data_5VFR
#
_model_server_result.job_id            n8JROs2OSaudx0fl-Gd-WQ 
_model_server_result.datetime_utc      '2024-11-04 20:34:48' 
_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":"WA","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 . . . WA 34 259.998 230.763 193.544 1 232.15 ? PG AGS 501 B 1 
HETATM 2 S S1G AGS . . . WA 34 261.924 230.547 193.71 1 232.15 ? S1G AGS 501 B 1 
HETATM 3 O O2G AGS . . . WA 34 259.534 231.938 194.441 1 232.15 ? O2G AGS 501 B 1 
HETATM 4 O O3G AGS . . . WA 34 259.297 229.448 193.989 1 232.15 ? O3G AGS 501 B 1 
HETATM 5 P PB AGS . . . WA 34 260.206 229.932 191.063 1 232.15 ? PB AGS 501 B 1 
HETATM 6 O O1B AGS . . . WA 34 261.715 230.172 190.993 1 232.15 ? O1B AGS 501 B 1 
HETATM 7 O O2B AGS . . . WA 34 259.832 228.58 191.536 1 232.15 ? O2B AGS 501 B 1 
HETATM 8 O O3B AGS . . . WA 34 259.661 231.027 192.053 1 232.15 ? O3B AGS 501 B 1 
HETATM 9 P PA AGS . . . WA 34 260.136 231.454 188.817 1 232.15 ? PA AGS 501 B 1 
HETATM 10 O O1A AGS . . . WA 34 261.602 231.54 188.742 1 232.15 ? O1A AGS 501 B 1 
HETATM 11 O O2A AGS . . . WA 34 259.44 232.64 189.491 1 232.15 ? O2A AGS 501 B 1 
HETATM 12 O O3A AGS . . . WA 34 259.695 230.172 189.601 1 232.15 ? O3A AGS 501 B 1 
HETATM 13 O O5' AGS . . . WA 34 259.585 231.153 187.375 1 232.15 ? O5' AGS 501 B 1 
HETATM 14 C C5' AGS . . . WA 34 259.469 232.192 186.409 1 232.15 ? C5' AGS 501 B 1 
HETATM 15 C C4' AGS . . . WA 34 258.27 231.934 185.536 1 232.15 ? C4' AGS 501 B 1 
HETATM 16 O O4' AGS . . . WA 34 257.953 233.137 184.828 1 232.15 ? O4' AGS 501 B 1 
HETATM 17 C C3' AGS . . . WA 34 258.529 230.873 184.473 1 232.15 ? C3' AGS 501 B 1 
HETATM 18 O O3' AGS . . . WA 34 258.06 229.598 184.911 1 232.15 ? O3' AGS 501 B 1 
HETATM 19 C C2' AGS . . . WA 34 257.731 231.367 183.25 1 232.15 ? C2' AGS 501 B 1 
HETATM 20 O O2' AGS . . . WA 34 256.526 230.659 183.025 1 232.15 ? O2' AGS 501 B 1 
HETATM 21 C C1' AGS . . . WA 34 257.449 232.844 183.543 1 232.15 ? C1' AGS 501 B 1 
HETATM 22 N N9 AGS . . . WA 34 258.09 233.734 182.589 1 232.15 ? N9 AGS 501 B 1 
HETATM 23 C C8 AGS . . . WA 34 259.246 233.505 181.908 1 232.15 ? C8 AGS 501 B 1 
HETATM 24 N N7 AGS . . . WA 34 259.601 234.481 181.111 1 232.15 ? N7 AGS 501 B 1 
HETATM 25 C C5 AGS . . . WA 34 258.6 235.412 181.27 1 232.15 ? C5 AGS 501 B 1 
HETATM 26 C C6 AGS . . . WA 34 258.402 236.688 180.718 1 232.15 ? C6 AGS 501 B 1 
HETATM 27 N N6 AGS . . . WA 34 259.219 237.259 179.822 1 232.15 ? N6 AGS 501 B 1 
HETATM 28 N N1 AGS . . . WA 34 257.293 237.373 181.101 1 232.15 ? N1 AGS 501 B 1 
HETATM 29 C C2 AGS . . . WA 34 256.466 236.822 181.99 1 232.15 ? C2 AGS 501 B 1 
HETATM 30 N N3 AGS . . . WA 34 256.57 235.633 182.583 1 232.15 ? N3 AGS 501 B 1 
HETATM 31 C C4 AGS . . . WA 34 257.668 234.974 182.187 1 232.15 ? C4 AGS 501 B 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    106 
_model_server_stats.query_time_ms           239 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#