data_4I81 # _model_server_result.job_id dp53hnSHr1x8arD-16HGvA _model_server_result.datetime_utc '2025-07-08 18:06:46' _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 4i81 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":601}' # _entry.id 4I81 # _exptl.entry_id 4I81 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 2 _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 4I81 _cell.length_a 57.935 _cell.length_b 199.167 _cell.length_c 211.891 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4I81 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,H,I,J,K,L _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 H N N ? 2 J N N ? 2 K N N # _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 4I81 _atom_sites.fract_transf_matrix[1][1] 0.017261 _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] 0.005021 _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] 0.004719 _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 2 AGS A 1 600 600 AGS AGS . H 2 AGS B 1 601 601 AGS AGS . I 3 SO4 C 1 500 500 SO4 SO4 . J 2 AGS D 1 501 602 AGS AGS . K 2 AGS E 1 501 603 AGS AGS . L 3 SO4 F 1 501 501 SO4 SO4 . # 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 . . . H 2 32.96 -43.294 -48.153 1 246.91 ? PG AGS 601 B 1 HETATM 2 S S1G AGS . . . H 2 33.945 -41.789 -47.118 1 247.38 ? S1G AGS 601 B 1 HETATM 3 O O2G AGS . . . H 2 32.585 -44.486 -47.138 1 242.34 ? O2G AGS 601 B 1 HETATM 4 O O3G AGS . . . H 2 31.723 -42.75 -48.755 1 247.59 ? O3G AGS 601 B 1 HETATM 5 P PB AGS . . . H 2 34.021 -45.444 -49.591 1 252.99 ? PB AGS 601 B 1 HETATM 6 O O1B AGS . . . H 2 34.86 -46.06 -48.497 1 248.76 ? O1B AGS 601 B 1 HETATM 7 O O2B AGS . . . H 2 32.631 -45.968 -49.859 1 251.8 ? O2B AGS 601 B 1 HETATM 8 O O3B AGS . . . H 2 33.919 -43.861 -49.316 1 252.24 ? O3B AGS 601 B 1 HETATM 9 P PA AGS . . . H 2 34.108 -45.756 -52.368 1 267.5 ? PA AGS 601 B 1 HETATM 10 O O1A AGS . . . H 2 33.089 -44.658 -52.559 1 265.62 ? O1A AGS 601 B 1 HETATM 11 O O2A AGS . . . H 2 33.676 -47.202 -52.424 1 266.84 ? O2A AGS 601 B 1 HETATM 12 O O3A AGS . . . H 2 34.858 -45.509 -50.965 1 260.83 ? O3A AGS 601 B 1 HETATM 13 O O5' AGS . . . H 2 35.288 -45.541 -53.441 1 276.74 ? O5' AGS 601 B 1 HETATM 14 C C5' AGS . . . H 2 36.435 -46.389 -53.435 1 280.77 ? C5' AGS 601 B 1 HETATM 15 C C4' AGS . . . H 2 36.436 -47.248 -54.693 1 287.38 ? C4' AGS 601 B 1 HETATM 16 O O4' AGS . . . H 2 37.248 -48.408 -54.485 1 285.44 ? O4' AGS 601 B 1 HETATM 17 C C3' AGS . . . H 2 35.033 -47.719 -55.041 1 279 ? C3' AGS 601 B 1 HETATM 18 O O3' AGS . . . H 2 34.669 -47.253 -56.343 1 283.08 ? O3' AGS 601 B 1 HETATM 19 C C2' AGS . . . H 2 35.077 -49.234 -55.026 1 270.62 ? C2' AGS 601 B 1 HETATM 20 O O2' AGS . . . H 2 34.738 -49.747 -56.317 1 269.66 ? O2' AGS 601 B 1 HETATM 21 C C1' AGS . . . H 2 36.505 -49.616 -54.671 1 272.89 ? C1' AGS 601 B 1 HETATM 22 N N9 AGS . . . H 2 36.515 -50.407 -53.415 1 267.15 ? N9 AGS 601 B 1 HETATM 23 C C8 AGS . . . H 2 36.496 -49.903 -52.167 1 266.22 ? C8 AGS 601 B 1 HETATM 24 N N7 AGS . . . H 2 36.511 -50.894 -51.238 1 260.72 ? N7 AGS 601 B 1 HETATM 25 C C5 AGS . . . H 2 36.541 -52.066 -51.899 1 258.82 ? C5 AGS 601 B 1 HETATM 26 C C6 AGS . . . H 2 36.571 -53.501 -51.528 1 254.99 ? C6 AGS 601 B 1 HETATM 27 N N6 AGS . . . H 2 36.571 -53.889 -50.229 1 251.71 ? N6 AGS 601 B 1 HETATM 28 N N1 AGS . . . H 2 36.597 -54.408 -52.528 1 255.2 ? N1 AGS 601 B 1 HETATM 29 C C2 AGS . . . H 2 36.597 -54.036 -53.822 1 258.69 ? C2 AGS 601 B 1 HETATM 30 N N3 AGS . . . H 2 36.571 -52.755 -54.23 1 262.23 ? N3 AGS 601 B 1 HETATM 31 C C4 AGS . . . H 2 36.543 -51.74 -53.333 1 262.49 ? C4 AGS 601 B 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #