data_6WVT # _model_server_result.job_id QpnbHvr7GjAExeP5yPlZAg _model_server_result.datetime_utc '2024-11-05 00:40:11' _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 6wvt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":802}' # _entry.id 6WVT # _exptl.entry_id 6WVT _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 6WVT _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WVT _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 N N N ? 4 P N N ? 4 R N N ? 4 T N N ? 4 V N N ? 4 X N 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 GLU 74 B GLU 72 1_555 A N HIC 75 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C HIC 75 B HIC 73 1_555 A N GLY 76 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 B C GLU 74 D GLU 72 1_555 B N HIC 75 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 B C HIC 75 D HIC 73 1_555 B N GLY 76 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 C C GLU 74 E GLU 72 1_555 C N HIC 75 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 C C HIC 75 E HIC 73 1_555 C N GLY 76 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale7 D C GLU 74 F GLU 72 1_555 D N HIC 75 F HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 D C HIC 75 F HIC 73 1_555 D N GLY 76 F GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale9 E C GLU 74 H GLU 72 1_555 E N HIC 75 H HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale10 E C HIC 75 H HIC 73 1_555 E N GLY 76 H GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale11 F C GLU 74 I GLU 72 1_555 F N HIC 75 I HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 F C HIC 75 I HIC 73 1_555 F N GLY 76 I GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? metalc ? metalc1 M MG MG . B MG 801 1_555 N O1B ADP . B ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc2 M MG MG . B MG 801 1_555 N O3B ADP . B ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc3 O MG MG . D MG 801 1_555 P O1B ADP . D ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc4 O MG MG . D MG 801 1_555 P O3B ADP . D ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc5 Q MG MG . E MG 801 1_555 R O3B ADP . E ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc6 Q MG MG . E MG 801 1_555 R O1B ADP . E ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc7 S MG MG . F MG 801 1_555 T O3B ADP . F ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc8 S MG MG . F MG 801 1_555 T O1B ADP . F ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc9 U MG MG . H MG 801 1_555 V O1B ADP . H ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc10 U MG MG . H MG 801 1_555 V O3B ADP . H ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc11 W MG MG . I MG 801 1_555 X O2B ADP . I ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc12 W MG MG . I MG 801 1_555 X O3B ADP . I ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? # _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 ? # _atom_sites.entry_id 6WVT _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 M 3 MG B 1 801 801 MG MG . N 4 ADP B 1 802 802 ADP ADP . O 3 MG D 1 801 801 MG MG . P 4 ADP D 1 802 802 ADP ADP . Q 3 MG E 1 801 801 MG MG . R 4 ADP E 1 802 802 ADP ADP . S 3 MG F 1 801 801 MG MG . T 4 ADP F 1 802 802 ADP ADP . U 3 MG H 1 801 801 MG MG . V 4 ADP H 1 802 802 ADP ADP . W 3 MG I 1 801 801 MG MG . X 4 ADP I 1 802 802 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 P PB ADP . . . V 4 124.354 106.384 61.431 1 57.95 ? PB ADP 802 H 1 HETATM 2 O O1B ADP . . . V 4 122.972 105.843 61.186 1 57.95 ? O1B ADP 802 H 1 HETATM 3 O O2B ADP . . . V 4 125.472 105.386 61.425 1 57.95 ? O2B ADP 802 H 1 HETATM 4 O O3B ADP . . . V 4 124.462 107.378 62.553 1 57.95 ? O3B ADP 802 H 1 HETATM 5 P PA ADP . . . V 4 124.152 108.744 60.09 1 57.95 ? PA ADP 802 H 1 HETATM 6 O O1A ADP . . . V 4 125.269 109.582 60.635 1 57.95 ? O1A ADP 802 H 1 HETATM 7 O O2A ADP . . . V 4 122.792 108.793 60.706 1 57.95 ? O2A ADP 802 H 1 HETATM 8 O O3A ADP . . . V 4 124.626 107.229 60.107 1 57.95 ? O3A ADP 802 H 1 HETATM 9 O O5' ADP . . . V 4 123.955 109.035 58.536 1 57.95 ? O5' ADP 802 H 1 HETATM 10 C C5' ADP . . . V 4 123.927 110.385 58.12 1 57.95 ? C5' ADP 802 H 1 HETATM 11 C C4' ADP . . . V 4 122.492 110.873 58.132 1 57.95 ? C4' ADP 802 H 1 HETATM 12 O O4' ADP . . . V 4 122.494 112.132 58.782 1 57.95 ? O4' ADP 802 H 1 HETATM 13 C C3' ADP . . . V 4 121.961 111.073 56.734 1 57.95 ? C3' ADP 802 H 1 HETATM 14 O O3' ADP . . . V 4 120.806 110.259 56.555 1 57.95 ? O3' ADP 802 H 1 HETATM 15 C C2' ADP . . . V 4 121.552 112.519 56.658 1 57.95 ? C2' ADP 802 H 1 HETATM 16 O O2' ADP . . . V 4 120.132 112.567 56.659 1 57.95 ? O2' ADP 802 H 1 HETATM 17 C C1' ADP . . . V 4 122.01 113.166 57.939 1 57.95 ? C1' ADP 802 H 1 HETATM 18 N N9 ADP . . . V 4 123.116 114.116 57.694 1 57.95 ? N9 ADP 802 H 1 HETATM 19 C C8 ADP . . . V 4 124.421 113.821 57.604 1 57.95 ? C8 ADP 802 H 1 HETATM 20 N N7 ADP . . . V 4 125.166 114.93 57.396 1 57.95 ? N7 ADP 802 H 1 HETATM 21 C C5 ADP . . . V 4 124.323 115.97 57.36 1 57.95 ? C5 ADP 802 H 1 HETATM 22 C C6 ADP . . . V 4 124.45 117.426 57.157 1 57.95 ? C6 ADP 802 H 1 HETATM 23 N N6 ADP . . . V 4 125.652 118.018 56.963 1 57.95 ? N6 ADP 802 H 1 HETATM 24 N N1 ADP . . . V 4 123.318 118.145 57.184 1 57.95 ? N1 ADP 802 H 1 HETATM 25 C C2 ADP . . . V 4 122.127 117.559 57.376 1 57.95 ? C2 ADP 802 H 1 HETATM 26 N N3 ADP . . . V 4 121.93 116.252 57.557 1 57.95 ? N3 ADP 802 H 1 HETATM 27 C C4 ADP . . . V 4 122.979 115.421 57.55 1 57.95 ? C4 ADP 802 H 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 266 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #