data_5VU8 # _model_server_result.job_id HbPJ6C8sDT3lzrJiEzy4lw _model_server_result.datetime_utc '2025-01-26 21:12:39' _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 5vu8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":801}' # _entry.id 5VU8 # _exptl.entry_id 5VU8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 477.155 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate' _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 5VU8 _cell.length_a 72.288 _cell.length_b 107.36 _cell.length_c 147.732 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VU8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 4 _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 disulf ? disulf1 A SG CYS 428 A CYS 428 1_555 A SG CYS 442 A CYS 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 506 A CYS 506 1_555 A SG CYS 509 A CYS 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 C O3' DG 11 P DG 11 1_555 C P 9O4 12 P 9O4 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? metalc ? metalc1 A OE1 GLU 580 A GLU 580 1_555 F MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc2 D O1A 9O7 . A 9O7 801 1_555 E MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc3 D O2G 9O7 . A 9O7 801 1_555 F MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc4 D O3G 9O7 . A 9O7 801 1_555 F MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? metalc ? metalc5 D O1G 9O7 . A 9O7 801 1_555 F MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc6 D O1A 9O7 . A 9O7 801 1_555 G MG MG . P MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc7 C O1P 9O4 12 P 9O4 12 1_555 G MG MG . P MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? hydrog WATSON-CRICK hydrog1 B N3 DC 6 T DC 6 1_555 C N1 DG 11 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 6 T DC 6 1_555 C O6 DG 11 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 6 T DC 6 1_555 C N2 DG 11 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 7 T DG 7 1_555 C N3 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 7 T DG 7 1_555 C O2 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 7 T DG 7 1_555 C N4 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog7 B O2 DC 8 T DC 8 1_555 C N2 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DA 9 T DA 9 1_555 C N3 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N6 DA 9 T DA 9 1_555 C O4 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DG 10 T DG 10 1_555 C N3 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N2 DG 10 T DG 10 1_555 C O2 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O6 DG 10 T DG 10 1_555 C N4 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N3 DT 11 T DT 11 1_555 C N1 DA 6 P DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O4 DT 11 T DT 11 1_555 C N6 DA 6 P DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 DT 12 T DT 12 1_555 C N1 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O4 DT 12 T DT 12 1_555 C N6 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DC 13 T DC 13 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N4 DC 13 T DC 13 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O2 DC 13 T DC 13 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog20 B N4 DC 15 T DC 15 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H14 N5 O12 P3' _chem_comp.formula_weight 477.155 _chem_comp.id 9O7 _chem_comp.mon_nstd_flag . _chem_comp.name '[(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate' _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 O4' C4' 9O7 sing 35 n n O4' C1' 9O7 sing 36 n n C4' C3' 9O7 sing 37 n n C2 N3 9O7 doub 38 n y C2 N1 9O7 sing 39 n y N3 C4 9O7 sing 40 n y N1 C6 9O7 doub 41 n y O1A PA 9O7 doub 42 n n C4 C5 9O7 doub 43 n y C4 N9 9O7 sing 44 n y C6 N6 9O7 sing 45 n n C6 C5 9O7 sing 46 n y O2A PA 9O7 sing 47 n n C1' N9 9O7 sing 48 n n C1' C2' 9O7 sing 49 n n C5 N7 9O7 sing 50 n y N9 C8 9O7 sing 51 n y C3' O3' 9O7 sing 52 n n C3' C2' 9O7 sing 53 n n C8 N7 9O7 doub 54 n y PA O3' 9O7 sing 55 n n PA O3A 9O7 sing 56 n n C2' O2' 9O7 sing 57 n n O3A PB 9O7 sing 58 n n O2B PB 9O7 doub 59 n n O2G PG 9O7 doub 60 n n PB O1B 9O7 sing 61 n n PB O3B 9O7 sing 62 n n PG O3B 9O7 sing 63 n n PG O3G 9O7 sing 64 n n PG O1G 9O7 sing 65 n n C2 H1 9O7 sing 66 n n N6 H2 9O7 sing 67 n n N6 H3 9O7 sing 68 n n C8 H4 9O7 sing 69 n n C1' H5 9O7 sing 70 n n O1B H6 9O7 sing 71 n n C2' H7 9O7 sing 72 n n O2' H8 9O7 sing 73 n n O2A H9 9O7 sing 74 n n C3' H10 9O7 sing 75 n n O3G H11 9O7 sing 76 n n C4' H12 9O7 sing 77 n n C4' H13 9O7 sing 78 n n O1G H14 9O7 sing 79 n n # _atom_sites.entry_id 5VU8 _atom_sites.fract_transf_matrix[1][1] 0.013834 _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] 0.009314 _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] 0.006769 _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 D 4 9O7 A 1 801 1 9O7 TAT . E 5 MG A 1 802 2 MG MG . F 5 MG A 1 803 3 MG MG . G 5 MG P 1 101 1 MG MG . H 6 HOH A 1 901 1 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 N N1 9O7 . . . D 4 93.233 123.434 462.233 0.59 80 ? N1 9O7 801 A 1 HETATM 2 C C2 9O7 . . . D 4 93.559 122.141 462.022 0.59 78.83 ? C2 9O7 801 A 1 HETATM 3 N N3 9O7 . . . D 4 92.778 121.061 462.22 0.59 78.56 ? N3 9O7 801 A 1 HETATM 4 C C4 9O7 . . . D 4 91.596 121.422 462.667 0.59 80.03 ? C4 9O7 801 A 1 HETATM 5 C C5 9O7 . . . D 4 91.142 122.75 462.925 0.59 79.43 ? C5 9O7 801 A 1 HETATM 6 C C6 9O7 . . . D 4 92.028 123.752 462.683 0.59 78.6 ? C6 9O7 801 A 1 HETATM 7 N N6 9O7 . . . D 4 91.657 125.136 462.914 0.59 78.96 ? N6 9O7 801 A 1 HETATM 8 N N7 9O7 . . . D 4 89.71 122.685 463.429 0.59 77.97 ? N7 9O7 801 A 1 HETATM 9 C C8 9O7 . . . D 4 89.55 121.351 463.389 0.59 80.66 ? C8 9O7 801 A 1 HETATM 10 N N9 9O7 . . . D 4 90.576 120.706 462.976 0.59 82.43 ? N9 9O7 801 A 1 HETATM 11 P PA 9O7 . . . D 4 85.891 118.859 463.448 0.59 86.49 ? PA 9O7 801 A 1 HETATM 12 P PB 9O7 . . . D 4 85.706 117.925 466.194 0.59 83.3 ? PB 9O7 801 A 1 HETATM 13 P PG 9O7 . . . D 4 83.159 117.306 467.426 0.59 98.98 ? PG 9O7 801 A 1 HETATM 14 C C1' 9O7 . . . D 4 90.593 119.27 462.867 0.59 81.73 ? C1' 9O7 801 A 1 HETATM 15 O O1A 9O7 . . . D 4 85.232 119.817 462.565 0.59 88.27 ? O1A 9O7 801 A 1 HETATM 16 O O1B 9O7 . . . D 4 87.037 118.378 466.593 0.59 82.23 ? O1B 9O7 801 A 1 HETATM 17 C C2' 9O7 . . . D 4 89.744 118.654 463.916 0.59 80.97 ? C2' 9O7 801 A 1 HETATM 18 O O2' 9O7 . . . D 4 90.271 117.648 464.255 0.59 79.25 ? O2' 9O7 801 A 1 HETATM 19 O O2A 9O7 . . . D 4 85.72 117.617 462.701 0.59 88.56 ? O2A 9O7 801 A 1 HETATM 20 O O2B 9O7 . . . D 4 85.97 116.535 465.829 0.59 70.32 ? O2B 9O7 801 A 1 HETATM 21 O O2G 9O7 . . . D 4 82.407 117.526 466.194 0.59 96.94 ? O2G 9O7 801 A 1 HETATM 22 C C3' 9O7 . . . D 4 88.494 118.293 463.266 0.59 79.86 ? C3' 9O7 801 A 1 HETATM 23 O O3' 9O7 . . . D 4 87.481 119.242 463.647 0.59 83.49 ? O3' 9O7 801 A 1 HETATM 24 O O3A 9O7 . . . D 4 85.14 118.791 464.912 0.59 86.01 ? O3A 9O7 801 A 1 HETATM 25 O O3B 9O7 . . . D 4 84.642 118.023 467.446 0.59 92.44 ? O3B 9O7 801 A 1 HETATM 26 O O3G 9O7 . . . D 4 83.205 115.855 467.573 0.59 97.81 ? O3G 9O7 801 A 1 HETATM 27 C C4' 9O7 . . . D 4 88.697 118.345 461.756 0.59 78.1 ? C4' 9O7 801 A 1 HETATM 28 O O4' 9O7 . . . D 4 90.078 118.857 461.548 0.59 78.37 ? O4' 9O7 801 A 1 HETATM 29 O O1G 9O7 . . . D 4 82.262 117.754 468.488 0.59 107.05 ? O1G 9O7 801 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 29 #