data_5J7I
#
_model_server_result.job_id            YoE_74tEEPoDZ_naMQMi1Q 
_model_server_result.datetime_utc      '2024-11-23 21:35:56' 
_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          5j7i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":501}' 
#
_entry.id    5J7I 
#
_exptl.entry_id    5J7I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ADENOSINE-5-DIPHOSPHORIBOSE 
_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            5J7I 
_cell.length_a            93.054 
_cell.length_b            109.543 
_cell.length_c            204.149 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5J7I 
_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        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 
_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                      3 
_struct_asym.id                             F 
_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 ILE 272 A ILE 272 1_555 A N SCY 273 A SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 A C SCY 273 A SCY 273 1_555 A N ALA 274 A ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale3 B C ILE 272 B ILE 272 1_555 B N SCY 273 B SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 B C SCY 273 B SCY 273 1_555 B N ALA 274 B ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale5 C C ILE 272 C ILE 272 1_555 C N SCY 273 C SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale6 C C SCY 273 C SCY 273 1_555 C N ALA 274 C ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale7 D C ILE 272 D ILE 272 1_555 D N SCY 273 D SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale8 D C SCY 273 D SCY 273 1_555 D N ALA 274 D ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
#
_chem_comp.formula           'C15 H23 N5 O14 P2' 
_chem_comp.formula_weight    559.316 
_chem_comp.id                APR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ADENOSINE-5-DIPHOSPHORIBOSE 
_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 APR sing 57 n y 
N1 C6 APR doub 58 n y 
C2 N3 APR doub 59 n y 
C2 H2 APR sing 60 n n 
N3 C4 APR sing 61 n y 
C4 C5 APR doub 62 n y 
C4 N9 APR sing 63 n y 
C5 C6 APR sing 64 n y 
C5 N7 APR sing 65 n y 
C6 N6 APR sing 66 n n 
N6 H61 APR sing 67 n n 
N6 H62 APR sing 68 n n 
N7 C8 APR doub 69 n y 
C8 N9 APR sing 70 n y 
C8 H8 APR sing 71 n n 
N9 C1' APR sing 72 n n 
C1' C2' APR sing 73 n n 
C1' O4' APR sing 74 n n 
C1' "H'1" APR sing 75 n n 
C2' O2' APR sing 76 n n 
C2' C3' APR sing 77 n n 
C2' "H'2" APR sing 78 n n 
O2' "HO'2" APR sing 79 n n 
C3' O3' APR sing 80 n n 
C3' C4' APR sing 81 n n 
C3' "H'3" APR sing 82 n n 
O3' "HO'3" APR sing 83 n n 
O4' C4' APR sing 84 n n 
C4' C5' APR sing 85 n n 
C4' "H'4" APR sing 86 n n 
C5' O5' APR sing 87 n n 
C5' "H5'1" APR sing 88 n n 
C5' "H5'2" APR sing 89 n n 
O5' PA APR sing 90 n n 
PA O1A APR doub 91 n n 
PA O2A APR sing 92 n n 
PA O3A APR sing 93 n n 
O2A HOA2 APR sing 94 n n 
O3A PB APR sing 95 n n 
PB O1B APR doub 96 n n 
PB O2B APR sing 97 n n 
PB O5D APR sing 98 n n 
O2B HOB2 APR sing 99 n n 
O5D C5D APR sing 100 n n 
C5D C4D APR sing 101 n n 
C5D H5R1 APR sing 102 n n 
C5D H5R2 APR sing 103 n n 
O4D C1D APR sing 104 n n 
O4D C4D APR sing 105 n n 
O1D C1D APR sing 106 n n 
O1D HOR1 APR sing 107 n n 
C1D C2D APR sing 108 n n 
C1D "HR'1" APR sing 109 n n 
O2D C2D APR sing 110 n n 
O2D HOR2 APR sing 111 n n 
C2D C3D APR sing 112 n n 
C2D "HR'2" APR sing 113 n n 
O3D C3D APR sing 114 n n 
O3D HOR3 APR sing 115 n n 
C3D C4D APR sing 116 n n 
C3D "HR'3" APR sing 117 n n 
C4D "HR'4" APR sing 118 n n 
#
_atom_sites.entry_id                     5J7I 
_atom_sites.fract_transf_matrix[1][1]    0.010746 
_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]    0.009129 
_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]    0.004898 
_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 ADP A 1 501 1 ADP ADP . 
F 3 APR B 1 501 2 APR APR . 
G 2 ADP C 1 501 3 ADP ADP . 
H 2 ADP D 1 501 4 ADP ADP . 
#
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 APR . . . F 3 18.123 -17.635 -16.73 1 47.66 ? N1 APR 501 B 1 
HETATM 2 C C2 APR . . . F 3 18.557 -18.547 -17.64 1 47.66 ? C2 APR 501 B 1 
HETATM 3 N N3 APR . . . F 3 18.608 -19.891 -17.312 1 47.66 ? N3 APR 501 B 1 
HETATM 4 C C4 APR . . . F 3 18.226 -20.295 -16.083 1 47.66 ? C4 APR 501 B 1 
HETATM 5 C C5 APR . . . F 3 17.789 -19.373 -15.164 1 47.66 ? C5 APR 501 B 1 
HETATM 6 C C6 APR . . . F 3 17.739 -18.029 -15.5 1 47.66 ? C6 APR 501 B 1 
HETATM 7 N N6 APR . . . F 3 17.328 -16.896 -14.736 1 47.66 ? N6 APR 501 B 1 
HETATM 8 N N7 APR . . . F 3 17.458 -20.037 -13.983 1 47.66 ? N7 APR 501 B 1 
HETATM 9 C C8 APR . . . F 3 17.687 -21.379 -14.166 1 47.66 ? C8 APR 501 B 1 
HETATM 10 N N9 APR . . . F 3 18.166 -21.53 -15.443 1 47.66 ? N9 APR 501 B 1 
HETATM 11 C C1' APR . . . F 3 18.552 -22.755 -16.134 1 47.66 ? C1' APR 501 B 1 
HETATM 12 C C2' APR . . . F 3 20.067 -22.781 -16.561 1 47.66 ? C2' APR 501 B 1 
HETATM 13 O O2' APR . . . F 3 20.19 -23.209 -17.855 1 47.66 ? O2' APR 501 B 1 
HETATM 14 C C3' APR . . . F 3 20.78 -23.737 -15.624 1 47.66 ? C3' APR 501 B 1 
HETATM 15 O O3' APR . . . F 3 21.308 -24.93 -16.335 1 47.66 ? O3' APR 501 B 1 
HETATM 16 O O4' APR . . . F 3 18.418 -23.782 -15.366 1 47.66 ? O4' APR 501 B 1 
HETATM 17 C C4' APR . . . F 3 19.866 -24.172 -14.774 1 47.66 ? C4' APR 501 B 1 
HETATM 18 C C5' APR . . . F 3 20.024 -23.557 -13.42 1 47.66 ? C5' APR 501 B 1 
HETATM 19 O O5' APR . . . F 3 18.718 -23.787 -12.775 1 47.66 ? O5' APR 501 B 1 
HETATM 20 P PA APR . . . F 3 18.544 -23.589 -11.199 1 47.66 ? PA APR 501 B 1 
HETATM 21 O O1A APR . . . F 3 17.558 -22.491 -10.898 1 47.66 ? O1A APR 501 B 1 
HETATM 22 O O2A APR . . . F 3 19.9 -23.241 -10.639 1 47.66 ? O2A APR 501 B 1 
HETATM 23 O O3A APR . . . F 3 18.035 -24.953 -10.619 1 47.66 ? O3A APR 501 B 1 
HETATM 24 P PB APR . . . F 3 17.7 -25.237 -9.072 1 47.66 ? PB APR 501 B 1 
HETATM 25 O O1B APR . . . F 3 17.485 -26.765 -8.886 1 47.66 ? O1B APR 501 B 1 
HETATM 26 O O2B APR . . . F 3 16.442 -24.474 -8.678 1 47.66 ? O2B APR 501 B 1 
HETATM 27 O O5D APR . . . F 3 18.922 -24.742 -8.151 1 47.66 ? O5D APR 501 B 1 
HETATM 28 C C5D APR . . . F 3 20.05 -25.557 -8.057 1 47.66 ? C5D APR 501 B 1 
HETATM 29 O O4D APR . . . F 3 21.124 -23.246 -8.098 1 47.66 ? O4D APR 501 B 1 
HETATM 30 O O1D APR . . . F 3 21.466 -21.961 -6.256 1 47.66 ? O1D APR 501 B 1 
HETATM 31 C C1D APR . . . F 3 21.986 -22.935 -7.166 1 47.66 ? C1D APR 501 B 1 
HETATM 32 O O2D APR . . . F 3 23.348 -24.268 -5.688 1 47.66 ? O2D APR 501 B 1 
HETATM 33 C C2D APR . . . F 3 22.22 -24.288 -6.442 1 47.66 ? C2D APR 501 B 1 
HETATM 34 O O3D APR . . . F 3 23.607 -25.075 -8.354 1 47.66 ? O3D APR 501 B 1 
HETATM 35 C C3D APR . . . F 3 22.307 -25.218 -7.61 1 47.66 ? C3D APR 501 B 1 
HETATM 36 C C4D APR . . . F 3 21.288 -24.8 -8.391 1 47.66 ? C4D APR 501 B 1 
HETATM 37 H H2 APR . . . F 3 18.831 -18.253 -18.525 1 19.86 ? H2 APR 501 B 1 
HETATM 38 H H61 APR . . . F 3 17.391 -16.066 -15.089 1 19.86 ? H61 APR 501 B 1 
HETATM 39 H H62 APR . . . F 3 16.98 -17.016 -13.835 1 19.86 ? H62 APR 501 B 1 
HETATM 40 H H8 APR . . . F 3 17.544 -22.104 -13.494 1 19.86 ? H8 APR 501 B 1 
HETATM 41 H "H'1" APR . . . F 3 18.001 -22.866 -16.914 1 19.86 ? "H'1" APR 501 B 1 
HETATM 42 H "H'2" APR . . . F 3 20.447 -21.891 -16.473 1 19.86 ? "H'2" APR 501 B 1 
HETATM 43 H "HO'2" APR . . . F 3 20.273 -22.488 -18.407 1 19.86 ? "HO'2" APR 501 B 1 
HETATM 44 H "H'3" APR . . . F 3 21.472 -23.293 -15.164 1 19.86 ? "H'3" APR 501 B 1 
HETATM 45 H "HO'3" APR . . . F 3 20.626 -25.399 -16.681 1 19.86 ? "HO'3" APR 501 B 1 
HETATM 46 H "H'4" APR . . . F 3 19.934 -25.155 -14.697 1 19.86 ? "H'4" APR 501 B 1 
HETATM 47 H "H5'1" APR . . . F 3 20.731 -24.015 -12.928 1 19.86 ? "H5'1" APR 501 B 1 
HETATM 48 H "H5'2" APR . . . F 3 20.224 -22.549 -13.497 1 19.86 ? "H5'2" APR 501 B 1 
HETATM 49 H H5R1 APR . . . F 3 19.956 -26.3 -8.673 1 19.86 ? H5R1 APR 501 B 1 
HETATM 50 H H5R2 APR . . . F 3 20.122 -25.908 -7.132 1 19.86 ? H5R2 APR 501 B 1 
HETATM 51 H HOR1 APR . . . F 3 21.666 -22.18 -5.463 1 19.86 ? HOR1 APR 501 B 1 
HETATM 52 H "HR'1" APR . . . F 3 22.828 -22.613 -7.573 1 19.86 ? "HR'1" APR 501 B 1 
HETATM 53 H HOR2 APR . . . F 3 23.328 -24.926 -5.113 1 19.86 ? HOR2 APR 501 B 1 
HETATM 54 H "HR'2" APR . . . F 3 21.47 -24.507 -5.906 1 19.86 ? "HR'2" APR 501 B 1 
HETATM 55 H HOR3 APR . . . F 3 24.268 -25.42 -7.866 1 19.86 ? HOR3 APR 501 B 1 
HETATM 56 H "HR'3" APR . . . F 3 22.168 -26.147 -7.324 1 19.86 ? "HR'3" APR 501 B 1 
HETATM 57 H "HR'4" APR . . . F 3 21.531 -24.944 -9.391 1 19.86 ? "HR'4" APR 501 B 1 
#
_model_server_stats.io_time_ms              149 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    48 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           57 
#