data_3VUF # _model_server_result.job_id Rhy-dsyf93fivkFUiWPFpQ _model_server_result.datetime_utc '2025-04-12 18:03:57' _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 3vuf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 3VUF # _exptl.entry_id 3VUF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 3VUF _cell.length_a 153.368 _cell.length_b 153.368 _cell.length_c 153.368 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VUF _symmetry.cell_setting ? _symmetry.Int_Tables_number 207 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 264 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 337 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 456 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 529 _struct_conn.ptnr2_symmetry 1_555 _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 2.037 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 3VUF _atom_sites.fract_transf_matrix[1][1] 0.00652 _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] 0.00652 _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] 0.00652 _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 ADP A 1 701 600 ADP ADP . C 3 SO4 A 1 702 611 SO4 SO4 . D 3 SO4 A 1 703 612 SO4 SO4 . E 3 SO4 A 1 704 613 SO4 SO4 . F 4 HOH A 1 801 701 HOH HOH . F 4 HOH A 2 802 702 HOH HOH . F 4 HOH A 3 803 703 HOH HOH . F 4 HOH A 4 804 704 HOH HOH . F 4 HOH A 5 805 705 HOH HOH . F 4 HOH A 6 806 706 HOH HOH . F 4 HOH A 7 807 707 HOH HOH . F 4 HOH A 8 808 708 HOH HOH . F 4 HOH A 9 809 709 HOH HOH . F 4 HOH A 10 810 710 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 P PB ADP . . . B 2 -52.847 -14.776 39.65 1 136.01 ? PB ADP 701 A 1 HETATM 2 O O1B ADP . . . B 2 -51.915 -15.85 39.104 1 136.05 ? O1B ADP 701 A 1 HETATM 3 O O2B ADP . . . B 2 -54.133 -15.354 40.213 1 135.83 ? O2B ADP 701 A 1 HETATM 4 O O3B ADP . . . B 2 -52.181 -13.783 40.597 1 136.25 ? O3B ADP 701 A 1 HETATM 5 P PA ADP . . . B 2 -54.509 -12.824 38.298 1 132.74 ? PA ADP 701 A 1 HETATM 6 O O1A ADP . . . B 2 -55.81 -13.588 38.055 1 132.24 ? O1A ADP 701 A 1 HETATM 7 O O2A ADP . . . B 2 -54.349 -11.951 39.533 1 132.48 ? O2A ADP 701 A 1 HETATM 8 O O3A ADP . . . B 2 -53.277 -13.893 38.334 1 134.23 ? O3A ADP 701 A 1 HETATM 9 O O5' ADP . . . B 2 -54.255 -11.868 37.007 1 130.58 ? O5' ADP 701 A 1 HETATM 10 C C5' ADP . . . B 2 -54.956 -10.622 36.812 1 128.71 ? C5' ADP 701 A 1 HETATM 11 C C4' ADP . . . B 2 -56.418 -10.613 37.34 1 127.74 ? C4' ADP 701 A 1 HETATM 12 O O4' ADP . . . B 2 -56.706 -9.479 38.196 1 126.83 ? O4' ADP 701 A 1 HETATM 13 C C3' ADP . . . B 2 -57.489 -10.59 36.243 1 126.6 ? C3' ADP 701 A 1 HETATM 14 O O3' ADP . . . B 2 -58.423 -11.661 36.461 1 126.64 ? O3' ADP 701 A 1 HETATM 15 C C2' ADP . . . B 2 -58.148 -9.201 36.298 1 125.33 ? C2' ADP 701 A 1 HETATM 16 O O2' ADP . . . B 2 -59.591 -9.245 36.288 1 122.98 ? O2' ADP 701 A 1 HETATM 17 C C1' ADP . . . B 2 -57.598 -8.527 37.564 1 125.1 ? C1' ADP 701 A 1 HETATM 18 N N9 ADP . . . B 2 -56.86 -7.238 37.296 1 123.46 ? N9 ADP 701 A 1 HETATM 19 C C8 ADP . . . B 2 -55.55 -7.144 36.935 1 123.38 ? C8 ADP 701 A 1 HETATM 20 N N7 ADP . . . B 2 -55.149 -5.853 36.771 1 123.19 ? N7 ADP 701 A 1 HETATM 21 C C5 ADP . . . B 2 -56.226 -5.076 37.042 1 122.4 ? C5 ADP 701 A 1 HETATM 22 C C6 ADP . . . B 2 -56.498 -3.611 37.073 1 121.47 ? C6 ADP 701 A 1 HETATM 23 N N6 ADP . . . B 2 -55.507 -2.737 36.768 1 119.69 ? N6 ADP 701 A 1 HETATM 24 N N1 ADP . . . B 2 -57.746 -3.192 37.407 1 120.11 ? N1 ADP 701 A 1 HETATM 25 C C2 ADP . . . B 2 -58.719 -4.08 37.707 1 119.89 ? C2 ADP 701 A 1 HETATM 26 N N3 ADP . . . B 2 -58.545 -5.418 37.707 1 120 ? N3 ADP 701 A 1 HETATM 27 C C4 ADP . . . B 2 -57.347 -5.982 37.39 1 121.98 ? C4 ADP 701 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #