data_7VAX # _model_server_result.job_id NE1EMCOekAC1xyocZfRJMQ _model_server_result.datetime_utc '2024-11-21 14:06:50' _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 7vax # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":602}' # _entry.id 7VAX # _exptl.entry_id 7VAX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 2 _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 7VAX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VAX _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 _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 ? 9 P N N ? 9 Q 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 metalc ? metalc1 A OG SER 235 A SER 235 1_555 M MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc2 M MG MG . A MG 601 1_555 N O3B ADP . A ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc3 C OG SER 235 C SER 235 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc4 O MG MG . C MG 601 1_555 P O2B AGS . C AGS 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc5 O MG MG . C MG 601 1_555 P O3B AGS . C AGS 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 PG S1G AGS doub 45 n n PG O2G AGS sing 46 n n PG O3G AGS sing 47 n n PG O3B AGS sing 48 n n PB O1B AGS doub 49 n n PB O2B AGS sing 50 n n PB O3B AGS sing 51 n n PB O3A AGS sing 52 n n PA O1A AGS doub 53 n n PA O2A AGS sing 54 n n PA O3A AGS sing 55 n n PA O5' AGS sing 56 n n O5' C5' AGS sing 57 n n C5' C4' AGS sing 58 n n C4' O4' AGS sing 59 n n C4' C3' AGS sing 60 n n O4' C1' AGS sing 61 n n C3' O3' AGS sing 62 n n C3' C2' AGS sing 63 n n C2' O2' AGS sing 64 n n C2' C1' AGS sing 65 n n C1' N9 AGS sing 66 n n N9 C8 AGS sing 67 n y N9 C4 AGS sing 68 n y C8 N7 AGS doub 69 n y N7 C5 AGS sing 70 n y C5 C6 AGS sing 71 n y C5 C4 AGS doub 72 n y C6 N6 AGS sing 73 n n C6 N1 AGS doub 74 n y N1 C2 AGS sing 75 n y C2 N3 AGS doub 76 n y N3 C4 AGS sing 77 n y O2G HOG2 AGS sing 78 n n O3G H21 AGS sing 79 n n O2B HOB2 AGS sing 80 n n O2A HOA2 AGS sing 81 n n C5' "H5'1" AGS sing 82 n n C5' "H5'2" AGS sing 83 n n C4' H4' AGS sing 84 n n C3' H3' AGS sing 85 n n O3' HO3' AGS sing 86 n n C2' H2' AGS sing 87 n n O2' HO2' AGS sing 88 n n C1' H1' AGS sing 89 n n C8 H8 AGS sing 90 n n N6 HN61 AGS sing 91 n n N6 HN62 AGS sing 92 n n C2 H2 AGS sing 93 n n # _atom_sites.entry_id 7VAX _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 7 MG A 1 601 602 MG MG . N 8 ADP A 1 602 601 ADP ADP . O 7 MG C 1 601 602 MG MG . P 9 AGS C 1 602 601 AGS AGS . Q 9 AGS D 1 601 601 AGS AGS . # 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 PG AGS . . . P 9 169.783 141.043 157.428 1 67.59 ? PG AGS 602 C 1 HETATM 2 S S1G AGS . . . P 9 170.487 140.629 159.196 1 67.59 ? S1G AGS 602 C 1 HETATM 3 O O2G AGS . . . P 9 168.253 140.764 157.396 1 67.59 ? O2G AGS 602 C 1 HETATM 4 O O3G AGS . . . P 9 170.036 142.547 157.116 1 67.59 ? O3G AGS 602 C 1 HETATM 5 P PB AGS . . . P 9 171.477 140.841 155.314 1 67.59 ? PB AGS 602 C 1 HETATM 6 O O1B AGS . . . P 9 171.214 142.292 155.216 1 67.59 ? O1B AGS 602 C 1 HETATM 7 O O2B AGS . . . P 9 172.89 140.498 155.79 1 67.59 ? O2B AGS 602 C 1 HETATM 8 O O3B AGS . . . P 9 170.488 140.168 156.349 1 67.59 ? O3B AGS 602 C 1 HETATM 9 P PA AGS . . . P 9 172.021 138.78 153.595 1 67.59 ? PA AGS 602 C 1 HETATM 10 O O1A AGS . . . P 9 171.419 137.688 154.389 1 67.59 ? O1A AGS 602 C 1 HETATM 11 O O2A AGS . . . P 9 173.516 138.988 153.849 1 67.59 ? O2A AGS 602 C 1 HETATM 12 O O3A AGS . . . P 9 171.311 140.162 153.895 1 67.59 ? O3A AGS 602 C 1 HETATM 13 O O5' AGS . . . P 9 171.719 138.498 152.069 1 67.59 ? O5' AGS 602 C 1 HETATM 14 C C5' AGS . . . P 9 170.378 138.235 151.61 1 67.59 ? C5' AGS 602 C 1 HETATM 15 C C4' AGS . . . P 9 170.455 137.396 150.361 1 67.59 ? C4' AGS 602 C 1 HETATM 16 O O4' AGS . . . P 9 171.01 138.183 149.287 1 67.59 ? O4' AGS 602 C 1 HETATM 17 C C3' AGS . . . P 9 171.357 136.173 150.461 1 67.59 ? C3' AGS 602 C 1 HETATM 18 O O3' AGS . . . P 9 170.649 135.06 150.993 1 67.59 ? O3' AGS 602 C 1 HETATM 19 C C2' AGS . . . P 9 171.761 135.944 149.004 1 67.59 ? C2' AGS 602 C 1 HETATM 20 O O2' AGS . . . P 9 170.784 135.191 148.296 1 67.59 ? O2' AGS 602 C 1 HETATM 21 C C1' AGS . . . P 9 171.832 137.376 148.463 1 67.59 ? C1' AGS 602 C 1 HETATM 22 N N9 AGS . . . P 9 173.175 137.945 148.457 1 67.59 ? N9 AGS 602 C 1 HETATM 23 C C8 AGS . . . P 9 173.665 138.915 149.29 1 67.59 ? C8 AGS 602 C 1 HETATM 24 N N7 AGS . . . P 9 174.915 139.238 149.059 1 67.59 ? N7 AGS 602 C 1 HETATM 25 C C5 AGS . . . P 9 175.272 138.42 147.999 1 67.59 ? C5 AGS 602 C 1 HETATM 26 C C6 AGS . . . P 9 176.475 138.272 147.279 1 67.59 ? C6 AGS 602 C 1 HETATM 27 N N6 AGS . . . P 9 177.581 138.975 147.53 1 67.59 ? N6 AGS 602 C 1 HETATM 28 N N1 AGS . . . P 9 176.498 137.365 146.277 1 67.59 ? N1 AGS 602 C 1 HETATM 29 C C2 AGS . . . P 9 175.392 136.66 146.022 1 67.59 ? C2 AGS 602 C 1 HETATM 30 N N3 AGS . . . P 9 174.205 136.712 146.631 1 67.59 ? N3 AGS 602 C 1 HETATM 31 C C4 AGS . . . P 9 174.212 137.617 147.616 1 67.59 ? C4 AGS 602 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 235 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #