDP . . . F 4 -7.395 0.473 -8.289 1 37.46 ? O4 UDP 503 A 1 HETATM 9 C C1' UDP . . . F 4 -12.822 0.75 -7.037 1 31.72 ? C1' UDP 503 A 1 HETATM 10 C C2' UDP . . . F 4 -13.281 -0.122 -5.83 1 30.98 ? C2' UDP 503 A 1 HETATM 11 O O2' UDP . . . F 4 -13.664 -1.376 -6.281 1 36.09 ? O2' UDP 503 A 1 HETATM 12 C C3' UDP . . . F 4 -14.375 0.777 -5.289 1 32.5 ? C3' UDP 503 A 1 HETATM 13 C C4' UDP . . . F 4 -14.035 2.09 -5.524 1 32.41 ? C4' UDP 503 A 1 HETATM 14 O O4' UDP . . . F 4 -12.968 2.017 -6.685 1 25.55 ? O4' UDP 503 A 1 HETATM 15 O O3' UDP . . . F 4 -15.622 0.471 -6.034 1 32.24 ? O3' UDP 503 A 1 HETATM 16 C C5' UDP . . . F 4 -13.388 2.774 -4.354 1 32.13 ? C5' UDP 503 A 1 HETATM 17 O O5' UDP . . . F 4 -14.459 3.193 -3.523 1 26.39 ? O5' UDP 503 A 1 HETATM 18 P PA UDP . . . F 4 -14.266 3.158 -1.886 1 32.03 ? PA UDP 503 A 1 HETATM 19 O O1A UDP . . . F 4 -13.581 1.883 -1.479 1 36.53 ? O1A UDP 503 A 1 HETATM 20 O O2A UDP . . . F 4 -15.582 3.497 -1.256 1 27.8 ? O2A UDP 503 A 1 HETATM 21 O O3A UDP . . . F 4 -13.139 4.299 -1.624 1 28.88 ? O3A UDP 503 A 1 HETATM 22 P PB UDP . . . F 4 -13.065 5.913 -1.896 1 30.59 ? PB UDP 503 A 1 HETATM 23 O O1B UDP . . . F 4 -12.431 5.868 -3.256 1 26.85 ? O1B UDP 503 A 1 HETATM 24 O O2B UDP . . . F 4 -12.203 6.515 -0.824 1 33.62 ? O2B UDP 503 A 1 HETATM 25 O O3B UDP . . . F 4 -14.475 6.422 -1.921 1 31.52 ? O3B UDP 503 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #