data_1V8R # _model_server_result.job_id Zblq1scTEbwwdZg1nrTCcA _model_server_result.datetime_utc '2025-09-06 22:02:36' _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 1v8r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":619}' # _entry.id 1V8R # _exptl.entry_id 1V8R _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 120 _cell.entry_id 1V8R _cell.length_a 49.71 _cell.length_b 49.71 _cell.length_c 118.14 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1V8R _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 118.14 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 A OE1 GLU 44 A GLU 44 6_655 C ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc2 A OE1 GLU 70 A GLU 70 1_555 C ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc3 A OE2 GLU 82 A GLU 82 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc4 B ZN ZN . A ZN 301 1_555 D O1A APR . A APR 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? metalc ? metalc5 B ZN ZN . A ZN 301 1_555 E O HOH . A HOH 655 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc6 B ZN ZN . A ZN 301 1_555 E O HOH . A HOH 669 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc7 B ZN ZN . A ZN 301 1_555 E O HOH . A HOH 673 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? # _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 13 n y N1 C6 APR doub 14 n y C2 N3 APR doub 15 n y C2 H2 APR sing 16 n n N3 C4 APR sing 17 n y C4 C5 APR doub 18 n y C4 N9 APR sing 19 n y C5 C6 APR sing 20 n y C5 N7 APR sing 21 n y C6 N6 APR sing 22 n n N6 H61 APR sing 23 n n N6 H62 APR sing 24 n n N7 C8 APR doub 25 n y C8 N9 APR sing 26 n y C8 H8 APR sing 27 n n N9 C1' APR sing 28 n n C1' C2' APR sing 29 n n C1' O4' APR sing 30 n n C1' "H'1" APR sing 31 n n C2' O2' APR sing 32 n n C2' C3' APR sing 33 n n C2' "H'2" APR sing 34 n n O2' "HO'2" APR sing 35 n n C3' O3' APR sing 36 n n C3' C4' APR sing 37 n n C3' "H'3" APR sing 38 n n O3' "HO'3" APR sing 39 n n O4' C4' APR sing 40 n n C4' C5' APR sing 41 n n C4' "H'4" APR sing 42 n n C5' O5' APR sing 43 n n C5' "H5'1" APR sing 44 n n C5' "H5'2" APR sing 45 n n O5' PA APR sing 46 n n PA O1A APR doub 47 n n PA O2A APR sing 48 n n PA O3A APR sing 49 n n O2A HOA2 APR sing 50 n n O3A PB APR sing 51 n n PB O1B APR doub 52 n n PB O2B APR sing 53 n n PB O5D APR sing 54 n n O2B HOB2 APR sing 55 n n O5D C5D APR sing 56 n n C5D C4D APR sing 57 n n C5D H5R1 APR sing 58 n n C5D H5R2 APR sing 59 n n O4D C1D APR sing 60 n n O4D C4D APR sing 61 n n O1D C1D APR sing 62 n n O1D HOR1 APR sing 63 n n C1D C2D APR sing 64 n n C1D "HR'1" APR sing 65 n n O2D C2D APR sing 66 n n O2D HOR2 APR sing 67 n n C2D C3D APR sing 68 n n C2D "HR'2" APR sing 69 n n O3D C3D APR sing 70 n n O3D HOR3 APR sing 71 n n C3D C4D APR sing 72 n n C3D "HR'3" APR sing 73 n n C4D "HR'4" APR sing 74 n n # _atom_sites.entry_id 1V8R _atom_sites.fract_transf_matrix[1][1] 0.020117 _atom_sites.fract_transf_matrix[1][2] 0.011614 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023229 _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] 0.008465 _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 ZN A 1 301 301 ZN ZN2 . C 2 ZN A 1 302 302 ZN ZN2 . D 3 APR A 1 619 619 APR APR . E 4 HOH A 1 620 1 HOH TIP . E 4 HOH A 2 621 2 HOH TIP . E 4 HOH A 3 622 3 HOH TIP . E 4 HOH A 4 623 4 HOH TIP . E 4 HOH A 5 624 5 HOH TIP . E 4 HOH A 6 625 6 HOH TIP . E 4 HOH A 7 626 7 HOH TIP . E 4 HOH A 8 627 8 HOH TIP . E 4 HOH A 9 628 9 HOH TIP . E 4 HOH A 10 629 10 HOH TIP . E 4 HOH A 11 630 11 HOH TIP . E 4 HOH A 12 631 12 HOH TIP . E 4 HOH A 13 632 13 HOH TIP . E 4 HOH A 14 633 14 HOH TIP . E 4 HOH A 15 634 15 HOH TIP . E 4 HOH A 16 635 16 HOH TIP . E 4 HOH A 17 636 17 HOH TIP . E 4 HOH A 18 637 18 HOH TIP . E 4 HOH A 19 638 19 HOH TIP . E 4 HOH A 20 639 20 HOH TIP . E 4 HOH A 21 640 21 HOH TIP . E 4 HOH A 22 641 22 HOH TIP . E 4 HOH A 23 642 23 HOH TIP . E 4 HOH A 24 643 24 HOH TIP . E 4 HOH A 25 644 25 HOH TIP . E 4 HOH A 26 645 26 HOH TIP . E 4 HOH A 27 646 27 HOH TIP . E 4 HOH A 28 647 28 HOH TIP . E 4 HOH A 29 648 29 HOH TIP . E 4 HOH A 30 649 30 HOH TIP . E 4 HOH A 31 650 31 HOH TIP . E 4 HOH A 32 651 32 HOH TIP . E 4 HOH A 33 652 33 HOH TIP . E 4 HOH A 34 653 34 HOH TIP . E 4 HOH A 35 654 35 HOH TIP . E 4 HOH A 36 655 36 HOH TIP . E 4 HOH A 37 656 37 HOH TIP . E 4 HOH A 38 657 38 HOH TIP . E 4 HOH A 39 658 39 HOH TIP . E 4 HOH A 40 659 40 HOH TIP . E 4 HOH A 41 660 41 HOH TIP . E 4 HOH A 42 661 42 HOH TIP . E 4 HOH A 43 662 43 HOH TIP . E 4 HOH A 44 663 44 HOH TIP . E 4 HOH A 45 664 45 HOH TIP . E 4 HOH A 46 665 46 HOH TIP . E 4 HOH A 47 666 47 HOH TIP . E 4 HOH A 48 667 49 HOH TIP . E 4 HOH A 49 668 50 HOH TIP . E 4 HOH A 50 669 52 HOH TIP . E 4 HOH A 51 670 53 HOH TIP . E 4 HOH A 52 671 54 HOH TIP . E 4 HOH A 53 672 55 HOH TIP . E 4 HOH A 54 673 56 HOH TIP . E 4 HOH A 55 674 57 HOH TIP . # 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 . . . D 3 1.776 5.752 48.874 1 29.7 ? N1 APR 619 A 1 HETATM 2 C C2 APR . . . D 3 2.31 5.034 47.77 1 49.73 ? C2 APR 619 A 1 HETATM 3 N N3 APR . . . D 3 3.008 5.56 46.746 1 55.17 ? N3 APR 619 A 1 HETATM 4 C C4 APR . . . D 3 3.195 6.984 46.838 1 52.56 ? C4 APR 619 A 1 HETATM 5 C C5 APR . . . D 3 2.733 7.85 47.865 1 58.17 ? C5 APR 619 A 1 HETATM 6 C C6 APR . . . D 3 1.969 7.175 48.955 1 49.48 ? C6 APR 619 A 1 HETATM 7 N N6 APR . . . D 3 1.451 7.816 50.012 1 21.95 ? N6 APR 619 A 1 HETATM 8 N N7 APR . . . D 3 3.114 9.161 47.597 1 55.56 ? N7 APR 619 A 1 HETATM 9 C C8 APR . . . D 3 3.79 9.085 46.438 1 57.47 ? C8 APR 619 A 1 HETATM 10 N N9 APR . . . D 3 3.865 7.802 45.946 1 52.01 ? N9 APR 619 A 1 HETATM 11 C C1' APR . . . D 3 4.555 7.187 44.611 1 54.06 ? C1' APR 619 A 1 HETATM 12 C C2' APR . . . D 3 4.017 7.898 43.344 1 55.86 ? C2' APR 619 A 1 HETATM 13 O O2' APR . . . D 3 3.375 6.948 42.513 1 65.62 ? O2' APR 619 A 1 HETATM 14 C C3' APR . . . D 3 5.259 8.554 42.629 1 55.59 ? C3' APR 619 A 1 HETATM 15 O O3' APR . . . D 3 5.425 8.074 41.299 1 67.12 ? O3' APR 619 A 1 HETATM 16 O O4' APR . . . D 3 5.918 7.427 44.606 1 50.91 ? O4' APR 619 A 1 HETATM 17 C C4' APR . . . D 3 6.437 8.241 43.449 1 61.02 ? C4' APR 619 A 1 HETATM 18 C C5' APR . . . D 3 7.034 9.51 43.916 1 56.5 ? C5' APR 619 A 1 HETATM 19 O O5' APR . . . D 3 8.321 9.234 44.476 1 67.82 ? O5' APR 619 A 1 HETATM 20 P PA APR . . . D 3 9.237 10.358 45.046 1 63.15 ? PA APR 619 A 1 HETATM 21 O O1A APR . . . D 3 10.185 10.64 44.085 1 67.85 ? O1A APR 619 A 1 HETATM 22 O O2A APR . . . D 3 9.827 9.866 46.183 1 57.03 ? O2A APR 619 A 1 HETATM 23 O O3A APR . . . D 3 8.403 11.792 45.459 1 64.69 ? O3A APR 619 A 1 HETATM 24 P PB APR . . . D 3 7.216 12.143 46.496 1 63.49 ? PB APR 619 A 1 HETATM 25 O O1B APR . . . D 3 7.171 11.118 47.571 1 70.81 ? O1B APR 619 A 1 HETATM 26 O O2B APR . . . D 3 5.915 12.172 45.784 1 57.23 ? O2B APR 619 A 1 HETATM 27 O O5D APR . . . D 3 7.589 13.632 47.23 1 44.29 ? O5D APR 619 A 1 HETATM 28 C C5D APR . . . D 3 9.007 13.654 47.725 1 47.02 ? C5D APR 619 A 1 HETATM 29 O O4D APR . . . D 3 8.086 14.672 50.019 1 66.26 ? O4D APR 619 A 1 HETATM 30 O O1D APR . . . D 3 6.727 13.622 51.622 1 46.57 ? O1D APR 619 A 1 HETATM 31 C C1D APR . . . D 3 8.036 13.816 51.183 1 45.37 ? C1D APR 619 A 1 HETATM 32 O O2D APR . . . D 3 9.068 11.697 51.866 1 16.41 ? O2D APR 619 A 1 HETATM 33 C C2D APR . . . D 3 8.715 12.516 50.747 1 41.34 ? C2D APR 619 A 1 HETATM 34 O O3D APR . . . D 3 11.036 13.455 50.846 1 51.29 ? O3D APR 619 A 1 HETATM 35 C C3D APR . . . D 3 9.915 13.016 49.928 1 43.96 ? C3D APR 619 A 1 HETATM 36 C C4D APR . . . D 3 9.357 14.162 49.169 1 41.29 ? C4D APR 619 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #