data_6XJI
#
_model_server_result.job_id            -uPOBAjdkCx8e0ckiKMr7g 
_model_server_result.datetime_utc      '2024-12-26 14:26:37' 
_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          6xji 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":301}' 
#
_entry.id    6XJI 
#
_exptl.entry_id    6XJI 
_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    2 
_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            6XJI 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XJI 
_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 
_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 E N N 
? 3 G 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 C OG1 THR 40 C THR 40 1_555 F MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc2 C OE2 GLU 70 C GLU 70 1_555 F MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? 
metalc ? metalc3 E O2G AGS . C AGS 301 1_555 F MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc4 E O2B AGS . C AGS 301 1_555 F MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? 
metalc ? metalc5 D OG1 THR 40 D THR 40 1_555 H MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc6 D OE2 GLU 70 D GLU 70 1_555 H MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? 
metalc ? metalc7 G O2G AGS . D AGS 301 1_555 H MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc8 G O2B AGS . D AGS 301 1_555 H MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? 
#
_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                     6XJI 
_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 3 AGS C 1 301 600 AGS AGS . 
F 4 MG C 1 302 701 MG MG . 
G 3 AGS D 1 301 301 AGS AGS . 
H 4 MG D 1 302 401 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 . . . G 3 86.57 110.663 74.931 1 121.48 ? PG AGS 301 D 1 
HETATM 2 S S1G AGS . . . G 3 87.632 110.411 73.377 1 122.45 ? S1G AGS 301 D 1 
HETATM 3 O O2G AGS . . . G 3 87.094 109.955 76.228 1 121.25 ? O2G AGS 301 D 1 
HETATM 4 O O3G AGS . . . G 3 86.343 112.074 75.516 1 120.89 ? O3G AGS 301 D 1 
HETATM 5 P PB AGS . . . G 3 84.736 108.609 74.172 1 122.59 ? PB AGS 301 D 1 
HETATM 6 O O1B AGS . . . G 3 83.929 108.66 72.933 1 123.47 -1 O1B AGS 301 D 1 
HETATM 7 O O2B AGS . . . G 3 86 107.753 74.12 1 121.83 ? O2B AGS 301 D 1 
HETATM 8 O O3B AGS . . . G 3 85.163 110.06 74.659 1 121.77 ? O3B AGS 301 D 1 
HETATM 9 P PA AGS . . . G 3 83.833 106.749 76.226 1 125.7 ? PA AGS 301 D 1 
HETATM 10 O O1A AGS . . . G 3 83.838 105.59 75.311 1 127.14 -1 O1A AGS 301 D 1 
HETATM 11 O O2A AGS . . . G 3 84.995 106.77 77.222 1 126.66 ? O2A AGS 301 D 1 
HETATM 12 O O3A AGS . . . G 3 83.879 108.114 75.416 1 123.93 ? O3A AGS 301 D 1 
HETATM 13 O O5' AGS . . . G 3 82.476 106.861 77.061 1 124.3 ? O5' AGS 301 D 1 
HETATM 14 C C5' AGS . . . G 3 81.202 107.162 76.459 1 123.91 ? C5' AGS 301 D 1 
HETATM 15 C C4' AGS . . . G 3 80.16 107.269 77.544 1 124.02 ? C4' AGS 301 D 1 
HETATM 16 O O4' AGS . . . G 3 80.205 106.097 78.386 1 124.11 ? O4' AGS 301 D 1 
HETATM 17 C C3' AGS . . . G 3 80.254 108.486 78.468 1 124.03 ? C3' AGS 301 D 1 
HETATM 18 O O3' AGS . . . G 3 78.989 109.124 78.612 1 124.24 ? O3' AGS 301 D 1 
HETATM 19 C C2' AGS . . . G 3 80.811 107.909 79.778 1 123.59 ? C2' AGS 301 D 1 
HETATM 20 O O2' AGS . . . G 3 80.316 108.579 80.933 1 122.48 ? O2' AGS 301 D 1 
HETATM 21 C C1' AGS . . . G 3 80.295 106.471 79.748 1 124.51 ? C1' AGS 301 D 1 
HETATM 22 N N9 AGS . . . G 3 81.157 105.507 80.431 1 126.01 ? N9 AGS 301 D 1 
HETATM 23 C C8 AGS . . . G 3 82.409 105.093 80.053 1 126.29 ? C8 AGS 301 D 1 
HETATM 24 N N7 AGS . . . G 3 82.963 104.237 80.877 1 126.1 ? N7 AGS 301 D 1 
HETATM 25 C C5 AGS . . . G 3 82.01 104.073 81.871 1 126.13 ? C5 AGS 301 D 1 
HETATM 26 C C6 AGS . . . G 3 81.987 103.301 83.049 1 126.37 ? C6 AGS 301 D 1 
HETATM 27 N N6 AGS . . . G 3 82.987 102.502 83.431 1 127.39 ? N6 AGS 301 D 1 
HETATM 28 N N1 AGS . . . G 3 80.884 103.372 83.829 1 125.82 ? N1 AGS 301 D 1 
HETATM 29 C C2 AGS . . . G 3 79.875 104.164 83.446 1 126.03 ? C2 AGS 301 D 1 
HETATM 30 N N3 AGS . . . G 3 79.782 104.933 82.356 1 126.12 ? N3 AGS 301 D 1 
HETATM 31 C C4 AGS . . . G 3 80.888 104.847 81.607 1 126.21 ? C4 AGS 301 D 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    57 
_model_server_stats.query_time_ms           370 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           31 
#