data_5VFR # _model_server_result.job_id 8cIGY156OSCLjreCNmYsTQ _model_server_result.datetime_utc '2024-11-04 20:30:49' _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 5vfr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"VA","auth_seq_id":501}' # _entry.id 5VFR # _exptl.entry_id 5VFR _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 34 _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 5VFR _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VFR _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 46-meric _pdbx_struct_assembly.oligomeric_count 46 _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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 34 VA N N ? 34 WA N N ? 34 XA N N ? 34 YA 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 R SG CYS 41 M CYS 41 1_555 R SG CYS 186 M CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 FA SG CYS 41 m CYS 41 1_555 FA SG CYS 186 m CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 I N SER 91 c SER 114 1_555 UA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc2 I O SER 91 c SER 114 1_555 UA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? # _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" # _atom_sites.entry_id 5VFR _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 UA 33 ZN c 1 401 401 ZN ZN . VA 34 AGS A 1 501 434 AGS AGS . WA 34 AGS B 1 501 441 AGS AGS . XA 34 AGS D 1 501 419 AGS AGS . YA 34 AGS F 1 501 440 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 . . . VA 34 253.402 254.713 218.311 1 187.96 ? PG AGS 501 A 1 HETATM 2 S S1G AGS . . . VA 34 254.443 254.755 219.952 1 187.96 ? S1G AGS 501 A 1 HETATM 3 O O2G AGS . . . VA 34 251.994 255.329 218.541 1 187.96 ? O2G AGS 501 A 1 HETATM 4 O O3G AGS . . . VA 34 253.266 253.243 217.819 1 187.96 ? O3G AGS 501 A 1 HETATM 5 P PB AGS . . . VA 34 253.448 255.634 215.818 1 187.96 ? PB AGS 501 A 1 HETATM 6 O O1B AGS . . . VA 34 253.053 254.294 215.334 1 187.96 ? O1B AGS 501 A 1 HETATM 7 O O2B AGS . . . VA 34 252.281 256.608 216.008 1 187.96 ? O2B AGS 501 A 1 HETATM 8 O O3B AGS . . . VA 34 254.138 255.533 217.224 1 187.96 ? O3B AGS 501 A 1 HETATM 9 P PA AGS . . . VA 34 254.18 257.734 214.288 1 187.96 ? PA AGS 501 A 1 HETATM 10 O O1A AGS . . . VA 34 255.411 258.376 213.785 1 187.96 ? O1A AGS 501 A 1 HETATM 11 O O2A AGS . . . VA 34 253.493 258.488 215.43 1 187.96 ? O2A AGS 501 A 1 HETATM 12 O O3A AGS . . . VA 34 254.464 256.282 214.807 1 187.96 ? O3A AGS 501 A 1 HETATM 13 O O5' AGS . . . VA 34 253.208 257.48 213.08 1 187.96 ? O5' AGS 501 A 1 HETATM 14 C C5' AGS . . . VA 34 251.915 258.08 213.063 1 187.96 ? C5' AGS 501 A 1 HETATM 15 C C4' AGS . . . VA 34 251.999 259.279 212.157 1 187.96 ? C4' AGS 501 A 1 HETATM 16 O O4' AGS . . . VA 34 250.709 259.49 211.541 1 187.96 ? O4' AGS 501 A 1 HETATM 17 C C3' AGS . . . VA 34 252.345 260.593 212.849 1 187.96 ? C3' AGS 501 A 1 HETATM 18 O O3' AGS . . . VA 34 253.749 260.823 212.857 1 187.96 ? O3' AGS 501 A 1 HETATM 19 C C2' AGS . . . VA 34 251.593 261.611 211.998 1 187.96 ? C2' AGS 501 A 1 HETATM 20 O O2' AGS . . . VA 34 252.294 261.898 210.795 1 187.96 ? O2' AGS 501 A 1 HETATM 21 C C1' AGS . . . VA 34 250.314 260.839 211.688 1 187.96 ? C1' AGS 501 A 1 HETATM 22 N N9 AGS . . . VA 34 249.293 260.893 212.731 1 187.96 ? N9 AGS 501 A 1 HETATM 23 C C8 AGS . . . VA 34 248.777 259.825 213.415 1 187.96 ? C8 AGS 501 A 1 HETATM 24 N N7 AGS . . . VA 34 247.859 260.145 214.293 1 187.96 ? N7 AGS 501 A 1 HETATM 25 C C5 AGS . . . VA 34 247.782 261.524 214.199 1 187.96 ? C5 AGS 501 A 1 HETATM 26 C C6 AGS . . . VA 34 247 262.477 214.879 1 187.96 ? C6 AGS 501 A 1 HETATM 27 N N6 AGS . . . VA 34 246.11 262.17 215.826 1 187.96 ? N6 AGS 501 A 1 HETATM 28 N N1 AGS . . . VA 34 247.153 263.775 214.534 1 187.96 ? N1 AGS 501 A 1 HETATM 29 C C2 AGS . . . VA 34 248.044 264.09 213.59 1 187.96 ? C2 AGS 501 A 1 HETATM 30 N N3 AGS . . . VA 34 248.822 263.278 212.87 1 187.96 ? N3 AGS 501 A 1 HETATM 31 C C4 AGS . . . VA 34 248.652 262.001 213.233 1 187.96 ? C4 AGS 501 A 1 # _model_server_stats.io_time_ms 263 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 138 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #