data_6RAK # _model_server_result.job_id izWV_R_lNEHJifIgtYa1YA _model_server_result.datetime_utc '2025-02-05 10:54:31' _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 6rak # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":701}' # _entry.id 6RAK # _exptl.entry_id 6RAK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 544.156 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADP ORTHOVANADATE' _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 6RAK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RAK _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 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 _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 C SG CYS 24 C CYS 22 1_555 C SG CYS 98 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 C SG CYS 52 C CYS 50 1_555 C SG CYS 110 C CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc1 A OG1 THR 400 A THR 400 1_555 E MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc2 A OE1 GLN 441 A GLN 441 1_555 E MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc3 D O2B AOV . A AOV 701 1_555 E MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc4 D O3G AOV . A AOV 701 1_555 E MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc5 B OG SER 378 B SER 378 1_555 G MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc6 B OE1 GLN 419 B GLN 419 1_555 G MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc7 F O2G ATP . B ATP 601 1_555 G MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc8 F O3B ATP . B ATP 601 1_555 G MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? # _chem_comp.formula 'C10 H17 N5 O14 P2 V' _chem_comp.formula_weight 544.156 _chem_comp.id AOV _chem_comp.mon_nstd_flag . _chem_comp.name 'ADP ORTHOVANADATE' _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 AOV doub 13 n n PB O2B AOV sing 14 n n PB O3B AOV sing 15 n n PB O3A AOV sing 16 n n O3B VG AOV sing 17 n n PA O1A AOV doub 18 n n PA O2A AOV sing 19 n n PA O3A AOV sing 20 n n PA O5' AOV sing 21 n n O5' C5' AOV sing 22 n n C5' C4' AOV sing 23 n n C4' O4' AOV sing 24 n n C4' C3' AOV sing 25 n n O4' C1' AOV sing 26 n n C3' O3' AOV sing 27 n n C3' C2' AOV sing 28 n n C2' O2' AOV sing 29 n n C2' C1' AOV sing 30 n n C1' N9 AOV sing 31 n n N9 C8 AOV sing 32 n y N9 C4 AOV sing 33 n y C8 N7 AOV doub 34 n y N7 C5 AOV sing 35 n y C5 C6 AOV sing 36 n y C5 C4 AOV doub 37 n y C6 N6 AOV sing 38 n n C6 N1 AOV doub 39 n y N1 C2 AOV sing 40 n y C2 N3 AOV doub 41 n y N3 C4 AOV sing 42 n y VG O1G AOV doub 43 n n VG O2G AOV sing 44 n n VG O3G AOV sing 45 n n VG O4G AOV sing 46 n n O2B H2B AOV sing 47 n n O2A H2A AOV sing 48 n n C5' "H5'1" AOV sing 49 n n C5' "H5'2" AOV sing 50 n n C4' H4' AOV sing 51 n n C3' H3' AOV sing 52 n n C1' H1' AOV sing 53 n n O3' HA AOV sing 54 n n C2' H2' AOV sing 55 n n O2' HB AOV sing 56 n n C8 H8 AOV sing 57 n n N6 H61N AOV sing 58 n n N6 H62N AOV sing 59 n n C2 H2 AOV sing 60 n n O2G H2G1 AOV sing 61 n n O3G H3G1 AOV sing 62 n n O4G H4G1 AOV sing 63 n n # _atom_sites.entry_id 6RAK _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 D 4 AOV A 1 701 1 AOV AOV . E 5 MG A 1 702 1 MG MG . F 6 ATP B 1 601 1 ATP ATP . G 5 MG B 1 602 2 MG MG . # 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 AOV . . . D 4 128.124 132.282 96.93 1 38.34 ? PB AOV 701 A 1 HETATM 2 O O1B AOV . . . D 4 127.439 131.617 95.806 1 38.34 ? O1B AOV 701 A 1 HETATM 3 O O2B AOV . . . D 4 128.593 131.189 98.011 1 38.34 ? O2B AOV 701 A 1 HETATM 4 O O3B AOV . . . D 4 129.398 133.093 96.375 1 38.34 ? O3B AOV 701 A 1 HETATM 5 P PA AOV . . . D 4 126.303 133.371 99.005 1 38.34 ? PA AOV 701 A 1 HETATM 6 O O1A AOV . . . D 4 127.171 132.906 100.103 1 38.34 ? O1A AOV 701 A 1 HETATM 7 O O2A AOV . . . D 4 124.998 132.445 98.909 1 38.34 ? O2A AOV 701 A 1 HETATM 8 O O3A AOV . . . D 4 127.106 133.319 97.617 1 38.34 ? O3A AOV 701 A 1 HETATM 9 O O5' AOV . . . D 4 125.833 134.876 99.291 1 38.34 ? O5' AOV 701 A 1 HETATM 10 C C5' AOV . . . D 4 125.082 135.636 98.346 1 38.34 ? C5' AOV 701 A 1 HETATM 11 C C4' AOV . . . D 4 124.75 136.991 98.964 1 38.34 ? C4' AOV 701 A 1 HETATM 12 O O4' AOV . . . D 4 124.312 136.779 100.312 1 38.34 ? O4' AOV 701 A 1 HETATM 13 C C3' AOV . . . D 4 126.004 137.872 99.002 1 38.34 ? C3' AOV 701 A 1 HETATM 14 O O3' AOV . . . D 4 125.701 139.167 98.49 1 38.34 ? O3' AOV 701 A 1 HETATM 15 C C2' AOV . . . D 4 126.37 137.971 100.495 1 38.34 ? C2' AOV 701 A 1 HETATM 16 O O2' AOV . . . D 4 126.745 139.31 100.806 1 38.34 ? O2' AOV 701 A 1 HETATM 17 C C1' AOV . . . D 4 125.054 137.613 101.221 1 38.34 ? C1' AOV 701 A 1 HETATM 18 N N9 AOV . . . D 4 125.344 136.826 102.414 1 38.34 ? N9 AOV 701 A 1 HETATM 19 C C8 AOV . . . D 4 125.895 135.583 102.427 1 38.34 ? C8 AOV 701 A 1 HETATM 20 N N7 AOV . . . D 4 126.012 135.161 103.65 1 38.34 ? N7 AOV 701 A 1 HETATM 21 C C5 AOV . . . D 4 125.541 136.105 104.492 1 38.34 ? C5 AOV 701 A 1 HETATM 22 C C6 AOV . . . D 4 125.414 136.207 105.886 1 38.34 ? C6 AOV 701 A 1 HETATM 23 N N6 AOV . . . D 4 125.828 135.174 106.707 1 38.34 ? N6 AOV 701 A 1 HETATM 24 N N1 AOV . . . D 4 124.89 137.315 106.395 1 38.34 ? N1 AOV 701 A 1 HETATM 25 C C2 AOV . . . D 4 124.493 138.308 105.62 1 38.34 ? C2 AOV 701 A 1 HETATM 26 N N3 AOV . . . D 4 124.593 138.255 104.31 1 38.34 ? N3 AOV 701 A 1 HETATM 27 C C4 AOV . . . D 4 125.104 137.186 103.712 1 38.34 ? C4 AOV 701 A 1 HETATM 28 V VG AOV . . . D 4 130.895 132.105 95.972 1 38.34 ? VG AOV 701 A 1 HETATM 29 O O1G AOV . . . D 4 131.705 133.444 95.775 1 38.34 ? O1G AOV 701 A 1 HETATM 30 O O2G AOV . . . D 4 130.039 131.346 94.538 1 38.34 ? O2G AOV 701 A 1 HETATM 31 O O3G AOV . . . D 4 130.84 131.3 97.619 1 38.34 ? O3G AOV 701 A 1 HETATM 32 O O4G AOV . . . D 4 132.402 131.137 95.566 1 38.34 ? O4G AOV 701 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #