data_9EMY
#
_model_server_result.job_id            Mgl9SKE2aXAZvQIaecFMow 
_model_server_result.datetime_utc      '2025-06-21 00:00:34' 
_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          9emy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":601}' 
#
_entry.id    9EMY 
#
_exptl.entry_id    9EMY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          4 
_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          90.02 
_cell.angle_gamma         90 
_cell.entry_id            9EMY 
_cell.length_a            82.397 
_cell.length_b            121.657 
_cell.length_c            151.059 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9EMY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA trimeric 3 author_defined_assembly 1 
PISA trimeric 3 author_defined_assembly 2 
PISA trimeric 3 author_defined_assembly 3 
PISA trimeric 3 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,M,N,R,T,U 1 1 
B,D,F,O,S 2 1 
G,I,K,P,V,X 3 1 
H,J,L,Q,W,Y 4 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    x,y,z 
_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
? 4 M N N 
? 4 O N N 
? 4 P N N 
? 4 Q 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 C SG CYS 22 C CYS 24 1_555 C SG CYS 96 C CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
disulf ? disulf2 D SG CYS 22 D CYS 24 1_555 D SG CYS 96 D CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
disulf ? disulf3 E SG CYS 22 E CYS 24 1_555 E SG CYS 96 E CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
disulf ? disulf4 F SG CYS 22 F CYS 24 1_555 F SG CYS 96 F CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf5 I SG CYS 22 I CYS 24 1_555 I SG CYS 96 I CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
disulf ? disulf6 J SG CYS 22 J CYS 24 1_555 J SG CYS 96 J CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf7 K SG CYS 22 K CYS 24 1_555 K SG CYS 96 K CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf8 L SG CYS 22 L CYS 24 1_555 L SG CYS 96 L CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
#
_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                     9EMY 
_atom_sites.fract_transf_matrix[1][1]    0.012136 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000004 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00822 
_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]    0.00662 
_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
M 4 AGS A 1 601 601 AGS AGS . 
N 5 PE4 A 1 602 602 PE4 PE4 . 
O 4 AGS B 1 601 601 AGS AGS . 
P 4 AGS G 1 601 601 AGS AGS . 
Q 4 AGS H 1 601 601 AGS AGS . 
R 6 HOH A 1 701 4 HOH HOH . 
S 6 HOH B 1 701 16 HOH HOH . 
S 6 HOH B 2 702 12 HOH HOH . 
S 6 HOH B 3 703 19 HOH HOH . 
S 6 HOH B 4 704 9 HOH HOH . 
T 6 HOH C 1 201 2 HOH HOH . 
U 6 HOH E 1 201 1 HOH HOH . 
V 6 HOH G 1 701 10 HOH HOH . 
V 6 HOH G 2 702 11 HOH HOH . 
W 6 HOH H 1 701 7 HOH HOH . 
W 6 HOH H 2 702 15 HOH HOH . 
W 6 HOH H 3 703 18 HOH HOH . 
W 6 HOH H 4 704 14 HOH HOH . 
W 6 HOH H 5 705 8 HOH HOH . 
W 6 HOH H 6 706 17 HOH HOH . 
X 6 HOH I 1 201 6 HOH HOH . 
X 6 HOH I 2 202 5 HOH HOH . 
Y 6 HOH L 1 201 3 HOH HOH . 
#
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 4 24.82 -7.962 11.811 0.7 82.31 ? PG AGS 601 A 1 
HETATM 2 S S1G AGS . . . M 4 26.229 -8.545 10.613 0.7 96.14 ? S1G AGS 601 A 1 
HETATM 3 O O2G AGS . . . M 4 23.409 -8.241 11.348 0.7 76.08 ? O2G AGS 601 A 1 
HETATM 4 O O3G AGS . . . M 4 24.969 -6.536 12.317 0.7 90.44 ? O3G AGS 601 A 1 
HETATM 5 P PB AGS . . . M 4 24.487 -10.062 13.898 0.7 86.45 ? PB AGS 601 A 1 
HETATM 6 O O1B AGS . . . M 4 23.982 -10.984 12.839 0.7 90.29 ? O1B AGS 601 A 1 
HETATM 7 O O2B AGS . . . M 4 23.604 -9.725 15.048 0.7 78.51 ? O2B AGS 601 A 1 
HETATM 8 O O3B AGS . . . M 4 24.907 -8.658 13.258 0.7 84.84 ? O3B AGS 601 A 1 
HETATM 9 P PA AGS . . . M 4 27.43 -10.206 13.838 0.7 96.64 ? PA AGS 601 A 1 
HETATM 10 O O1A AGS . . . M 4 27.468 -8.917 13.086 0.7 89.18 ? O1A AGS 601 A 1 
HETATM 11 O O2A AGS . . . M 4 28.356 -10.297 15.006 0.7 90.23 ? O2A AGS 601 A 1 
HETATM 12 O O3A AGS . . . M 4 25.942 -10.556 14.358 0.7 90.69 ? O3A AGS 601 A 1 
HETATM 13 O O5' AGS . . . M 4 27.736 -11.419 12.818 0.7 110.82 ? O5' AGS 601 A 1 
HETATM 14 C C5' AGS . . . M 4 26.983 -11.721 11.594 1 111.08 ? C5' AGS 601 A 1 
HETATM 15 C C4' AGS . . . M 4 26.666 -13.201 11.548 1 110.08 ? C4' AGS 601 A 1 
HETATM 16 O O4' AGS . . . M 4 27.839 -13.979 11.92 1 104.68 ? O4' AGS 601 A 1 
HETATM 17 C C3' AGS . . . M 4 25.552 -13.678 12.492 1 110.63 ? C3' AGS 601 A 1 
HETATM 18 O O3' AGS . . . M 4 24.792 -14.75 11.949 1 120.12 ? O3' AGS 601 A 1 
HETATM 19 C C2' AGS . . . M 4 26.315 -14.182 13.718 1 103.9 ? C2' AGS 601 A 1 
HETATM 20 O O2' AGS . . . M 4 25.597 -15.234 14.318 1 107.01 ? O2' AGS 601 A 1 
HETATM 21 C C1' AGS . . . M 4 27.625 -14.695 13.123 1 97.02 ? C1' AGS 601 A 1 
HETATM 22 N N9 AGS . . . M 4 28.793 -14.509 13.986 1 87.36 ? N9 AGS 601 A 1 
HETATM 23 C C8 AGS . . . M 4 29.218 -13.33 14.548 1 84.64 ? C8 AGS 601 A 1 
HETATM 24 N N7 AGS . . . M 4 30.319 -13.437 15.246 1 80.27 ? N7 AGS 601 A 1 
HETATM 25 C C5 AGS . . . M 4 30.636 -14.781 15.17 1 80.59 ? C5 AGS 601 A 1 
HETATM 26 C C6 AGS . . . M 4 31.693 -15.532 15.722 1 81.33 ? C6 AGS 601 A 1 
HETATM 27 N N6 AGS . . . M 4 32.657 -15.016 16.481 1 78.12 ? N6 AGS 601 A 1 
HETATM 28 N N1 AGS . . . M 4 31.723 -16.857 15.445 1 83.17 ? N1 AGS 601 A 1 
HETATM 29 C C2 AGS . . . M 4 30.752 -17.367 14.674 1 87.55 ? C2 AGS 601 A 1 
HETATM 30 N N3 AGS . . . M 4 29.71 -16.76 14.107 1 87.5 ? N3 AGS 601 A 1 
HETATM 31 C C4 AGS . . . M 4 29.708 -15.45 14.392 1 83.4 ? C4 AGS 601 A 1 
#
_model_server_stats.io_time_ms              48 
_model_server_stats.parse_time_ms           32 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#