data_7E21 # _model_server_result.job_id XHwBXATgehKBk0QQcc2SYw _model_server_result.datetime_utc '2024-12-21 14:51:36' _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 7e21 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1106}' # _entry.id 7E21 # _exptl.entry_id 7E21 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 7 _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 7E21 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7E21 _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 7 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 D 1 NAG B 401 NAG 4 n D NAG 2 D 2 NAG B 402 NAG # 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 A SG CYS 211 A CYS 211 1_555 A SG CYS 249 A CYS 249 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf2 A SG CYS 518 A CYS 518 1_555 A SG CYS 556 A CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 B SG CYS 126 B CYS 126 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 B SG CYS 159 B CYS 159 1_555 B SG CYS 175 B CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? disulf ? disulf5 B SG CYS 213 B CYS 213 1_555 B SG CYS 276 B CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 B ND2 ASN 158 B ASN 158 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 B ND2 ASN 265 B ASN 265 1_555 R C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? metalc ? metalc1 A O VAL 329 A VAL 329 1_555 F NA NA . A NA 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc2 A O ALA 330 A ALA 330 1_555 E NA NA . A NA 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc3 A O ALA 728 A ALA 728 1_555 H NA NA . A NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.181 ? metalc ? metalc4 A OD2 ASP 747 A ASP 747 1_555 H NA NA . A NA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc5 A O TYR 778 A TYR 778 1_555 G NA NA . A NA 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc6 A OG1 THR 781 A THR 781 1_555 G NA NA . A NA 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc7 A OG SER 782 A SER 782 1_555 G NA NA . A NA 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.025 ? metalc ? metalc8 A OD1 ASN 783 A ASN 783 1_555 E NA NA . A NA 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc9 A OE1 GLU 786 A GLU 786 1_555 E NA NA . A NA 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? metalc ? metalc10 A OE1 GLN 930 A GLN 930 1_555 G NA NA . A NA 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? metalc ? metalc11 E NA NA . A NA 1101 1_555 T O HOH . A HOH 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? # _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 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 7E21 _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 5 NA A 1 1101 1101 NA NA . F 5 NA A 1 1102 1102 NA NA . G 5 NA A 1 1103 1103 NA NA . H 5 NA A 1 1104 1104 NA NA . I 6 MG A 1 1105 1301 MG MG . J 7 AGS A 1 1106 1401 AGS LIG . K 8 Y01 A 1 1107 1502 Y01 LIG . L 8 Y01 A 1 1108 1503 Y01 LIG . M 8 Y01 A 1 1109 1504 Y01 LIG . N 8 Y01 A 1 1110 1506 Y01 LIG . O 9 PC1 A 1 1111 1602 PC1 LIG . P 8 Y01 B 1 401 1505 Y01 LIG . Q 9 PC1 B 1 402 1601 PC1 LIG . R 10 NAG B 1 403 403 NAG NAG . S 8 Y01 C 1 1501 1501 Y01 LIG . T 11 HOH A 1 1201 1203 HOH HOH . T 11 HOH A 2 1202 1201 HOH HOH . T 11 HOH A 3 1203 1205 HOH HOH . T 11 HOH A 4 1204 1204 HOH HOH . T 11 HOH A 5 1205 1202 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 PG AGS . . . J 7 114.83 116.167 49.571 1 102.04 ? PG AGS 1106 A 1 HETATM 2 S S1G AGS . . . J 7 115.447 114.393 49.225 1 102.04 ? S1G AGS 1106 A 1 HETATM 3 O O2G AGS . . . J 7 116.154 117.188 49.726 1 102.04 ? O2G AGS 1106 A 1 HETATM 4 O O3G AGS . . . J 7 113.966 116.182 50.976 1 102.04 ? O3G AGS 1106 A 1 HETATM 5 P PB AGS . . . J 7 114.013 116.221 46.767 1 102.04 ? PB AGS 1106 A 1 HETATM 6 O O1B AGS . . . J 7 112.671 116.432 46.067 1 102.04 ? O1B AGS 1106 A 1 HETATM 7 O O2B AGS . . . J 7 114.373 114.782 46.684 1 102.04 ? O2B AGS 1106 A 1 HETATM 8 O O3B AGS . . . J 7 113.873 116.683 48.359 1 102.04 ? O3B AGS 1106 A 1 HETATM 9 P PA AGS . . . J 7 116.656 116.583 45.617 1 102.04 ? PA AGS 1106 A 1 HETATM 10 O O1A AGS . . . J 7 116.73 115.099 45.761 1 102.04 ? O1A AGS 1106 A 1 HETATM 11 O O2A AGS . . . J 7 117.67 117.229 46.527 1 102.04 ? O2A AGS 1106 A 1 HETATM 12 O O3A AGS . . . J 7 115.146 117.12 46.024 1 102.04 ? O3A AGS 1106 A 1 HETATM 13 O O5' AGS . . . J 7 116.965 116.985 44.094 1 102.04 ? O5' AGS 1106 A 1 HETATM 14 C C5' AGS . . . J 7 116.641 118.335 43.645 1 102.04 ? C5' AGS 1106 A 1 HETATM 15 C C4' AGS . . . J 7 115.427 118.31 42.625 1 102.04 ? C4' AGS 1106 A 1 HETATM 16 O O4' AGS . . . J 7 115.889 117.846 41.202 1 102.04 ? O4' AGS 1106 A 1 HETATM 17 C C3' AGS . . . J 7 114.551 117.44 42.964 1 102.04 ? C3' AGS 1106 A 1 HETATM 18 O O3' AGS . . . J 7 113.615 118.023 43.895 1 102.04 ? O3' AGS 1106 A 1 HETATM 19 C C2' AGS . . . J 7 113.799 117.07 41.562 1 102.04 ? C2' AGS 1106 A 1 HETATM 20 O O2' AGS . . . J 7 112.925 118.17 41.155 1 102.04 ? O2' AGS 1106 A 1 HETATM 21 C C1' AGS . . . J 7 114.769 116.925 40.698 1 102.04 ? C1' AGS 1106 A 1 HETATM 22 N N9 AGS . . . J 7 115.245 115.51 40.664 1 102.04 ? N9 AGS 1106 A 1 HETATM 23 C C8 AGS . . . J 7 115.316 114.661 41.706 1 102.04 ? C8 AGS 1106 A 1 HETATM 24 N N7 AGS . . . J 7 115.8 113.482 41.254 1 102.04 ? N7 AGS 1106 A 1 HETATM 25 C C5 AGS . . . J 7 116.028 113.604 39.957 1 102.04 ? C5 AGS 1106 A 1 HETATM 26 C C6 AGS . . . J 7 116.568 112.621 38.925 1 102.04 ? C6 AGS 1106 A 1 HETATM 27 N N6 AGS . . . J 7 116.928 111.296 39.319 1 102.04 ? N6 AGS 1106 A 1 HETATM 28 N N1 AGS . . . J 7 116.713 113.024 37.569 1 102.04 ? N1 AGS 1106 A 1 HETATM 29 C C2 AGS . . . J 7 116.352 114.349 37.177 1 102.04 ? C2 AGS 1106 A 1 HETATM 30 N N3 AGS . . . J 7 115.835 115.287 38.173 1 102.04 ? N3 AGS 1106 A 1 HETATM 31 C C4 AGS . . . J 7 115.685 114.863 39.585 1 102.04 ? C4 AGS 1106 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #