data_3VAD # _model_server_result.job_id mLNmpeA5Jb6Vkpbw25ARdw _model_server_result.datetime_utc '2024-11-15 14:25:54' _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 3vad # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 3VAD # _exptl.entry_id 3VAD _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 3VAD _cell.length_a 128.079 _cell.length_b 128.079 _cell.length_c 74.035 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VAD _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 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 # 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 OD1 ASN 279 A ASN 249 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc2 A O VAL 328 A VAL 298 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc3 A O ASP 330 A ASP 300 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc4 A O PHE 333 A PHE 303 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc5 A O GLY 367 A GLY 337 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? metalc ? metalc6 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc7 B O2B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc8 B O1A ADP . A ADP 401 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc9 C MG MG . A MG 402 1_555 G O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc10 C MG MG . A MG 402 1_555 G O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? # _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 20 n n PB O2B ADP sing 21 n n PB O3B ADP sing 22 n n PB O3A ADP sing 23 n n O2B HOB2 ADP sing 24 n n O3B HOB3 ADP sing 25 n n PA O1A ADP doub 26 n n PA O2A ADP sing 27 n n PA O3A ADP sing 28 n n PA O5' ADP sing 29 n n O2A HOA2 ADP sing 30 n n O5' C5' ADP sing 31 n n C5' C4' ADP sing 32 n n C5' "H5'1" ADP sing 33 n n C5' "H5'2" ADP sing 34 n n C4' O4' ADP sing 35 n n C4' C3' ADP sing 36 n n C4' H4' ADP sing 37 n n O4' C1' ADP sing 38 n n C3' O3' ADP sing 39 n n C3' C2' ADP sing 40 n n C3' H3' ADP sing 41 n n O3' HO3' ADP sing 42 n n C2' O2' ADP sing 43 n n C2' C1' ADP sing 44 n n C2' H2' ADP sing 45 n n O2' HO2' ADP sing 46 n n C1' N9 ADP sing 47 n n C1' H1' ADP sing 48 n n N9 C8 ADP sing 49 n y N9 C4 ADP sing 50 n y C8 N7 ADP doub 51 n y C8 H8 ADP sing 52 n n N7 C5 ADP sing 53 n y C5 C6 ADP sing 54 n y C5 C4 ADP doub 55 n y C6 N6 ADP sing 56 n n C6 N1 ADP doub 57 n y N6 HN61 ADP sing 58 n n N6 HN62 ADP sing 59 n n N1 C2 ADP sing 60 n y C2 N3 ADP doub 61 n y C2 H2 ADP sing 62 n n N3 C4 ADP sing 63 n y # _atom_sites.entry_id 3VAD _atom_sites.fract_transf_matrix[1][1] 0.007808 _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] 0.007808 _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] 0.013507 _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 1 401 1 ADP ADP . C 3 MG A 1 402 1 MG MG . D 4 K A 1 403 1 K K . E 5 0F1 A 1 404 1 0F1 BT2 . F 5 0F1 A 1 405 1 0F1 BT2 . G 6 HOH A 1 501 1 HOH HOH . G 6 HOH A 2 502 2 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 5.03 -32.911 -4.64 1 76.83 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 4.992 -32.653 -6.126 1 70.31 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 6.405 -33.295 -4.139 1 66.96 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 3.914 -33.781 -4.109 1 73 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 5.674 -30.522 -3.156 1 60.46 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 4.915 -29.333 -2.657 1 56.33 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 6.44 -31.381 -2.174 1 67.24 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 4.638 -31.472 -3.975 1 73.27 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 6.721 -30.091 -4.297 1 62.9 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 6.33 -29.169 -5.312 1 60.22 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 7.14 -29.382 -6.577 1 63.12 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 8.341 -28.613 -6.521 1 61.68 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 7.573 -30.821 -6.811 1 58.58 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 6.574 -31.523 -7.54 1 66.85 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 8.832 -30.667 -7.614 1 63.32 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 8.55 -30.377 -8.983 1 61.79 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 9.411 -29.379 -7.073 1 66.84 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 10.452 -29.669 -6.059 1 57.78 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 10.33 -29.663 -4.719 1 54.75 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 11.511 -29.964 -4.128 1 54.5 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 12.41 -30.163 -5.095 1 54.43 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 13.835 -30.521 -5.191 1 47.25 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 14.61 -30.74 -4.103 1 44.08 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 14.353 -30.632 -6.435 1 54.91 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 13.65 -30.444 -7.556 1 50.17 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 12.354 -30.124 -7.531 1 60.74 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 11.698 -29.976 -6.364 1 56.15 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 27 #