data_8WK0
#
_model_server_result.job_id            DYejzxKTY08h28r3wIJKgg 
_model_server_result.datetime_utc      '2024-10-10 00:27:23' 
_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          8wk0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":701}' 
#
_entry.id    8WK0 
#
_exptl.entry_id    8WK0 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    5 
_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            8WK0 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8WK0 
_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    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_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
? 2 G N N 
? 2 I N N 
? 2 K N N 
? 2 M N N 
? 2 O 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 B OG SER 174 D SER 174 1_555 H MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? 
metalc ? metalc2 G O3B AGS . D AGS 701 1_555 H MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc3 C OG SER 174 M SER 174 1_555 J MG MG . M MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? 
metalc ? metalc4 I O2G AGS . M AGS 701 1_555 J MG MG . M MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? 
metalc ? metalc5 I O3G AGS . M AGS 701 1_555 J MG MG . M MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? 
metalc ? metalc6 I O1B AGS . M AGS 701 1_555 J MG MG . M MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? 
metalc ? metalc7 I O3B AGS . M AGS 701 1_555 J MG MG . M MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc8 I O2A AGS . M AGS 701 1_555 J MG MG . M MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc9 I O3A AGS . M AGS 701 1_555 J MG MG . M MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc10 K O1B AGS . N AGS 701 1_555 L MG MG . N MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? 
metalc ? metalc11 K O3B AGS . N AGS 701 1_555 L MG MG . N MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc12 K O1A AGS . N AGS 701 1_555 L MG MG . N MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 ? 
metalc ? metalc13 K O3A AGS . N AGS 701 1_555 L MG MG . N MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? 
metalc ? metalc14 E OG SER 174 O SER 174 1_555 N MG MG . O MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
metalc ? metalc15 E OE1 GLU 203 O GLU 203 1_555 N MG MG . O MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? 
metalc ? metalc16 M O3G AGS . O AGS 701 1_555 N MG MG . O MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? 
metalc ? metalc17 M O3B AGS . O AGS 701 1_555 N MG MG . O MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc18 F OG SER 174 L SER 174 1_555 P MG MG . L MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc19 O O2G AGS . L AGS 701 1_555 P MG MG . L MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.854 ? 
metalc ? metalc20 O O3B AGS . L AGS 701 1_555 P MG MG . L MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? 
metalc ? metalc21 O O3A AGS . L AGS 701 1_555 P MG MG . L MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? 
#
_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                     8WK0 
_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
G 2 AGS D 1 701 701 AGS AGS . 
H 3 MG D 1 702 6 MG MG . 
I 2 AGS M 1 701 701 AGS AGS . 
J 3 MG M 1 702 2 MG MG . 
K 2 AGS N 1 701 701 AGS AGS . 
L 3 MG N 1 702 5 MG MG . 
M 2 AGS O 1 701 701 AGS AGS . 
N 3 MG O 1 702 3 MG MG . 
O 2 AGS L 1 701 701 AGS AGS . 
P 3 MG L 1 702 4 MG MG . 
#
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 . . . M 2 158.523 118.467 123.707 1 53.22 ? PG AGS 701 O 1 
HETATM 2 S S1G AGS . . . M 2 156.735 117.798 123.594 1 53.22 ? S1G AGS 701 O 1 
HETATM 3 O O2G AGS . . . M 2 158.497 119.92 124.478 1 53.22 ? O2G AGS 701 O 1 
HETATM 4 O O3G AGS . . . M 2 159.18 118.668 122.213 1 53.22 ? O3G AGS 701 O 1 
HETATM 5 P PB AGS . . . M 2 161.083 117.615 124.709 1 53.22 ? PB AGS 701 O 1 
HETATM 6 O O1B AGS . . . M 2 161.479 118.905 124.05 1 53.22 ? O1B AGS 701 O 1 
HETATM 7 O O2B AGS . . . M 2 161.444 117.658 126.171 1 53.22 ? O2B AGS 701 O 1 
HETATM 8 O O3B AGS . . . M 2 159.464 117.402 124.53 1 53.22 ? O3B AGS 701 O 1 
HETATM 9 P PA AGS . . . M 2 163.524 116.363 123.912 1 53.22 ? PA AGS 701 O 1 
HETATM 10 O O1A AGS . . . M 2 164.045 117.665 124.447 1 53.22 ? O1A AGS 701 O 1 
HETATM 11 O O2A AGS . . . M 2 164.021 115.24 124.776 1 53.22 ? O2A AGS 701 O 1 
HETATM 12 O O3A AGS . . . M 2 161.886 116.387 123.976 1 53.22 ? O3A AGS 701 O 1 
HETATM 13 O O5' AGS . . . M 2 164.053 116.166 122.37 1 53.22 ? O5' AGS 701 O 1 
HETATM 14 C C5' AGS . . . M 2 165.124 115.293 122.15 1 53.22 ? C5' AGS 701 O 1 
HETATM 15 C C4' AGS . . . M 2 166.48 116.019 122.451 1 53.22 ? C4' AGS 701 O 1 
HETATM 16 O O4' AGS . . . M 2 166.518 116.578 123.905 1 53.22 ? O4' AGS 701 O 1 
HETATM 17 C C3' AGS . . . M 2 167.451 115.192 122.402 1 53.22 ? C3' AGS 701 O 1 
HETATM 18 O O3' AGS . . . M 2 167.995 115.126 121.052 1 53.22 ? O3' AGS 701 O 1 
HETATM 19 C C2' AGS . . . M 2 168.575 115.815 123.437 1 53.22 ? C2' AGS 701 O 1 
HETATM 20 O O2' AGS . . . M 2 169.185 116.989 122.827 1 53.22 ? O2' AGS 701 O 1 
HETATM 21 C C1' AGS . . . M 2 167.91 116.162 124.469 1 53.22 ? C1' AGS 701 O 1 
HETATM 22 N N9 AGS . . . M 2 167.726 115.05 125.443 1 53.22 ? N9 AGS 701 O 1 
HETATM 23 C C8 AGS . . . M 2 166.739 114.243 125.828 1 53.22 ? C8 AGS 701 O 1 
HETATM 24 N N7 AGS . . . M 2 167.203 113.439 126.783 1 53.22 ? N7 AGS 701 O 1 
HETATM 25 C C5 AGS . . . M 2 168.481 113.753 127 1 53.22 ? C5 AGS 701 O 1 
HETATM 26 C C6 AGS . . . M 2 169.412 113.238 127.868 1 53.22 ? C6 AGS 701 O 1 
HETATM 27 N N6 AGS . . . M 2 169.207 112.161 128.816 1 53.22 ? N6 AGS 701 O 1 
HETATM 28 N N1 AGS . . . M 2 170.632 113.731 127.89 1 53.22 ? N1 AGS 701 O 1 
HETATM 29 C C2 AGS . . . M 2 170.963 114.743 127.057 1 53.22 ? C2 AGS 701 O 1 
HETATM 30 N N3 AGS . . . M 2 170.048 115.248 126.203 1 53.22 ? N3 AGS 701 O 1 
HETATM 31 C C4 AGS . . . M 2 168.805 114.75 126.179 1 53.22 ? C4 AGS 701 O 1 
HETATM 32 H HOG2 AGS . . . M 2 157.607 120.14 124.704 1 53.22 ? HOG2 AGS 701 O 1 
HETATM 33 H H21 AGS . . . M 2 158.494 118.802 121.581 1 53.22 ? H21 AGS 701 O 1 
HETATM 34 H "H5'1" AGS . . . M 2 165.017 114.426 122.792 1 53.22 ? "H5'1" AGS 701 O 1 
HETATM 35 H "H5'2" AGS . . . M 2 165.116 114.97 121.114 1 53.22 ? "H5'2" AGS 701 O 1 
HETATM 36 H H4' AGS . . . M 2 166.643 116.823 121.742 1 53.22 ? H4' AGS 701 O 1 
HETATM 37 H H3' AGS . . . M 2 167.143 114.208 122.739 1 53.22 ? H3' AGS 701 O 1 
HETATM 38 H HO3' AGS . . . M 2 168.343 115.97 120.81 1 53.22 ? HO3' AGS 701 O 1 
HETATM 39 H H2' AGS . . . M 2 169.33 115.071 123.667 1 53.22 ? H2' AGS 701 O 1 
HETATM 40 H HO2' AGS . . . M 2 168.546 117.68 122.764 1 53.22 ? HO2' AGS 701 O 1 
HETATM 41 H H1' AGS . . . M 2 168.385 117.012 124.949 1 53.22 ? H1' AGS 701 O 1 
HETATM 42 H H8 AGS . . . M 2 165.736 114.23 125.429 1 53.22 ? H8 AGS 701 O 1 
HETATM 43 H HN61 AGS . . . M 2 168.751 111.316 128.524 1 53.22 ? HN61 AGS 701 O 1 
HETATM 44 H HN62 AGS . . . M 2 169.521 112.259 129.762 1 53.22 ? HN62 AGS 701 O 1 
HETATM 45 H H2 AGS . . . M 2 171.967 115.15 127.075 1 53.22 ? H2 AGS 701 O 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    67 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           45 
#