data_6QV2 # _model_server_result.job_id 3FXKzybk3EExjyACA3QmHQ _model_server_result.datetime_utc '2024-11-08 03:53:41' _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 6qv2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":600}' # _entry.id 6QV2 # _exptl.entry_id 6QV2 _exptl.method 'X-RAY DIFFRACTION' # _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 83.18 _cell.angle_beta 73 _cell.angle_gamma 67.37 _cell.entry_id 6QV2 _cell.length_a 88.6 _cell.length_b 113.07 _cell.length_c 126.89 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QV2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,G,H,I,J 1 1 C,D,F,K,L,M,N 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 I N N ? 4 K N N ? 4 M 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 disulf ? disulf1 E SG CYS 25 E CYS 22 1_555 E SG CYS 99 E CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 E SG CYS 53 E CYS 50 1_555 E SG CYS 112 E CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 F SG CYS 25 F CYS 22 1_555 F SG CYS 99 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 F SG CYS 53 F CYS 50 1_555 F SG CYS 112 F CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc1 A OG SER 383 A SER 373 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc2 A OE1 GLN 424 A GLN 414 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc3 G O2G AGS . A AGS 600 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc4 G O2B AGS . A AGS 600 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc5 B OG1 THR 395 B THR 395 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc6 I O3G AGS . B AGS 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc7 I O2B AGS . B AGS 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc8 I O3A AGS . B AGS 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc9 C OG SER 383 C SER 373 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc10 C OE1 GLN 424 C GLN 414 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc11 K O2G AGS . C AGS 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc12 K O2B AGS . C AGS 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc13 D OG1 THR 395 D THR 395 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc14 M O1B AGS . D AGS 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc15 M O2B AGS . D AGS 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc16 M O1A AGS . D AGS 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc17 M O3A AGS . D AGS 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? # _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 6QV2 _atom_sites.fract_transf_matrix[1][1] 0.011287 _atom_sites.fract_transf_matrix[1][2] -0.004705 _atom_sites.fract_transf_matrix[1][3] -0.003417 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009582 _atom_sites.fract_transf_matrix[2][3] -0.000068 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008241 _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 G 4 AGS A 1 600 600 AGS AGS . H 5 MG A 1 601 601 MG MG . I 4 AGS B 1 600 600 AGS AGS . J 5 MG B 1 601 601 MG MG . K 4 AGS C 1 600 600 AGS AGS . L 5 MG C 1 601 601 MG MG . M 4 AGS D 1 600 600 AGS AGS . N 5 MG D 1 601 601 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 PG AGS . . . I 4 72.959 64.642 48.748 1 78.42 ? PG AGS 600 B 1 HETATM 2 S S1G AGS . . . I 4 72.396 66.365 48.18 1 82.09 ? S1G AGS 600 B 1 HETATM 3 O O2G AGS . . . I 4 72.759 63.505 47.686 1 79.04 ? O2G AGS 600 B 1 HETATM 4 O O3G AGS . . . I 4 72.287 63.935 49.967 1 74.96 ? O3G AGS 600 B 1 HETATM 5 P PB AGS . . . I 4 75.32 65.108 50.355 1 75.95 ? PB AGS 600 B 1 HETATM 6 O O1B AGS . . . I 4 76.654 65.645 50.01 1 77.34 ? O1B AGS 600 B 1 HETATM 7 O O2B AGS . . . I 4 74.421 66.029 51.173 1 76.28 ? O2B AGS 600 B 1 HETATM 8 O O3B AGS . . . I 4 74.498 64.691 49.057 1 77.51 ? O3B AGS 600 B 1 HETATM 9 P PA AGS . . . I 4 76.653 62.871 51.675 1 60.8 ? PA AGS 600 B 1 HETATM 10 O O1A AGS . . . I 4 77.636 63.748 52.347 1 63.93 ? O1A AGS 600 B 1 HETATM 11 O O2A AGS . . . I 4 76.078 61.788 52.578 1 15.89 ? O2A AGS 600 B 1 HETATM 12 O O3A AGS . . . I 4 75.421 63.724 51.137 1 72.05 ? O3A AGS 600 B 1 HETATM 13 O O5' AGS . . . I 4 77.244 62.105 50.387 1 55.61 ? O5' AGS 600 B 1 HETATM 14 C C5' AGS . . . I 4 78.525 62.402 49.794 1 70.37 ? C5' AGS 600 B 1 HETATM 15 C C4' AGS . . . I 4 79.289 61.124 49.551 1 63.99 ? C4' AGS 600 B 1 HETATM 16 O O4' AGS . . . I 4 79.223 60.267 50.712 1 26.13 ? O4' AGS 600 B 1 HETATM 17 C C3' AGS . . . I 4 78.847 60.284 48.345 1 66.59 ? C3' AGS 600 B 1 HETATM 18 O O3' AGS . . . I 4 79.94 60.061 47.461 1 73.01 ? O3' AGS 600 B 1 HETATM 19 C C2' AGS . . . I 4 78.311 58.991 48.977 1 26.31 ? C2' AGS 600 B 1 HETATM 20 O O2' AGS . . . I 4 78.575 57.834 48.191 1 25.24 ? O2' AGS 600 B 1 HETATM 21 C C1' AGS . . . I 4 79.104 58.929 50.278 1 14.16 ? C1' AGS 600 B 1 HETATM 22 N N9 AGS . . . I 4 78.466 58.14 51.331 1 9.19 ? N9 AGS 600 B 1 HETATM 23 C C8 AGS . . . I 4 77.544 58.57 52.251 1 7.35 ? C8 AGS 600 B 1 HETATM 24 N N7 AGS . . . I 4 77.12 57.633 53.063 1 5.79 ? N7 AGS 600 B 1 HETATM 25 C C5 AGS . . . I 4 77.807 56.502 52.648 1 5.19 ? C5 AGS 600 B 1 HETATM 26 C C6 AGS . . . I 4 77.803 55.166 53.1 1 4.4 ? C6 AGS 600 B 1 HETATM 27 N N6 AGS . . . I 4 77.055 54.728 54.12 1 4.19 ? N6 AGS 600 B 1 HETATM 28 N N1 AGS . . . I 4 78.607 54.283 52.462 1 4.12 ? N1 AGS 600 B 1 HETATM 29 C C2 AGS . . . I 4 79.361 54.716 51.444 1 5.01 ? C2 AGS 600 B 1 HETATM 30 N N3 AGS . . . I 4 79.449 55.948 50.933 1 7.54 ? N3 AGS 600 B 1 HETATM 31 C C4 AGS . . . I 4 78.643 56.801 51.582 1 6.49 ? C4 AGS 600 B 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #