data_8SEV
#
_model_server_result.job_id            nMIMUI_fsTgFK7QiVy053A 
_model_server_result.datetime_utc      '2024-12-21 17:44:50' 
_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          8sev 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":5101}' 
#
_entry.id    8SEV 
#
_exptl.entry_id    8SEV 
_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    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            8SEV 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8SEV 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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 E N N 
? 2 G N N 
? 2 I N N 
? 2 K 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 A SG CYS 4876 A CYS 4876 1_555 A SG CYS 4882 A CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 B SG CYS 4876 B CYS 4876 1_555 B SG CYS 4882 B CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 C SG CYS 4876 C CYS 4876 1_555 C SG CYS 4882 C CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 D SG CYS 4876 D CYS 4876 1_555 D SG CYS 4882 D CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc1 A SG CYS 4958 A CYS 4958 1_555 F ZN ZN . A ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc2 A SG CYS 4961 A CYS 4961 1_555 F ZN ZN . A ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc3 A NE2 HIS 4978 A HIS 4978 1_555 F ZN ZN . A ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc4 A ND1 HIS 4983 A HIS 4983 1_555 F ZN ZN . A ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc5 B SG CYS 4958 B CYS 4958 1_555 H ZN ZN . B ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc6 B SG CYS 4961 B CYS 4961 1_555 H ZN ZN . B ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc7 B NE2 HIS 4978 B HIS 4978 1_555 H ZN ZN . B ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc8 B ND1 HIS 4983 B HIS 4983 1_555 H ZN ZN . B ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc9 C SG CYS 4958 C CYS 4958 1_555 J ZN ZN . C ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc10 C SG CYS 4961 C CYS 4961 1_555 J ZN ZN . C ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc11 C NE2 HIS 4978 C HIS 4978 1_555 J ZN ZN . C ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc12 C ND1 HIS 4983 C HIS 4983 1_555 J ZN ZN . C ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc13 D SG CYS 4958 D CYS 4958 1_555 L ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc14 D SG CYS 4961 D CYS 4961 1_555 L ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc15 D NE2 HIS 4978 D HIS 4978 1_555 L ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc16 D ND1 HIS 4983 D HIS 4983 1_555 L ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_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                     8SEV 
_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
E 2 AGS A 1 5101 5101 AGS AGS . 
F 3 ZN A 1 5102 5103 ZN ZN . 
G 2 AGS B 1 5101 5101 AGS AGS . 
H 3 ZN B 1 5102 5103 ZN ZN . 
I 2 AGS C 1 5101 5101 AGS AGS . 
J 3 ZN C 1 5102 5103 ZN ZN . 
K 2 AGS D 1 5101 5101 AGS AGS . 
L 3 ZN D 1 5102 5103 ZN ZN . 
#
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 . . . K 2 265.328 281.743 220.843 1 72.97 ? PG AGS 5101 D 1 
HETATM 2 S S1G AGS . . . K 2 263.898 282.138 222.107 1 72.97 ? S1G AGS 5101 D 1 
HETATM 3 O O2G AGS . . . K 2 266.698 282.113 221.483 1 72.97 ? O2G AGS 5101 D 1 
HETATM 4 O O3G AGS . . . K 2 265.121 282.595 219.556 1 72.97 ? O3G AGS 5101 D 1 
HETATM 5 P PB AGS . . . K 2 264.94 279.133 221.542 1 72.97 ? PB AGS 5101 D 1 
HETATM 6 O O1B AGS . . . K 2 263.471 279.068 221.708 1 72.97 ? O1B AGS 5101 D 1 
HETATM 7 O O2B AGS . . . K 2 265.532 277.814 221.04 1 72.97 ? O2B AGS 5101 D 1 
HETATM 8 O O3B AGS . . . K 2 265.324 280.231 220.466 1 72.97 ? O3B AGS 5101 D 1 
HETATM 9 P PA AGS . . . K 2 265.144 278.901 224.304 1 72.97 ? PA AGS 5101 D 1 
HETATM 10 O O1A AGS . . . K 2 263.673 279.014 224.42 1 72.97 ? O1A AGS 5101 D 1 
HETATM 11 O O2A AGS . . . K 2 265.914 279.651 225.395 1 72.97 ? O2A AGS 5101 D 1 
HETATM 12 O O3A AGS . . . K 2 265.675 279.456 222.912 1 72.97 ? O3A AGS 5101 D 1 
HETATM 13 O O5' AGS . . . K 2 265.504 277.36 224.291 1 72.97 ? O5' AGS 5101 D 1 
HETATM 14 C C5' AGS . . . K 2 264.549 276.375 223.85 1 72.97 ? C5' AGS 5101 D 1 
HETATM 15 C C4' AGS . . . K 2 264.155 275.513 225.023 1 72.97 ? C4' AGS 5101 D 1 
HETATM 16 O O4' AGS . . . K 2 265.336 275.034 225.688 1 72.97 ? O4' AGS 5101 D 1 
HETATM 17 C C3' AGS . . . K 2 263.313 276.208 226.098 1 72.97 ? C3' AGS 5101 D 1 
HETATM 18 O O3' AGS . . . K 2 261.958 275.78 226.036 1 72.97 ? O3' AGS 5101 D 1 
HETATM 19 C C2' AGS . . . K 2 263.974 275.798 227.428 1 72.97 ? C2' AGS 5101 D 1 
HETATM 20 O O2' AGS . . . K 2 263.021 275.28 228.35 1 72.97 ? O2' AGS 5101 D 1 
HETATM 21 C C1' AGS . . . K 2 264.968 274.716 227.007 1 72.97 ? C1' AGS 5101 D 1 
HETATM 22 N N9 AGS . . . K 2 266.172 274.655 227.828 1 72.97 ? N9 AGS 5101 D 1 
HETATM 23 C C8 AGS . . . K 2 266.619 273.584 228.556 1 72.97 ? C8 AGS 5101 D 1 
HETATM 24 N N7 AGS . . . K 2 267.734 273.808 229.208 1 72.97 ? N7 AGS 5101 D 1 
HETATM 25 C C5 AGS . . . K 2 268.044 275.121 228.886 1 72.97 ? C5 AGS 5101 D 1 
HETATM 26 C C6 AGS . . . K 2 269.11 275.961 229.258 1 72.97 ? C6 AGS 5101 D 1 
HETATM 27 N N6 AGS . . . K 2 270.102 275.587 230.068 1 72.97 ? N6 AGS 5101 D 1 
HETATM 28 N N1 AGS . . . K 2 269.121 277.218 228.76 1 72.97 ? N1 AGS 5101 D 1 
HETATM 29 C C2 AGS . . . K 2 268.129 277.597 227.949 1 72.97 ? C2 AGS 5101 D 1 
HETATM 30 N N3 AGS . . . K 2 267.075 276.894 227.529 1 72.97 ? N3 AGS 5101 D 1 
HETATM 31 C C4 AGS . . . K 2 267.09 275.655 228.037 1 72.97 ? C4 AGS 5101 D 1 
#
_model_server_stats.io_time_ms              108 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    97 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           31 
#