data_2H4L
#
_model_server_result.job_id            aGArO_ocLxQZYHAnvnCoDw 
_model_server_result.datetime_utc      '2024-11-14 06:54:32' 
_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              71 
_model_server_stats.parse_time_ms           39 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           243 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           15 
#