data_1XPR
#
_model_server_result.job_id            6susB5icIZuW1o9B8b1e-Q 
_model_server_result.datetime_utc      '2025-02-05 06:50:04' 
_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          1xpr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":2600}' 
#
_entry.id    1XPR 
#
_exptl.entry_id    1XPR 
_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    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          108.16 
_cell.angle_gamma         90 
_cell.entry_id            1XPR 
_cell.length_a            210.526 
_cell.length_b            109.679 
_cell.length_c            160.046 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1XPR 
_symmetry.cell_setting             monoclinic 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
? dimeric 2 author_defined_assembly 3 
? dimeric 2 author_defined_assembly 4 
? dimeric 2 author_defined_assembly 5 
? dimeric 2 author_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,G,M,N 1 1 
B,H,O,P,Q 2 1 
C,I,R,S,T 3 1 
D,J,U,V,W 4 1 
E,K,X,Y,Z 5 1 
F,L,AA,BA,CA 6 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 N N N 
? 4 P N N 
? 4 S N N 
? 4 V N N 
? 4 Y N N 
? 4 BA 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 G OG1 THR 185 A THR 185 1_555 M MG MG . A MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc2 N O2G AGS . A AGS 1600 1_555 M MG MG . A MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? 
metalc ? metalc3 H OG1 THR 185 B THR 185 1_555 O MG MG . B MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc4 P O2B AGS . B AGS 2600 1_555 O MG MG . B MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc5 P O2G AGS . B AGS 2600 1_555 O MG MG . B MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc6 S O2G AGS . C AGS 3600 1_555 R MG MG . C MG 3601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc7 S O2B AGS . C AGS 3600 1_555 R MG MG . C MG 3601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? 
metalc ? metalc8 J OG1 THR 185 D THR 185 1_555 U MG MG . D MG 4601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc9 V O2G AGS . D AGS 4600 1_555 U MG MG . D MG 4601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? 
metalc ? metalc10 K OG1 THR 185 E THR 185 1_555 X MG MG . E MG 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
metalc ? metalc11 Y O2G AGS . E AGS 5600 1_555 X MG MG . E MG 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? 
metalc ? metalc12 L OG1 THR 185 F THR 185 1_555 AA MG MG . F MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc13 L OE1 GLU 215 F GLU 215 1_555 AA MG MG . F MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc14 BA O2G AGS . F AGS 6600 1_555 AA MG MG . F MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? 
#
_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                     1XPR 
_atom_sites.fract_transf_matrix[1][1]    0.00475 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001558 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009118 
_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]    0.006576 
_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 3 MG A 1 1601 1601 MG MG . 
N 4 AGS A 1 1600 1600 AGS AGS . 
O 3 MG B 1 2601 2601 MG MG . 
P 4 AGS B 1 2600 2600 AGS AGS . 
Q 5 FB B 1 2701 2701 FB FB . 
R 3 MG C 1 3601 3601 MG MG . 
S 4 AGS C 1 3600 3600 AGS AGS . 
T 5 FB C 1 3701 3701 FB FB . 
U 3 MG D 1 4601 4601 MG MG . 
V 4 AGS D 1 4600 4600 AGS AGS . 
W 5 FB D 1 4701 4701 FB FB . 
X 3 MG E 1 5601 5601 MG MG . 
Y 4 AGS E 1 5600 5600 AGS AGS . 
Z 5 FB E 1 5701 5701 FB FB . 
AA 3 MG F 1 6601 6601 MG MG . 
BA 4 AGS F 1 6600 6600 AGS AGS . 
CA 5 FB F 1 6701 6701 FB FB . 
#
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 . . . P 4 -10.875 -8.188 36.685 1 88.33 ? PG AGS 2600 B 1 
HETATM 2 S S1G AGS . . . P 4 -11.41 -10.088 36.078 1 88.57 ? S1G AGS 2600 B 1 
HETATM 3 O O2G AGS . . . P 4 -11.482 -7.141 35.659 1 88.46 ? O2G AGS 2600 B 1 
HETATM 4 O O3G AGS . . . P 4 -9.293 -8.05 36.715 1 88.4 ? O3G AGS 2600 B 1 
HETATM 5 P PB AGS . . . P 4 -11.994 -6.577 38.739 1 86.43 ? PB AGS 2600 B 1 
HETATM 6 O O1B AGS . . . P 4 -10.814 -5.866 39.533 1 86.48 ? O1B AGS 2600 B 1 
HETATM 7 O O2B AGS . . . P 4 -12.56 -5.612 37.613 1 86.44 ? O2B AGS 2600 B 1 
HETATM 8 O O3B AGS . . . P 4 -11.513 -7.996 38.154 1 87.48 ? O3B AGS 2600 B 1 
HETATM 9 P PA AGS . . . P 4 -14.284 -8.086 39.583 1 84.12 ? PA AGS 2600 B 1 
HETATM 10 O O1A AGS . . . P 4 -14.434 -8.53 38.06 1 84.2 ? O1A AGS 2600 B 1 
HETATM 11 O O2A AGS . . . P 4 -15.681 -7.641 40.194 1 84.19 ? O2A AGS 2600 B 1 
HETATM 12 O O3A AGS . . . P 4 -13.168 -6.935 39.789 1 85.32 ? O3A AGS 2600 B 1 
HETATM 13 O O5' AGS . . . P 4 -13.686 -9.318 40.424 1 83.14 ? O5' AGS 2600 B 1 
HETATM 14 C C5' AGS . . . P 4 -13.028 -9.107 41.673 1 81.48 ? C5' AGS 2600 B 1 
HETATM 15 C C4' AGS . . . P 4 -13.484 -10.065 42.77 1 80.23 ? C4' AGS 2600 B 1 
HETATM 16 O O4' AGS . . . P 4 -13.612 -9.283 43.946 1 79.65 ? O4' AGS 2600 B 1 
HETATM 17 C C3' AGS . . . P 4 -14.839 -10.711 42.499 1 79.71 ? C3' AGS 2600 B 1 
HETATM 18 O O3' AGS . . . P 4 -14.707 -12.125 42.492 1 79.74 ? O3' AGS 2600 B 1 
HETATM 19 C C2' AGS . . . P 4 -15.781 -10.251 43.601 1 79.34 ? C2' AGS 2600 B 1 
HETATM 20 O O2' AGS . . . P 4 -16.256 -11.351 44.363 1 79.33 ? O2' AGS 2600 B 1 
HETATM 21 C C1' AGS . . . P 4 -14.94 -9.355 44.488 1 79 ? C1' AGS 2600 B 1 
HETATM 22 N N9 AGS . . . P 4 -15.467 -7.98 44.729 1 78.19 ? N9 AGS 2600 B 1 
HETATM 23 C C8 AGS . . . P 4 -15.034 -6.821 44.161 1 77.92 ? C8 AGS 2600 B 1 
HETATM 24 N N7 AGS . . . P 4 -15.702 -5.716 44.631 1 77.73 ? N7 AGS 2600 B 1 
HETATM 25 C C5 AGS . . . P 4 -16.585 -6.169 45.536 1 77.58 ? C5 AGS 2600 B 1 
HETATM 26 C C6 AGS . . . P 4 -17.633 -5.637 46.446 1 77.41 ? C6 AGS 2600 B 1 
HETATM 27 N N6 AGS . . . P 4 -17.892 -4.309 46.482 1 77.37 ? N6 AGS 2600 B 1 
HETATM 28 N N1 AGS . . . P 4 -18.328 -6.494 47.242 1 77.4 ? N1 AGS 2600 B 1 
HETATM 29 C C2 AGS . . . P 4 -18.117 -7.829 47.25 1 77.44 ? C2 AGS 2600 B 1 
HETATM 30 N N3 AGS . . . P 4 -17.2 -8.426 46.466 1 77.55 ? N3 AGS 2600 B 1 
HETATM 31 C C4 AGS . . . P 4 -16.41 -7.603 45.582 1 77.75 ? C4 AGS 2600 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           722 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           31 
#