data_6NYB # _model_server_result.job_id lLsdkAbncAJ_bZKJblh7ew _model_server_result.datetime_utc '2024-11-26 08:27:44' _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 6nyb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 6NYB # _exptl.entry_id 6NYB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 6NYB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NYB _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 covale ? covale1 A C SER 391 A SER 364 1_555 A N SEP 392 A SEP 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 A C SEP 392 A SEP 365 1_555 A N ALA 393 A ALA 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale3 A C ALA 755 A ALA 728 1_555 A N SEP 756 A SEP 729 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale4 A C SEP 756 A SEP 729 1_555 A N GLU 757 A GLU 730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? metalc ? metalc1 A NE2 HIS 262 A HIS 235 1_555 G ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc2 A SG CYS 275 A CYS 248 1_555 F ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc3 A SG CYS 278 A CYS 251 1_555 F ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc4 A SG CYS 288 A CYS 261 1_555 G ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? metalc ? metalc5 A SG CYS 291 A CYS 264 1_555 G ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc6 B OD1 ASN 217 B ASN 195 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc7 B OD2 ASP 230 B ASP 208 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc8 H O2B ADP . B ADP 601 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc9 H O1A ADP . B ADP 601 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? # _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 6NYB _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 E 4 AGS A 1 801 801 AGS AGS . F 5 ZN A 1 901 901 ZN ZN . G 5 ZN A 1 902 902 ZN ZN . H 6 ADP B 1 601 601 ADP ADP . I 7 MG B 1 602 602 MG MG . J 8 LCJ B 1 901 901 LCJ GDC . # 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 . . . E 4 106.087 117.227 124.935 1 92.79 ? PG AGS 801 A 1 HETATM 2 S S1G AGS . . . E 4 104.435 116.117 124.35 1 92.79 ? S1G AGS 801 A 1 HETATM 3 O O2G AGS . . . E 4 107.256 117.08 123.838 1 92.79 ? O2G AGS 801 A 1 HETATM 4 O O3G AGS . . . E 4 106.571 116.73 126.242 1 92.79 ? O3G AGS 801 A 1 HETATM 5 P PB AGS . . . E 4 105.377 119.704 123.806 1 92.79 ? PB AGS 801 A 1 HETATM 6 O O1B AGS . . . E 4 106.38 119.387 122.725 1 92.79 ? O1B AGS 801 A 1 HETATM 7 O O2B AGS . . . E 4 103.9 119.635 123.5 1 92.79 ? O2B AGS 801 A 1 HETATM 8 O O3B AGS . . . E 4 105.67 118.773 125.087 1 92.79 ? O3B AGS 801 A 1 HETATM 9 P PA AGS . . . E 4 107.073 121.464 125.174 1 92.79 ? PA AGS 801 A 1 HETATM 10 O O1A AGS . . . E 4 108.205 120.803 124.423 1 92.79 ? O1A AGS 801 A 1 HETATM 11 O O2A AGS . . . E 4 106.847 121.114 126.625 1 92.79 ? O2A AGS 801 A 1 HETATM 12 O O3A AGS . . . E 4 105.703 121.173 124.378 1 92.79 ? O3A AGS 801 A 1 HETATM 13 O O5' AGS . . . E 4 107.261 123.063 125.076 1 92.79 ? O5' AGS 801 A 1 HETATM 14 C C5' AGS . . . E 4 106.439 123.897 124.256 1 92.79 ? C5' AGS 801 A 1 HETATM 15 C C4' AGS . . . E 4 107.255 125.065 123.702 1 92.79 ? C4' AGS 801 A 1 HETATM 16 O O4' AGS . . . E 4 108.579 125.056 124.247 1 92.79 ? O4' AGS 801 A 1 HETATM 17 C C3' AGS . . . E 4 107.395 125.037 122.183 1 92.79 ? C3' AGS 801 A 1 HETATM 18 O O3' AGS . . . E 4 106.605 126.074 121.588 1 92.79 ? O3' AGS 801 A 1 HETATM 19 C C2' AGS . . . E 4 108.873 125.224 121.886 1 92.79 ? C2' AGS 801 A 1 HETATM 20 O O2' AGS . . . E 4 109.112 126.404 121.11 1 92.79 ? O2' AGS 801 A 1 HETATM 21 C C1' AGS . . . E 4 109.559 125.326 123.239 1 92.79 ? C1' AGS 801 A 1 HETATM 22 N N9 AGS . . . E 4 110.694 124.381 123.354 1 92.79 ? N9 AGS 801 A 1 HETATM 23 C C8 AGS . . . E 4 110.662 123.133 123.854 1 92.79 ? C8 AGS 801 A 1 HETATM 24 N N7 AGS . . . E 4 111.893 122.561 123.81 1 92.79 ? N7 AGS 801 A 1 HETATM 25 C C5 AGS . . . E 4 112.736 123.458 123.269 1 92.79 ? C5 AGS 801 A 1 HETATM 26 C C6 AGS . . . E 4 114.177 123.512 122.927 1 92.79 ? C6 AGS 801 A 1 HETATM 27 N N6 AGS . . . E 4 114.991 122.455 123.165 1 92.79 ? N6 AGS 801 A 1 HETATM 28 N N1 AGS . . . E 4 114.644 124.658 122.373 1 92.79 ? N1 AGS 801 A 1 HETATM 29 C C2 AGS . . . E 4 113.843 125.72 122.131 1 92.79 ? C2 AGS 801 A 1 HETATM 30 N N3 AGS . . . E 4 112.532 125.732 122.417 1 92.79 ? N3 AGS 801 A 1 HETATM 31 C C4 AGS . . . E 4 111.936 124.655 122.975 1 92.79 ? C4 AGS 801 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #