data_2H4L # _model_server_result.job_id 4mwmyhSjweKEorfKRDvKRg _model_server_result.datetime_utc '2024-11-23 19:00:46' _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 2h4l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":600}' # _entry.id 2H4L # _exptl.entry_id 2H4L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 230.11 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 1-O-phosphono-alpha-D-ribofuranose _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 90 _cell.entry_id 2H4L _cell.length_a 70.717 _cell.length_b 74.095 _cell.length_c 84.347 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2H4L _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 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 covale ? covale1 A C GLY 107 X GLY 107 1_555 A N SEP 108 X SEP 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale2 A C SEP 108 X SEP 108 1_555 A N HIS 109 X HIS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A OG SEP 108 X SEP 108 1_555 C ZN ZN . X ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc2 A OD2 ASP 242 X ASP 242 1_555 C ZN ZN . X ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.775 ? metalc ? metalc3 A OD1 ASP 244 X ASP 244 1_555 C ZN ZN . X ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc4 A OD1 ASP 246 X ASP 246 1_555 C ZN ZN . X ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? # _chem_comp.formula 'C5 H11 O8 P' _chem_comp.formula_weight 230.11 _chem_comp.id R1P _chem_comp.mon_nstd_flag n _chem_comp.name 1-O-phosphono-alpha-D-ribofuranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms RIBOSE-1-PHOSPHATE;1-O-phosphono-alpha-D-ribose;1-O-phosphono-D-ribose;1-O-phosphono-ribose # 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 C5 O5 R1P sing 277 n n C5 C4 R1P sing 278 n n C5 H51 R1P sing 279 n n C5 H52 R1P sing 280 n n O5 HO5 R1P sing 281 n n C4 O4 R1P sing 282 n n C4 C3 R1P sing 283 n n C4 H4 R1P sing 284 n n O4 C1 R1P sing 285 n n C1 C2 R1P sing 286 n n C1 O1 R1P sing 287 n n C1 H1 R1P sing 288 n n C2 O2 R1P sing 289 n n C2 C3 R1P sing 290 n n C2 H2 R1P sing 291 n n O2 HO2 R1P sing 292 n n C3 O3 R1P sing 293 n n C3 H3 R1P sing 294 n n O3 HO3 R1P sing 295 n n O1 P R1P sing 296 n n P O1P R1P doub 297 n n P O2P R1P sing 298 n n P O3P R1P sing 299 n n O2P HOP2 R1P sing 300 n n O3P HOP3 R1P sing 301 n n # _pdbx_chem_comp_identifier.comp_id R1P _pdbx_chem_comp_identifier.identifier a-D-Ribf1PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 2H4L _atom_sites.fract_transf_matrix[1][1] 0.014141 _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] 0.013496 _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] 0.011856 _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 R1P X 1 600 600 R1P R1P . C 3 ZN X 1 500 500 ZN ZN . D 4 HOH X 1 601 1 HOH HOH . D 4 HOH X 2 602 2 HOH HOH . D 4 HOH X 3 603 3 HOH HOH . D 4 HOH X 4 604 4 HOH HOH . D 4 HOH X 5 605 5 HOH HOH . D 4 HOH X 6 606 6 HOH HOH . D 4 HOH X 7 607 7 HOH HOH . D 4 HOH X 8 608 8 HOH HOH . D 4 HOH X 9 609 9 HOH HOH . D 4 HOH X 10 610 10 HOH HOH . D 4 HOH X 11 611 11 HOH HOH . D 4 HOH X 12 612 12 HOH HOH . D 4 HOH X 13 613 13 HOH HOH . D 4 HOH X 14 614 14 HOH HOH . D 4 HOH X 15 615 15 HOH HOH . D 4 HOH X 16 616 16 HOH HOH . D 4 HOH X 17 617 17 HOH HOH . D 4 HOH X 18 618 18 HOH HOH . D 4 HOH X 19 619 19 HOH HOH . D 4 HOH X 20 620 20 HOH HOH . D 4 HOH X 21 621 21 HOH HOH . D 4 HOH X 22 622 22 HOH HOH . D 4 HOH X 23 623 23 HOH HOH . D 4 HOH X 24 624 24 HOH HOH . D 4 HOH X 25 625 25 HOH HOH . D 4 HOH X 26 626 26 HOH HOH . D 4 HOH X 27 627 27 HOH HOH . D 4 HOH X 28 628 28 HOH HOH . D 4 HOH X 29 629 29 HOH HOH . D 4 HOH X 30 630 30 HOH HOH . D 4 HOH X 31 631 31 HOH HOH . D 4 HOH X 32 632 32 HOH HOH . D 4 HOH X 33 633 33 HOH HOH . D 4 HOH X 34 634 34 HOH HOH . D 4 HOH X 35 635 35 HOH HOH . D 4 HOH X 36 636 36 HOH HOH . D 4 HOH X 37 637 37 HOH HOH . D 4 HOH X 38 638 38 HOH HOH . D 4 HOH X 39 639 39 HOH HOH . D 4 HOH X 40 640 40 HOH HOH . D 4 HOH X 41 641 41 HOH HOH . D 4 HOH X 42 642 42 HOH HOH . D 4 HOH X 43 643 43 HOH HOH . D 4 HOH X 44 644 44 HOH HOH . D 4 HOH X 45 645 45 HOH HOH . D 4 HOH X 46 646 46 HOH HOH . D 4 HOH X 47 647 47 HOH HOH . D 4 HOH X 48 648 48 HOH HOH . D 4 HOH X 49 649 49 HOH HOH . D 4 HOH X 50 650 50 HOH HOH . D 4 HOH X 51 651 51 HOH HOH . D 4 HOH X 52 652 52 HOH HOH . D 4 HOH X 53 653 53 HOH HOH . D 4 HOH X 54 654 54 HOH HOH . D 4 HOH X 55 655 55 HOH HOH . D 4 HOH X 56 656 56 HOH HOH . D 4 HOH X 57 657 57 HOH HOH . D 4 HOH X 58 658 58 HOH HOH . D 4 HOH X 59 659 59 HOH HOH . D 4 HOH X 60 660 60 HOH HOH . D 4 HOH X 61 661 61 HOH HOH . D 4 HOH X 62 662 62 HOH HOH . D 4 HOH X 63 663 63 HOH HOH . D 4 HOH X 64 664 64 HOH HOH . D 4 HOH X 65 665 65 HOH HOH . D 4 HOH X 66 666 66 HOH HOH . D 4 HOH X 67 667 67 HOH HOH . D 4 HOH X 68 668 68 HOH HOH . D 4 HOH X 69 669 69 HOH HOH . D 4 HOH X 70 670 70 HOH HOH . D 4 HOH X 71 671 71 HOH HOH . D 4 HOH X 72 672 72 HOH HOH . D 4 HOH X 73 673 73 HOH HOH . D 4 HOH X 74 674 74 HOH HOH . D 4 HOH X 75 675 75 HOH HOH . D 4 HOH X 76 676 76 HOH HOH . D 4 HOH X 77 677 77 HOH HOH . D 4 HOH X 78 678 78 HOH HOH . D 4 HOH X 79 679 79 HOH HOH . D 4 HOH X 80 680 80 HOH HOH . D 4 HOH X 81 681 81 HOH HOH . D 4 HOH X 82 682 82 HOH HOH . D 4 HOH X 83 683 83 HOH HOH . D 4 HOH X 84 684 84 HOH HOH . D 4 HOH X 85 685 85 HOH HOH . D 4 HOH X 86 686 86 HOH HOH . D 4 HOH X 87 687 87 HOH HOH . D 4 HOH X 88 688 88 HOH HOH . D 4 HOH X 89 689 89 HOH HOH . D 4 HOH X 90 690 90 HOH HOH . D 4 HOH X 91 691 91 HOH HOH . D 4 HOH X 92 692 92 HOH HOH . D 4 HOH X 93 693 93 HOH HOH . D 4 HOH X 94 694 94 HOH HOH . D 4 HOH X 95 695 95 HOH HOH . D 4 HOH X 96 696 96 HOH HOH . D 4 HOH X 97 697 97 HOH HOH . D 4 HOH X 98 698 98 HOH HOH . D 4 HOH X 99 699 99 HOH HOH . D 4 HOH X 100 700 100 HOH HOH . D 4 HOH X 101 701 101 HOH HOH . D 4 HOH X 102 702 102 HOH HOH . D 4 HOH X 103 703 103 HOH HOH . D 4 HOH X 104 704 104 HOH HOH . D 4 HOH X 105 705 105 HOH HOH . D 4 HOH X 106 706 106 HOH HOH . D 4 HOH X 107 707 107 HOH HOH . D 4 HOH X 108 708 108 HOH HOH . D 4 HOH X 109 709 109 HOH HOH . D 4 HOH X 110 710 110 HOH HOH . D 4 HOH X 111 711 111 HOH HOH . D 4 HOH X 112 712 112 HOH HOH . D 4 HOH X 113 713 113 HOH HOH . D 4 HOH X 114 714 114 HOH HOH . D 4 HOH X 115 715 115 HOH HOH . D 4 HOH X 116 716 116 HOH HOH . D 4 HOH X 117 717 117 HOH HOH . D 4 HOH X 118 718 118 HOH HOH . D 4 HOH X 119 719 119 HOH HOH . D 4 HOH X 120 720 120 HOH HOH . D 4 HOH X 121 721 121 HOH HOH . D 4 HOH X 122 722 122 HOH HOH . D 4 HOH X 123 723 123 HOH HOH . D 4 HOH X 124 724 124 HOH HOH . D 4 HOH X 125 725 125 HOH HOH . D 4 HOH X 126 726 126 HOH HOH . D 4 HOH X 127 727 127 HOH HOH . D 4 HOH X 128 728 128 HOH HOH . D 4 HOH X 129 729 129 HOH HOH . D 4 HOH X 130 730 130 HOH HOH . D 4 HOH X 131 731 131 HOH HOH . D 4 HOH X 132 732 132 HOH HOH . D 4 HOH X 133 733 133 HOH HOH . D 4 HOH X 134 734 134 HOH HOH . D 4 HOH X 135 735 135 HOH HOH . D 4 HOH X 136 736 136 HOH HOH . D 4 HOH X 137 737 137 HOH HOH . D 4 HOH X 138 738 138 HOH HOH . D 4 HOH X 139 739 139 HOH HOH . D 4 HOH X 140 740 140 HOH HOH . D 4 HOH X 141 741 141 HOH HOH . D 4 HOH X 142 742 142 HOH HOH . D 4 HOH X 143 743 143 HOH HOH . D 4 HOH X 144 744 144 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 C C5 R1P . . . B 2 -49.674 -13.393 13.72 1 40.53 ? C5 R1P 600 X 1 HETATM 2 O O5 R1P . A . B 2 -49.358 -13.538 12.336 0.5 38.65 ? O5 R1P 600 X 1 HETATM 3 O O5 R1P . B . B 2 -50.732 -13.191 14.657 0.5 39.2 ? O5 R1P 600 X 1 HETATM 4 C C4 R1P . . . B 2 -48.457 -13.839 14.51 1 39.89 ? C4 R1P 600 X 1 HETATM 5 O O4 R1P . . . B 2 -48.33 -13.076 15.712 1 40.11 ? O4 R1P 600 X 1 HETATM 6 C C1 R1P . . . B 2 -48.268 -13.902 16.865 1 38.24 ? C1 R1P 600 X 1 HETATM 7 C C2 R1P . . . B 2 -48.49 -15.336 16.421 1 39.56 ? C2 R1P 600 X 1 HETATM 8 O O2 R1P . . . B 2 -47.503 -16.244 16.903 1 40.25 ? O2 R1P 600 X 1 HETATM 9 C C3 R1P . . . B 2 -48.551 -15.298 14.904 1 39.72 ? C3 R1P 600 X 1 HETATM 10 O O3 R1P . . . B 2 -47.392 -15.914 14.377 1 39.91 ? O3 R1P 600 X 1 HETATM 11 O O1 R1P . . . B 2 -46.882 -13.827 17.16 1 35.76 ? O1 R1P 600 X 1 HETATM 12 P P R1P . . . B 2 -46.213 -12.784 18.167 1 34.8 ? P R1P 600 X 1 HETATM 13 O O1P R1P . . . B 2 -44.879 -12.231 17.504 1 33.98 ? O1P R1P 600 X 1 HETATM 14 O O2P R1P . . . B 2 -47.193 -11.592 18.528 1 34.6 ? O2P R1P 600 X 1 HETATM 15 O O3P R1P . . . B 2 -45.871 -13.553 19.523 1 34.91 ? O3P R1P 600 X 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 15 #