data_5VFQ
#
_model_server_result.job_id            YWPz8OKG5YDqfp_w0ahIcw 
_model_server_result.datetime_utc      '2024-11-24 12:21:11' 
_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          5vfq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"WA","auth_seq_id":501}' 
#
_entry.id    5VFQ 
#
_exptl.entry_id    5VFQ 
_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            5VFQ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VFQ 
_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 G SG CYS 41 M CYS 41 1_555 G SG CYS 186 M CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 O SG CYS 627 U CYS 633 1_555 O SG CYS 653 U CYS 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 FA SG CYS 41 m CYS 41 1_555 FA SG CYS 186 m CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc1 W O SER 91 c SER 114 1_555 UA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc2 W ND1 HIS 92 c HIS 115 1_555 UA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? 
metalc ? metalc3 W NE2 HIS 92 c HIS 115 1_555 UA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? 
#
_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                     5VFQ 
_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 C 1 501 407 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 34 257.334 200.622 200.219 1 180.35 ? PG AGS 501 C 1 
HETATM 2 S S1G AGS . . . WA 34 256.821 200.899 202.075 1 180.35 ? S1G AGS 501 C 1 
HETATM 3 O O2G AGS . . . WA 34 258.398 201.686 199.842 1 180.35 ? O2G AGS 501 C 1 
HETATM 4 O O3G AGS . . . WA 34 256.087 200.743 199.298 1 180.35 ? O3G AGS 501 C 1 
HETATM 5 P PB AGS . . . WA 34 257.136 198.087 199.31 1 180.35 ? PB AGS 501 C 1 
HETATM 6 O O1B AGS . . . WA 34 256.988 198.51 197.861 1 180.35 ? O1B AGS 501 C 1 
HETATM 7 O O2B AGS . . . WA 34 255.796 197.872 199.893 1 180.35 ? O2B AGS 501 C 1 
HETATM 8 O O3B AGS . . . WA 34 257.959 199.217 200.032 1 180.35 ? O3B AGS 501 C 1 
HETATM 9 P PA AGS . . . WA 34 259.116 196.834 198.045 1 180.35 ? PA AGS 501 C 1 
HETATM 10 O O1A AGS . . . WA 34 259.099 198.054 197.242 1 180.35 ? O1A AGS 501 C 1 
HETATM 11 O O2A AGS . . . WA 34 260.459 196.589 198.726 1 180.35 ? O2A AGS 501 C 1 
HETATM 12 O O3A AGS . . . WA 34 258.021 196.801 199.193 1 180.35 ? O3A AGS 501 C 1 
HETATM 13 O O5' AGS . . . WA 34 258.751 195.666 197.074 1 180.35 ? O5' AGS 501 C 1 
HETATM 14 C C5' AGS . . . WA 34 257.577 194.899 197.328 1 180.35 ? C5' AGS 501 C 1 
HETATM 15 C C4' AGS . . . WA 34 257.978 193.467 197.574 1 180.35 ? C4' AGS 501 C 1 
HETATM 16 O O4' AGS . . . WA 34 257.642 192.661 196.42 1 180.35 ? O4' AGS 501 C 1 
HETATM 17 C C3' AGS . . . WA 34 259.452 193.221 197.886 1 180.35 ? C3' AGS 501 C 1 
HETATM 18 O O3' AGS . . . WA 34 259.63 192.404 199.022 1 180.35 ? O3' AGS 501 C 1 
HETATM 19 C C2' AGS . . . WA 34 260.021 192.587 196.601 1 180.35 ? C2' AGS 501 C 1 
HETATM 20 O O2' AGS . . . WA 34 260.799 191.427 196.864 1 180.35 ? O2' AGS 501 C 1 
HETATM 21 C C1' AGS . . . WA 34 258.803 192.233 195.752 1 180.35 ? C1' AGS 501 C 1 
HETATM 22 N N9 AGS . . . WA 34 258.847 192.875 194.441 1 180.35 ? N9 AGS 501 C 1 
HETATM 23 C C8 AGS . . . WA 34 258.237 194.021 194.058 1 180.35 ? C8 AGS 501 C 1 
HETATM 24 N N7 AGS . . . WA 34 258.495 194.368 192.804 1 180.35 ? N7 AGS 501 C 1 
HETATM 25 C C5 AGS . . . WA 34 259.347 193.379 192.363 1 180.35 ? C5 AGS 501 C 1 
HETATM 26 C C6 AGS . . . WA 34 259.991 193.151 191.125 1 180.35 ? C6 AGS 501 C 1 
HETATM 27 N N6 AGS . . . WA 34 259.858 193.958 190.075 1 180.35 ? N6 AGS 501 C 1 
HETATM 28 N N1 AGS . . . WA 34 260.775 192.067 191.016 1 180.35 ? N1 AGS 501 C 1 
HETATM 29 C C2 AGS . . . WA 34 260.911 191.254 192.071 1 180.35 ? C2 AGS 501 C 1 
HETATM 30 N N3 AGS . . . WA 34 260.363 191.359 193.281 1 180.35 ? N3 AGS 501 C 1 
HETATM 31 C C4 AGS . . . WA 34 259.593 192.44 193.354 1 180.35 ? C4 AGS 501 C 1 
#
_model_server_stats.io_time_ms              253 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    127 
_model_server_stats.query_time_ms           339 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           31 
#