data_8PEX
#
_model_server_result.job_id            MFehjE3hUQSCkiqE-ZneJg 
_model_server_result.datetime_utc      '2024-10-11 10:18:44' 
_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          8pex 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"AA","auth_seq_id":501}' 
#
_entry.id    8PEX 
#
_exptl.entry_id    8PEX 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    12 
_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            8PEX 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8PEX 
_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    22-meric 
_pdbx_struct_assembly.oligomeric_count      22 
_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 
_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
? 3 W N N 
? 3 Y N N 
? 3 AA N N 
? 3 CA N N 
? 3 EA N N 
? 3 GA N N 
? 3 IA N N 
? 3 KA N N 
? 3 MA N N 
? 3 OA N N 
? 3 QA N N 
? 3 SA 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 OG1 THR 185 A THR 185 1_555 X MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc2 W O2G AGS . A AGS 501 1_555 X MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
metalc ? metalc3 W O1B AGS . A AGS 501 1_555 X MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc4 B OG1 THR 185 B THR 185 1_555 Z MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc5 Y O2G AGS . B AGS 501 1_555 Z MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc6 Y O1B AGS . B AGS 501 1_555 Z MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc7 C OG1 THR 185 C THR 185 1_555 BA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc8 AA O2G AGS . C AGS 501 1_555 BA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc9 AA O1B AGS . C AGS 501 1_555 BA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc10 D OG1 THR 185 D THR 185 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc11 CA O2G AGS . D AGS 501 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc12 CA O1B AGS . D AGS 501 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc13 E OG1 THR 185 E THR 185 1_555 FA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc14 EA O2G AGS . E AGS 501 1_555 FA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc15 EA O1B AGS . E AGS 501 1_555 FA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc16 F OG1 THR 185 F THR 185 1_555 HA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc17 GA O2G AGS . F AGS 501 1_555 HA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc18 GA O3G AGS . F AGS 501 1_555 HA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? 
metalc ? metalc19 GA O1B AGS . F AGS 501 1_555 HA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc20 G OG1 THR 185 I THR 185 1_555 JA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc21 IA O2G AGS . I AGS 501 1_555 JA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc22 IA O1B AGS . I AGS 501 1_555 JA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc23 H OG1 THR 185 J THR 185 1_555 LA MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc24 KA O2G AGS . J AGS 501 1_555 LA MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc25 KA O1B AGS . J AGS 501 1_555 LA MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc26 I OG1 THR 185 K THR 185 1_555 NA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc27 MA O2G AGS . K AGS 501 1_555 NA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc28 MA O1B AGS . K AGS 501 1_555 NA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc29 J OG1 THR 185 L THR 185 1_555 PA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc30 OA O2G AGS . L AGS 501 1_555 PA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc31 OA O1B AGS . L AGS 501 1_555 PA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc32 K OG1 THR 185 M THR 185 1_555 RA MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc33 QA O2G AGS . M AGS 501 1_555 RA MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc34 QA O1B AGS . M AGS 501 1_555 RA MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc35 L OG1 THR 185 N THR 185 1_555 TA MG MG . N MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc36 SA O2G AGS . N AGS 501 1_555 TA MG MG . N MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc37 SA O1B AGS . N AGS 501 1_555 TA MG MG . N MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
#
_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                     8PEX 
_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
W 3 AGS A 1 501 501 AGS AGS . 
X 4 MG A 1 502 502 MG MG . 
Y 3 AGS B 1 501 501 AGS AGS . 
Z 4 MG B 1 502 502 MG MG . 
AA 3 AGS C 1 501 501 AGS AGS . 
BA 4 MG C 1 502 502 MG MG . 
CA 3 AGS D 1 501 501 AGS AGS . 
DA 4 MG D 1 502 502 MG MG . 
EA 3 AGS E 1 501 501 AGS AGS . 
FA 4 MG E 1 502 502 MG MG . 
GA 3 AGS F 1 501 501 AGS AGS . 
HA 4 MG F 1 502 502 MG MG . 
IA 3 AGS I 1 501 501 AGS AGS . 
JA 4 MG I 1 502 502 MG MG . 
KA 3 AGS J 1 501 501 AGS AGS . 
LA 4 MG J 1 502 502 MG MG . 
MA 3 AGS K 1 501 501 AGS AGS . 
NA 4 MG K 1 502 502 MG MG . 
OA 3 AGS L 1 501 501 AGS AGS . 
PA 4 MG L 1 502 502 MG MG . 
QA 3 AGS M 1 501 501 AGS AGS . 
RA 4 MG M 1 502 502 MG MG . 
SA 3 AGS N 1 501 501 AGS AGS . 
TA 4 MG N 1 502 502 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 . . . AA 3 208.421 166.027 158.684 1 104.82 ? PG AGS 501 C 1 
HETATM 2 S S1G AGS . . . AA 3 206.623 166.207 157.96 1 121.22 ? S1G AGS 501 C 1 
HETATM 3 O O2G AGS . . . AA 3 209.157 164.854 157.974 1 106.18 ? O2G AGS 501 C 1 
HETATM 4 O O3G AGS . . . AA 3 209.209 167.347 158.443 1 102.71 ? O3G AGS 501 C 1 
HETATM 5 P PB AGS . . . AA 3 209.651 165.28 160.98 1 99.91 ? PB AGS 501 C 1 
HETATM 6 O O1B AGS . . . AA 3 210.416 164.305 160.171 1 107 ? O1B AGS 501 C 1 
HETATM 7 O O2B AGS . . . AA 3 209.165 164.707 162.312 1 107.8 ? O2B AGS 501 C 1 
HETATM 8 O O3B AGS . . . AA 3 208.349 165.739 160.211 1 97.58 ? O3B AGS 501 C 1 
HETATM 9 P PA AGS . . . AA 3 212.09 166.34 161.627 1 114.31 ? PA AGS 501 C 1 
HETATM 10 O O1A AGS . . . AA 3 212.835 166.058 160.381 1 111.55 ? O1A AGS 501 C 1 
HETATM 11 O O2A AGS . . . AA 3 212.204 165.242 162.687 1 98.22 ? O2A AGS 501 C 1 
HETATM 12 O O3A AGS . . . AA 3 210.545 166.535 161.34 1 105.94 ? O3A AGS 501 C 1 
HETATM 13 O O5' AGS . . . AA 3 212.575 167.737 162.184 1 109.29 ? O5' AGS 501 C 1 
HETATM 14 C C5' AGS . . . AA 3 212.29 168.126 163.539 1 101.36 ? C5' AGS 501 C 1 
HETATM 15 C C4' AGS . . . AA 3 212.773 169.537 163.756 1 102.94 ? C4' AGS 501 C 1 
HETATM 16 O O4' AGS . . . AA 3 212.911 169.783 165.169 1 110.83 ? O4' AGS 501 C 1 
HETATM 17 C C3' AGS . . . AA 3 214.14 169.858 163.166 1 104.12 ? C3' AGS 501 C 1 
HETATM 18 O O3' AGS . . . AA 3 214.258 171.246 162.877 1 109.04 ? O3' AGS 501 C 1 
HETATM 19 C C2' AGS . . . AA 3 215.093 169.427 164.283 1 103.09 ? C2' AGS 501 C 1 
HETATM 20 O O2' AGS . . . AA 3 216.285 170.204 164.289 1 107.8 ? O2' AGS 501 C 1 
HETATM 21 C C1' AGS . . . AA 3 214.272 169.698 165.55 1 108.04 ? C1' AGS 501 C 1 
HETATM 22 N N9 AGS . . . AA 3 214.396 168.657 166.564 1 105.07 ? N9 AGS 501 C 1 
HETATM 23 C C8 AGS . . . AA 3 213.517 167.636 166.812 1 104.5 ? C8 AGS 501 C 1 
HETATM 24 N N7 AGS . . . AA 3 213.882 166.84 167.788 1 100.35 ? N7 AGS 501 C 1 
HETATM 25 C C5 AGS . . . AA 3 215.092 167.372 168.208 1 99.99 ? C5 AGS 501 C 1 
HETATM 26 C C6 AGS . . . AA 3 215.997 166.987 169.216 1 104.95 ? C6 AGS 501 C 1 
HETATM 27 N N6 AGS . . . AA 3 215.816 165.932 170.014 1 107.93 ? N6 AGS 501 C 1 
HETATM 28 N N1 AGS . . . AA 3 217.111 167.736 169.377 1 109.89 ? N1 AGS 501 C 1 
HETATM 29 C C2 AGS . . . AA 3 217.297 168.793 168.581 1 110.2 ? C2 AGS 501 C 1 
HETATM 30 N N3 AGS . . . AA 3 216.515 169.251 167.6 1 108.66 ? N3 AGS 501 C 1 
HETATM 31 C C4 AGS . . . AA 3 215.421 168.491 167.464 1 104.38 ? C4 AGS 501 C 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    64 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          19 
_model_server_stats.element_count           31 
#