data_5J7I # _model_server_result.job_id hSEd96VWbgEYcJ0qMxy40w _model_server_result.datetime_utc '2024-12-06 22:37:00' _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 137 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 405 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 57 #