data_1JLS
#
_model_server_result.job_id            -xFQm63x3thgLLlSWGijHA 
_model_server_result.datetime_utc      '2024-10-24 04:22:13' 
_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          1jls 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":301}' 
#
_entry.id    1JLS 
#
_exptl.entry_id    1JLS 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              390.07 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-O-pyrophosphono-5-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          97.7 
_cell.angle_gamma         90 
_cell.entry_id            1JLS 
_cell.length_a            71.4 
_cell.length_b            111.4 
_cell.length_c            71.9 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1JLS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W 
_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                      5 
_struct_asym.id                             H 
_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 H O1B PRP . B PRP 301 1_555 F MG MG . B MG 3756 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? 
metalc ? metalc2 H O2B PRP . B PRP 301 1_555 F MG MG . B MG 3756 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc3 H O3A PRP . B PRP 301 1_555 F MG MG . B MG 3756 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.071 ? 
#
_chem_comp.formula           'C5 H13 O14 P3' 
_chem_comp.formula_weight    390.07 
_chem_comp.id                PRP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose 
_chem_comp.type              d-saccharide 
_chem_comp.pdbx_synonyms     'ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID;1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose;1-O-pyrophosphono-5-O-phosphono-D-ribose;1-O-pyrophosphono-5-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
C1 C2 PRP sing 281 n n 
C1 O1 PRP sing 282 n n 
C1 O4 PRP sing 283 n n 
C1 H1 PRP sing 284 n n 
C2 C3 PRP sing 285 n n 
C2 O2 PRP sing 286 n n 
C2 H2 PRP sing 287 n n 
C3 C4 PRP sing 288 n n 
C3 O3 PRP sing 289 n n 
C3 H3 PRP sing 290 n n 
C4 C5 PRP sing 291 n n 
C4 O4 PRP sing 292 n n 
C4 H4 PRP sing 293 n n 
C5 O5 PRP sing 294 n n 
C5 H51 PRP sing 295 n n 
C5 H52 PRP sing 296 n n 
O1 PA PRP sing 297 n n 
O2 HO2 PRP sing 298 n n 
O3 HO3 PRP sing 299 n n 
O5 P PRP sing 300 n n 
P O1P PRP doub 301 n n 
P O2P PRP sing 302 n n 
P O3P PRP sing 303 n n 
O2P HOP2 PRP sing 304 n n 
O3P HOP3 PRP sing 305 n n 
PA O1A PRP doub 306 n n 
PA O2A PRP sing 307 n n 
PA O3A PRP sing 308 n n 
O2A HOA2 PRP sing 309 n n 
O3A PB PRP sing 310 n n 
PB O1B PRP doub 311 n n 
PB O2B PRP sing 312 n n 
PB O3B PRP sing 313 n n 
O2B HOB2 PRP sing 314 n n 
O3B HOB3 PRP sing 315 n n 
#
_pdbx_chem_comp_identifier.comp_id            PRP 
_pdbx_chem_comp_identifier.identifier         a-D-Ribf1PO35PO3 
_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                     1JLS 
_atom_sites.fract_transf_matrix[1][1]    0.014006 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001894 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008977 
_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]    0.014035 
_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 2 PO4 B 1 3699 699 PO4 PO4 . 
F 3 MG B 1 3756 756 MG MG2 . 
G 4 URA B 1 300 0 URA URA . 
H 5 PRP B 1 301 1 PRP PRP . 
I 2 PO4 A 1 1599 599 PO4 PO4 . 
J 2 PO4 A 1 3199 199 PO4 PO4 . 
K 2 PO4 A 1 3599 599 PO4 PO4 . 
L 4 URA A 1 400 0 URA URA . 
M 2 PO4 D 1 3399 399 PO4 PO4 . 
N 2 PO4 D 1 3499 499 PO4 PO4 . 
O 2 PO4 D 1 3799 799 PO4 PO4 . 
P 4 URA D 1 500 0 URA URA . 
Q 2 PO4 C 1 2599 599 PO4 PO4 . 
R 2 PO4 C 1 3299 299 PO4 PO4 . 
S 4 URA C 1 600 0 URA URA . 
T 6 HOH B 1 706 706 HOH WAT . 
T 6 HOH B 2 709 709 HOH WAT . 
T 6 HOH B 3 723 723 HOH WAT . 
T 6 HOH B 4 726 726 HOH WAT . 
T 6 HOH B 5 728 728 HOH WAT . 
T 6 HOH B 6 735 735 HOH WAT . 
T 6 HOH B 7 737 737 HOH WAT . 
T 6 HOH B 8 738 738 HOH WAT . 
T 6 HOH B 9 741 741 HOH WAT . 
T 6 HOH B 10 745 745 HOH WAT . 
T 6 HOH B 11 758 758 HOH WAT . 
T 6 HOH B 12 770 770 HOH WAT . 
T 6 HOH B 13 774 774 HOH WAT . 
T 6 HOH B 14 776 776 HOH WAT . 
T 6 HOH B 15 781 781 HOH WAT . 
T 6 HOH B 16 791 791 HOH WAT . 
T 6 HOH B 17 793 793 HOH WAT . 
T 6 HOH B 18 800 800 HOH WAT . 
T 6 HOH B 19 803 803 HOH WAT . 
T 6 HOH B 20 819 819 HOH WAT . 
T 6 HOH B 21 830 830 HOH WAT . 
T 6 HOH B 22 838 838 HOH WAT . 
T 6 HOH B 23 839 839 HOH WAT . 
T 6 HOH B 24 840 840 HOH WAT . 
U 6 HOH A 1 710 710 HOH WAT . 
U 6 HOH A 2 711 711 HOH WAT . 
U 6 HOH A 3 714 714 HOH WAT . 
U 6 HOH A 4 718 718 HOH WAT . 
U 6 HOH A 5 719 719 HOH WAT . 
U 6 HOH A 6 724 724 HOH WAT . 
U 6 HOH A 7 727 727 HOH WAT . 
U 6 HOH A 8 734 734 HOH WAT . 
U 6 HOH A 9 739 739 HOH WAT . 
U 6 HOH A 10 743 743 HOH WAT . 
U 6 HOH A 11 746 746 HOH WAT . 
U 6 HOH A 12 747 747 HOH WAT . 
U 6 HOH A 13 749 749 HOH WAT . 
U 6 HOH A 14 752 752 HOH WAT . 
U 6 HOH A 15 763 763 HOH WAT . 
U 6 HOH A 16 769 769 HOH WAT . 
U 6 HOH A 17 771 771 HOH WAT . 
U 6 HOH A 18 773 773 HOH WAT . 
U 6 HOH A 19 777 777 HOH WAT . 
U 6 HOH A 20 778 778 HOH WAT . 
U 6 HOH A 21 779 779 HOH WAT . 
U 6 HOH A 22 788 788 HOH WAT . 
U 6 HOH A 23 789 789 HOH WAT . 
U 6 HOH A 24 794 794 HOH WAT . 
U 6 HOH A 25 795 795 HOH WAT . 
U 6 HOH A 26 796 796 HOH WAT . 
U 6 HOH A 27 799 799 HOH WAT . 
U 6 HOH A 28 810 810 HOH WAT . 
U 6 HOH A 29 818 818 HOH WAT . 
U 6 HOH A 30 826 826 HOH WAT . 
U 6 HOH A 31 833 833 HOH WAT . 
U 6 HOH A 32 835 835 HOH WAT . 
U 6 HOH A 33 836 836 HOH WAT . 
U 6 HOH A 34 841 841 HOH WAT . 
U 6 HOH A 35 847 847 HOH WAT . 
V 6 HOH D 1 700 700 HOH WAT . 
V 6 HOH D 2 701 701 HOH WAT . 
V 6 HOH D 3 704 704 HOH WAT . 
V 6 HOH D 4 705 705 HOH WAT . 
V 6 HOH D 5 707 707 HOH WAT . 
V 6 HOH D 6 712 712 HOH WAT . 
V 6 HOH D 7 716 716 HOH WAT . 
V 6 HOH D 8 725 725 HOH WAT . 
V 6 HOH D 9 729 729 HOH WAT . 
V 6 HOH D 10 736 736 HOH WAT . 
V 6 HOH D 11 740 740 HOH WAT . 
V 6 HOH D 12 742 742 HOH WAT . 
V 6 HOH D 13 744 744 HOH WAT . 
V 6 HOH D 14 748 748 HOH WAT . 
V 6 HOH D 15 751 751 HOH WAT . 
V 6 HOH D 16 754 754 HOH WAT . 
V 6 HOH D 17 761 761 HOH WAT . 
V 6 HOH D 18 762 762 HOH WAT . 
V 6 HOH D 19 765 765 HOH WAT . 
V 6 HOH D 20 767 767 HOH WAT . 
V 6 HOH D 21 772 772 HOH WAT . 
V 6 HOH D 22 775 775 HOH WAT . 
V 6 HOH D 23 780 780 HOH WAT . 
V 6 HOH D 24 797 797 HOH WAT . 
V 6 HOH D 25 798 798 HOH WAT . 
V 6 HOH D 26 801 801 HOH WAT . 
V 6 HOH D 27 804 804 HOH WAT . 
V 6 HOH D 28 805 805 HOH WAT . 
V 6 HOH D 29 806 806 HOH WAT . 
V 6 HOH D 30 813 813 HOH WAT . 
V 6 HOH D 31 817 817 HOH WAT . 
V 6 HOH D 32 829 829 HOH WAT . 
V 6 HOH D 33 834 834 HOH WAT . 
V 6 HOH D 34 842 842 HOH WAT . 
V 6 HOH D 35 843 843 HOH WAT . 
V 6 HOH D 36 844 844 HOH WAT . 
V 6 HOH D 37 845 845 HOH WAT . 
V 6 HOH D 38 846 846 HOH WAT . 
W 6 HOH C 1 702 702 HOH WAT . 
W 6 HOH C 2 715 715 HOH WAT . 
W 6 HOH C 3 720 720 HOH WAT . 
W 6 HOH C 4 730 730 HOH WAT . 
W 6 HOH C 5 733 733 HOH WAT . 
W 6 HOH C 6 750 750 HOH WAT . 
W 6 HOH C 7 753 753 HOH WAT . 
W 6 HOH C 8 759 759 HOH WAT . 
W 6 HOH C 9 764 764 HOH WAT . 
W 6 HOH C 10 766 766 HOH WAT . 
W 6 HOH C 11 768 768 HOH WAT . 
W 6 HOH C 12 790 790 HOH WAT . 
W 6 HOH C 13 802 802 HOH WAT . 
W 6 HOH C 14 808 808 HOH WAT . 
W 6 HOH C 15 809 809 HOH WAT . 
W 6 HOH C 16 816 816 HOH WAT . 
W 6 HOH C 17 820 820 HOH WAT . 
W 6 HOH C 18 825 825 HOH WAT . 
W 6 HOH C 19 828 828 HOH WAT . 
W 6 HOH C 20 831 831 HOH WAT . 
W 6 HOH C 21 837 837 HOH WAT . 
#
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 C1 PRP . . . H 5 45.96 54.106 38.321 1 31.36 ? C1 PRP 301 B 1 
HETATM 2 C C2 PRP . . . H 5 44.464 54.007 37.904 1 27.03 ? C2 PRP 301 B 1 
HETATM 3 C C3 PRP . . . H 5 44.251 52.594 37.232 1 30.67 ? C3 PRP 301 B 1 
HETATM 4 C C4 PRP . . . H 5 45.575 52.557 36.452 1 32.8 ? C4 PRP 301 B 1 
HETATM 5 C C5 PRP . . . H 5 45.465 53.372 35.118 1 33.83 ? C5 PRP 301 B 1 
HETATM 6 O O1 PRP . . . H 5 46.238 53.684 39.795 1 44.21 ? O1 PRP 301 B 1 
HETATM 7 O O2 PRP . . . H 5 43.621 54.211 39.058 1 38.54 ? O2 PRP 301 B 1 
HETATM 8 O O3 PRP . . . H 5 44.226 51.458 38.211 1 40.46 ? O3 PRP 301 B 1 
HETATM 9 O O4 PRP . . . H 5 46.61 53.137 37.337 1 31.1 ? O4 PRP 301 B 1 
HETATM 10 O O5 PRP . . . H 5 46.753 53.118 34.398 1 33.73 ? O5 PRP 301 B 1 
HETATM 11 P P PRP . . . H 5 47.338 51.842 33.863 1 45.97 ? P PRP 301 B 1 
HETATM 12 O O1P PRP . . . H 5 47.833 51.046 35.119 1 33.7 ? O1P PRP 301 B 1 
HETATM 13 O O2P PRP . . . H 5 46.119 51.226 33.098 1 33.07 ? O2P PRP 301 B 1 
HETATM 14 O O3P PRP . . . H 5 48.619 52.254 32.837 1 37.98 ? O3P PRP 301 B 1 
HETATM 15 P PA PRP . . . H 5 47.125 54.672 40.905 1 58.96 ? PA PRP 301 B 1 
HETATM 16 O O1A PRP . . . H 5 48.519 54.111 41.024 1 50.53 ? O1A PRP 301 B 1 
HETATM 17 O O2A PRP . . . H 5 47.12 56.109 40.403 1 45.49 ? O2A PRP 301 B 1 
HETATM 18 O O3A PRP . . . H 5 46.726 54.225 42.483 1 52.36 ? O3A PRP 301 B 1 
HETATM 19 P PB PRP . . . H 5 45.311 54.369 43.41 1 61.26 ? PB PRP 301 B 1 
HETATM 20 O O1B PRP . . . H 5 44.845 52.998 43.828 1 46.43 ? O1B PRP 301 B 1 
HETATM 21 O O2B PRP . . . H 5 44.315 55.036 42.535 1 50.11 ? O2B PRP 301 B 1 
HETATM 22 O O3B PRP . . . H 5 45.693 55.218 44.586 1 50.23 ? O3B PRP 301 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           22 
#