data_3KFK # _model_server_result.job_id k01puifVklGWl7UO_Rg5jg _model_server_result.datetime_utc '2025-03-06 08:38:54' _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 3kfk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":544}' # _entry.id 3KFK # _exptl.entry_id 3KFK _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 3KFK _cell.length_a 150.533 _cell.length_b 209.527 _cell.length_c 266.862 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KFK _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -209.527 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_545 x,-y-1,-z 1 0 0 0 -1 0 0 0 -1 0 -209.527 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H 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 A SG CYS 448 A CYS 470 1_555 A SG CYS 462 A CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? disulf ? disulf2 B SG CYS 448 B CYS 470 1_555 B SG CYS 462 B CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? disulf ? disulf3 C SG CYS 448 C CYS 470 1_555 C SG CYS 462 C CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? disulf ? disulf4 D SG CYS 448 D CYS 470 1_555 D SG CYS 462 D CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? # _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 3KFK _atom_sites.fract_transf_matrix[1][1] 0.006643 _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] 0.004773 _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] 0.003747 _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 2 AGS A 1 544 544 AGS AGS . F 2 AGS B 1 544 544 AGS AGS . G 2 AGS C 1 544 544 AGS AGS . H 2 AGS D 1 544 544 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 . . . E 2 -27.752 -57.624 -25.921 1 475.08 ? PG AGS 544 A 1 HETATM 2 S S1G AGS . . . E 2 -26.453 -58.317 -25.682 1 549.51 ? S1G AGS 544 A 1 HETATM 3 O O2G AGS . . . E 2 -28.57 -58.093 -27.071 1 349.08 ? O2G AGS 544 A 1 HETATM 4 O O3G AGS . . . E 2 -27.501 -56.159 -26.016 1 455.96 ? O3G AGS 544 A 1 HETATM 5 P PB AGS . . . E 2 -29.293 -56.796 -23.6 1 399.84 ? PB AGS 544 A 1 HETATM 6 O O1B AGS . . . E 2 -29.667 -55.544 -24.296 1 350.97 ? O1B AGS 544 A 1 HETATM 7 O O2B AGS . . . E 2 -30.262 -57.452 -22.706 1 319.72 ? O2B AGS 544 A 1 HETATM 8 O O3B AGS . . . E 2 -28.803 -57.875 -24.707 1 358.73 ? O3B AGS 544 A 1 HETATM 9 P PA AGS . . . E 2 -27.032 -55.262 -22.383 1 549.51 ? PA AGS 544 A 1 HETATM 10 O O1A AGS . . . E 2 -25.831 -55.726 -21.679 1 549.51 ? O1A AGS 544 A 1 HETATM 11 O O2A AGS . . . E 2 -26.851 -54.468 -23.611 1 549.51 ? O2A AGS 544 A 1 HETATM 12 O O3A AGS . . . E 2 -27.97 -56.56 -22.672 1 549.51 ? O3A AGS 544 A 1 HETATM 13 O O5' AGS . . . E 2 -27.867 -54.432 -21.3 1 437.71 ? O5' AGS 544 A 1 HETATM 14 C C5' AGS . . . E 2 -29.117 -53.807 -21.578 1 376.55 ? C5' AGS 544 A 1 HETATM 15 C C4' AGS . . . E 2 -29.853 -53.483 -20.291 1 260.41 ? C4' AGS 544 A 1 HETATM 16 O O4' AGS . . . E 2 -29.182 -52.388 -19.624 1 273.65 ? O4' AGS 544 A 1 HETATM 17 C C3' AGS . . . E 2 -31.278 -53.048 -20.529 1 282.06 ? C3' AGS 544 A 1 HETATM 18 O O3' AGS . . . E 2 -32.092 -53.709 -19.543 1 319.72 ? O3' AGS 544 A 1 HETATM 19 C C2' AGS . . . E 2 -31.178 -51.518 -20.43 1 384.86 ? C2' AGS 544 A 1 HETATM 20 O O2' AGS . . . E 2 -32.42 -50.884 -20.077 1 406.87 ? O2' AGS 544 A 1 HETATM 21 C C1' AGS . . . E 2 -30.083 -51.28 -19.414 1 407.9 ? C1' AGS 544 A 1 HETATM 22 N N9 AGS . . . E 2 -29.348 -49.997 -19.647 1 502.55 ? N9 AGS 544 A 1 HETATM 23 C C8 AGS . . . E 2 -28.809 -49.458 -20.809 1 517.64 ? C8 AGS 544 A 1 HETATM 24 N N7 AGS . . . E 2 -28.223 -48.299 -20.649 1 512.92 ? N7 AGS 544 A 1 HETATM 25 C C5 AGS . . . E 2 -28.371 -48.033 -19.288 1 496.98 ? C5 AGS 544 A 1 HETATM 26 C C6 AGS . . . E 2 -27.972 -46.946 -18.425 1 438.86 ? C6 AGS 544 A 1 HETATM 27 N N6 AGS . . . E 2 -27.305 -45.863 -18.831 1 341.71 ? N6 AGS 544 A 1 HETATM 28 N N1 AGS . . . E 2 -28.294 -47.02 -17.09 1 467.56 ? N1 AGS 544 A 1 HETATM 29 C C2 AGS . . . E 2 -28.965 -48.089 -16.622 1 485.16 ? C2 AGS 544 A 1 HETATM 30 N N3 AGS . . . E 2 -29.392 -49.164 -17.332 1 519.1 ? N3 AGS 544 A 1 HETATM 31 C C4 AGS . . . E 2 -29.058 -49.067 -18.669 1 520.96 ? C4 AGS 544 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #