data_5GRB # _model_server_result.job_id -oJVkYS9_c5JAMpqX3p-eg _model_server_result.datetime_utc '2025-03-04 07:50:57' _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 5grb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 5GRB # _exptl.entry_id 5GRB _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 89.98 _cell.angle_gamma 90 _cell.entry_id 5GRB _cell.length_a 73.668 _cell.length_b 54.912 _cell.length_c 163.097 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GRB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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 ? tetrameric 4 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,H,K,L,O,P,Q,R,S,U 1 1 B,I,J,T 2 1 D,M,N,V 3 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 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q 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 metalc ? metalc1 A SG CYS 155 A CYS 270 1_555 H ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc2 A SG CYS 166 A CYS 281 1_555 H ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc3 A SG CYS 171 A CYS 286 1_555 H ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc4 H ZN ZN . A ZN 402 1_555 S O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc5 B SG CYS 155 B CYS 270 1_555 J ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc6 B SG CYS 166 B CYS 281 1_555 J ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc7 B SG CYS 171 B CYS 286 1_555 J ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc8 C SG CYS 155 C CYS 270 1_555 L ZN ZN . C ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc9 C SG CYS 166 C CYS 281 1_555 L ZN ZN . C ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc10 D SG CYS 155 D CYS 270 1_555 N ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc11 D SG CYS 166 D CYS 281 1_555 N ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc12 D SG CYS 171 D CYS 286 1_555 N ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc13 E SG CYS 155 E CYS 270 1_555 P ZN ZN . E ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc14 E SG CYS 166 E CYS 281 1_555 P ZN ZN . E ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc15 E SG CYS 171 E CYS 286 1_555 P ZN ZN . E ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc16 F SG CYS 155 F CYS 270 1_555 R ZN ZN . F ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc17 F SG CYS 166 F CYS 281 1_555 R ZN ZN . F ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc18 F SG CYS 171 F CYS 286 1_555 R ZN ZN . F ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? # _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 5GRB _atom_sites.fract_transf_matrix[1][1] 0.013574 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] -0.000005 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018211 _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] 0.006131 _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 1 401 10 AGS AGS . H 3 ZN A 1 402 2 ZN ZN . I 2 AGS B 1 401 11 AGS AGS . J 3 ZN B 1 402 3 ZN ZN . K 2 AGS C 1 401 12 AGS AGS . L 3 ZN C 1 402 4 ZN ZN . M 2 AGS D 1 401 13 AGS AGS . N 3 ZN D 1 402 5 ZN ZN . O 2 AGS E 1 401 4 AGS AGS . P 3 ZN E 1 402 6 ZN ZN . Q 2 AGS F 1 401 9 AGS AGS . R 3 ZN F 1 402 1 ZN ZN . S 4 HOH A 1 501 13 HOH HOH . S 4 HOH A 2 502 3 HOH HOH . T 4 HOH B 1 501 4 HOH HOH . T 4 HOH B 2 502 7 HOH HOH . U 4 HOH C 1 501 5 HOH HOH . U 4 HOH C 2 502 6 HOH HOH . U 4 HOH C 3 503 8 HOH HOH . U 4 HOH C 4 504 1 HOH HOH . V 4 HOH D 1 501 10 HOH HOH . V 4 HOH D 2 502 2 HOH HOH . V 4 HOH D 3 503 12 HOH HOH . V 4 HOH D 4 504 9 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 . . . G 2 -24.677 14.457 -31.273 0.86 96.39 ? PG AGS 401 A 1 HETATM 2 S S1G AGS . . . G 2 -25.444 15.157 -29.616 0.86 75.92 ? S1G AGS 401 A 1 HETATM 3 O O2G AGS . . . G 2 -25.497 15.011 -32.476 0.86 81.94 ? O2G AGS 401 A 1 HETATM 4 O O3G AGS . . . G 2 -24.671 12.915 -31.179 0.86 85.01 ? O3G AGS 401 A 1 HETATM 5 P PB AGS . . . G 2 -22.149 13.361 -31.138 0.86 71.79 ? PB AGS 401 A 1 HETATM 6 O O1B AGS . . . G 2 -22.308 12.145 -31.969 0.86 70.37 ? O1B AGS 401 A 1 HETATM 7 O O2B AGS . . . G 2 -20.725 13.898 -31.252 0.86 76.05 ? O2B AGS 401 A 1 HETATM 8 O O3B AGS . . . G 2 -23.138 14.583 -31.507 0.86 86.11 ? O3B AGS 401 A 1 HETATM 9 P PA AGS . . . G 2 -21.818 14.204 -28.737 0.86 74.11 ? PA AGS 401 A 1 HETATM 10 O O1A AGS . . . G 2 -21.628 13.825 -27.341 0.86 75.6 ? O1A AGS 401 A 1 HETATM 11 O O2A AGS . . . G 2 -20.414 14.298 -29.278 0.86 81.73 ? O2A AGS 401 A 1 HETATM 12 O O3A AGS . . . G 2 -22.406 13.072 -29.628 0.86 64.29 ? O3A AGS 401 A 1 HETATM 13 O O5' AGS . . . G 2 -22.574 15.598 -28.999 0.86 77.86 ? O5' AGS 401 A 1 HETATM 14 C C5' AGS . . . G 2 -21.846 16.757 -29.473 0.86 68.85 ? C5' AGS 401 A 1 HETATM 15 C C4' AGS . . . G 2 -22.419 17.381 -30.726 0.86 82.96 ? C4' AGS 401 A 1 HETATM 16 O O4' AGS . . . G 2 -22.356 18.809 -30.585 0.86 104.55 ? O4' AGS 401 A 1 HETATM 17 C C3' AGS . . . G 2 -21.682 17.02 -32.017 0.86 94.43 ? C3' AGS 401 A 1 HETATM 18 O O3' AGS . . . G 2 -22.484 16.12 -32.773 0.86 84.27 ? O3' AGS 401 A 1 HETATM 19 C C2' AGS . . . G 2 -21.549 18.341 -32.788 0.86 104.51 ? C2' AGS 401 A 1 HETATM 20 O O2' AGS . . . G 2 -22.441 18.412 -33.897 0.86 100.08 ? O2' AGS 401 A 1 HETATM 21 C C1' AGS . . . G 2 -21.866 19.427 -31.757 0.86 110.13 ? C1' AGS 401 A 1 HETATM 22 N N9 AGS . . . G 2 -20.727 20.262 -31.396 0.86 114.85 ? N9 AGS 401 A 1 HETATM 23 C C8 AGS . . . G 2 -19.53 19.875 -30.848 0.86 110.38 ? C8 AGS 401 A 1 HETATM 24 N N7 AGS . . . G 2 -18.701 20.864 -30.623 0.86 110.88 ? N7 AGS 401 A 1 HETATM 25 C C5 AGS . . . G 2 -19.402 21.983 -31.048 0.86 118.57 ? C5 AGS 401 A 1 HETATM 26 C C6 AGS . . . G 2 -19.079 23.354 -31.078 0.86 124.48 ? C6 AGS 401 A 1 HETATM 27 N N6 AGS . . . G 2 -17.913 23.851 -30.655 0.86 125.34 ? N6 AGS 401 A 1 HETATM 28 N N1 AGS . . . G 2 -20.009 24.21 -31.567 0.86 118.02 ? N1 AGS 401 A 1 HETATM 29 C C2 AGS . . . G 2 -21.175 23.716 -31.994 0.86 108.14 ? C2 AGS 401 A 1 HETATM 30 N N3 AGS . . . G 2 -21.59 22.448 -32.014 0.86 111.29 ? N3 AGS 401 A 1 HETATM 31 C C4 AGS . . . G 2 -20.652 21.627 -31.525 0.86 116.95 ? C4 AGS 401 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #