data_4PD6 # _model_server_result.job_id xYeZT3m6C4zMQ_Slon1uCw _model_server_result.datetime_utc '2024-11-01 19:39:30' _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 4pd6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4PD6 # _exptl.entry_id 4PD6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE _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 4PD6 _cell.length_a 119.65 _cell.length_b 119.65 _cell.length_c 83.11 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PD6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 59.825 -103.61994 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 119.65 0 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 # 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 O ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc2 A OD1 ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc3 A O VAL 158 A VAL 152 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc4 A OG SER 189 A SER 183 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc5 A O ILE 190 A ILE 184 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc6 C NA NA . A NA 502 1_555 E O HOH . A HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? # _chem_comp.formula 'C9 H12 N2 O6' _chem_comp.formula_weight 244.201 _chem_comp.id URI _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE _chem_comp.type non-polymer _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 URI sing 413 n n N1 C6 URI sing 414 n n N1 C1' URI sing 415 n n C2 N3 URI sing 416 n n C2 O2 URI doub 417 n n N3 C4 URI sing 418 n n N3 H3 URI sing 419 n n C4 C5 URI sing 420 n n C4 O4 URI doub 421 n n C5 C6 URI doub 422 n n C5 H5 URI sing 423 n n C6 H6 URI sing 424 n n C1' C2' URI sing 425 n n C1' O4' URI sing 426 n n C1' H1' URI sing 427 n n C2' C3' URI sing 428 n n C2' O2' URI sing 429 n n C2' H2' URI sing 430 n n C3' C4' URI sing 431 n n C3' O3' URI sing 432 n n C3' H3' URI sing 433 n n C4' O4' URI sing 434 n n C4' C5' URI sing 435 n n C4' H4' URI sing 436 n n O2' HO2' URI sing 437 n n O3' HO3' URI sing 438 n n C5' O5' URI sing 439 n n C5' "H5'1" URI sing 440 n n C5' "H5'2" URI sing 441 n n O5' HO5' URI sing 442 n n # _atom_sites.entry_id 4PD6 _atom_sites.fract_transf_matrix[1][1] 0.008358 _atom_sites.fract_transf_matrix[1][2] 0.004825 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009651 _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] 0.012032 _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 URI A 1 501 501 URI URI . C 3 NA A 1 502 502 NA NA . D 4 DMU A 1 503 503 DMU LMT . E 5 HOH A 1 601 601 HOH HOH . E 5 HOH A 2 602 602 HOH HOH . E 5 HOH A 3 603 603 HOH HOH . E 5 HOH A 4 604 604 HOH HOH . E 5 HOH A 5 605 605 HOH HOH . E 5 HOH A 6 606 606 HOH HOH . E 5 HOH A 7 607 607 HOH HOH . E 5 HOH A 8 608 608 HOH HOH . E 5 HOH A 9 609 609 HOH HOH . E 5 HOH A 10 610 610 HOH HOH . E 5 HOH A 11 611 611 HOH HOH . E 5 HOH A 12 612 612 HOH HOH . E 5 HOH A 13 613 613 HOH HOH . E 5 HOH A 14 614 614 HOH HOH . E 5 HOH A 15 615 615 HOH HOH . E 5 HOH A 16 616 616 HOH HOH . E 5 HOH A 17 617 617 HOH HOH . E 5 HOH A 18 618 618 HOH HOH . E 5 HOH A 19 619 619 HOH HOH . E 5 HOH A 20 620 620 HOH HOH . E 5 HOH A 21 621 621 HOH HOH . E 5 HOH A 22 622 622 HOH HOH . E 5 HOH A 23 623 623 HOH HOH . E 5 HOH A 24 624 624 HOH HOH . E 5 HOH A 25 625 625 HOH HOH . E 5 HOH A 26 626 626 HOH HOH . E 5 HOH A 27 627 627 HOH HOH . E 5 HOH A 28 628 628 HOH HOH . E 5 HOH A 29 629 629 HOH HOH . E 5 HOH A 30 630 630 HOH HOH . E 5 HOH A 31 631 631 HOH HOH . E 5 HOH A 32 632 632 HOH HOH . E 5 HOH A 33 633 633 HOH HOH . E 5 HOH A 34 634 634 HOH HOH . E 5 HOH A 35 635 635 HOH HOH . E 5 HOH A 36 636 636 HOH HOH . E 5 HOH A 37 637 637 HOH HOH . E 5 HOH A 38 638 638 HOH HOH . E 5 HOH A 39 639 639 HOH HOH . E 5 HOH A 40 640 640 HOH HOH . E 5 HOH A 41 641 641 HOH HOH . E 5 HOH A 42 642 642 HOH HOH . E 5 HOH A 43 643 643 HOH HOH . E 5 HOH A 44 644 644 HOH HOH . E 5 HOH A 45 645 645 HOH HOH . E 5 HOH A 46 646 646 HOH HOH . E 5 HOH A 47 647 647 HOH HOH . E 5 HOH A 48 648 648 HOH HOH . E 5 HOH A 49 649 649 HOH HOH . E 5 HOH A 50 650 650 HOH HOH . E 5 HOH A 51 651 651 HOH HOH . E 5 HOH A 52 652 652 HOH HOH . E 5 HOH A 53 653 653 HOH HOH . E 5 HOH A 54 654 654 HOH HOH . E 5 HOH A 55 655 655 HOH HOH . E 5 HOH A 56 656 656 HOH HOH . E 5 HOH A 57 657 657 HOH HOH . E 5 HOH A 58 658 658 HOH HOH . E 5 HOH A 59 659 659 HOH HOH . E 5 HOH A 60 660 660 HOH HOH . E 5 HOH A 61 661 661 HOH HOH . E 5 HOH A 62 662 662 HOH HOH . E 5 HOH A 63 663 663 HOH HOH . E 5 HOH A 64 664 664 HOH HOH . E 5 HOH A 65 665 665 HOH HOH . E 5 HOH A 66 666 666 HOH HOH . E 5 HOH A 67 667 667 HOH HOH . E 5 HOH A 68 668 668 HOH HOH . E 5 HOH A 69 669 669 HOH HOH . E 5 HOH A 70 670 670 HOH HOH . E 5 HOH A 71 671 671 HOH HOH . E 5 HOH A 72 672 672 HOH HOH . E 5 HOH A 73 673 673 HOH HOH . E 5 HOH A 74 674 674 HOH HOH . E 5 HOH A 75 675 675 HOH HOH . E 5 HOH A 76 676 676 HOH HOH . E 5 HOH A 77 677 677 HOH HOH . E 5 HOH A 78 678 678 HOH HOH . E 5 HOH A 79 679 679 HOH HOH . E 5 HOH A 80 680 680 HOH HOH . E 5 HOH A 81 681 681 HOH HOH . E 5 HOH A 82 682 682 HOH HOH . E 5 HOH A 83 683 683 HOH HOH . E 5 HOH A 84 684 684 HOH HOH . E 5 HOH A 85 685 685 HOH HOH . E 5 HOH A 86 686 686 HOH HOH . E 5 HOH A 87 687 687 HOH HOH . E 5 HOH A 88 688 688 HOH HOH . E 5 HOH A 89 689 689 HOH HOH . E 5 HOH A 90 690 690 HOH HOH . E 5 HOH A 91 691 691 HOH HOH . E 5 HOH A 92 692 692 HOH HOH . E 5 HOH A 93 693 693 HOH HOH . E 5 HOH A 94 694 694 HOH HOH . E 5 HOH A 95 695 695 HOH HOH . E 5 HOH A 96 696 696 HOH HOH . E 5 HOH A 97 697 697 HOH HOH . E 5 HOH A 98 698 698 HOH HOH . E 5 HOH A 99 699 699 HOH HOH . E 5 HOH A 100 700 700 HOH HOH . E 5 HOH A 101 701 701 HOH HOH . E 5 HOH A 102 702 702 HOH HOH . E 5 HOH A 103 703 703 HOH HOH . E 5 HOH A 104 704 704 HOH HOH . E 5 HOH A 105 705 705 HOH HOH . E 5 HOH A 106 706 706 HOH HOH . E 5 HOH A 107 707 707 HOH HOH . E 5 HOH A 108 708 708 HOH HOH . E 5 HOH A 109 709 709 HOH HOH . E 5 HOH A 110 710 710 HOH HOH . E 5 HOH A 111 711 711 HOH HOH . E 5 HOH A 112 712 712 HOH HOH . E 5 HOH A 113 713 713 HOH HOH . E 5 HOH A 114 714 714 HOH HOH . E 5 HOH A 115 715 715 HOH HOH . E 5 HOH A 116 716 716 HOH HOH . E 5 HOH A 117 717 717 HOH HOH . E 5 HOH A 118 718 718 HOH HOH . E 5 HOH A 119 719 719 HOH HOH . E 5 HOH A 120 720 720 HOH HOH . E 5 HOH A 121 721 721 HOH HOH . E 5 HOH A 122 722 722 HOH HOH . E 5 HOH A 123 723 723 HOH HOH . E 5 HOH A 124 724 724 HOH HOH . E 5 HOH A 125 725 725 HOH HOH . E 5 HOH A 126 726 726 HOH HOH . E 5 HOH A 127 727 727 HOH HOH . E 5 HOH A 128 728 728 HOH HOH . E 5 HOH A 129 729 729 HOH HOH . E 5 HOH A 130 730 730 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 URI . . . B 2 51.324 -20.255 -8.972 1 34.21 ? N1 URI 501 A 1 HETATM 2 C C2 URI . . . B 2 50.65 -20.548 -10.142 1 34.21 ? C2 URI 501 A 1 HETATM 3 N N3 URI . . . B 2 49.586 -21.402 -9.998 1 34.21 ? N3 URI 501 A 1 HETATM 4 C C4 URI . . . B 2 49.136 -21.98 -8.828 1 34.21 ? C4 URI 501 A 1 HETATM 5 C C5 URI . . . B 2 49.884 -21.629 -7.661 1 34.21 ? C5 URI 501 A 1 HETATM 6 C C6 URI . . . B 2 50.927 -20.799 -7.771 1 34.21 ? C6 URI 501 A 1 HETATM 7 O O2 URI . . . B 2 50.966 -20.093 -11.226 1 34.21 ? O2 URI 501 A 1 HETATM 8 O O4 URI . . . B 2 48.161 -22.728 -8.862 1 34.21 ? O4 URI 501 A 1 HETATM 9 C C1' URI . . . B 2 52.489 -19.342 -9.055 1 34.21 ? C1' URI 501 A 1 HETATM 10 C C2' URI . . . B 2 52.069 -17.89 -9.261 1 34.21 ? C2' URI 501 A 1 HETATM 11 C C3' URI . . . B 2 52.048 -17.379 -7.825 1 34.21 ? C3' URI 501 A 1 HETATM 12 C C4' URI . . . B 2 53.215 -18.117 -7.193 1 34.21 ? C4' URI 501 A 1 HETATM 13 O O2' URI . . . B 2 53.081 -17.234 -10.008 1 34.21 ? O2' URI 501 A 1 HETATM 14 O O3' URI . . . B 2 52.157 -15.971 -7.729 1 34.21 ? O3' URI 501 A 1 HETATM 15 O O4' URI . . . B 2 53.21 -19.417 -7.841 1 34.21 ? O4' URI 501 A 1 HETATM 16 C C5' URI . . . B 2 53.151 -18.298 -5.694 1 34.21 ? C5' URI 501 A 1 HETATM 17 O O5' URI . . . B 2 51.901 -18.836 -5.29 1 34.21 ? O5' URI 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 17 #