data_4J9V
#
_model_server_result.job_id            aIJAT1AhAZT-zBEb1QK8fw 
_model_server_result.datetime_utc      '2025-03-04 23:06:27' 
_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          4j9v 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    4J9V 
#
_exptl.entry_id    4J9V 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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         120 
_cell.entry_id            4J9V 
_cell.length_a            109.324 
_cell.length_b            109.324 
_cell.length_c            337.656 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4J9V 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               software_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 10_444 -y-1,-x-1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -54.662 -94.677361 -56.276 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
? 2 F N N 
? 2 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 A OE1 GLN 84 A GLN 84 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? 
metalc ? metalc2 A O ALA 116 A ALA 116 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? 
metalc ? metalc3 B OE1 GLN 84 B GLN 84 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? 
metalc ? metalc4 B O ALA 116 B ALA 116 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
#
_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                     4J9V 
_atom_sites.fract_transf_matrix[1][1]    0.009147 
_atom_sites.fract_transf_matrix[1][2]    0.005281 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010562 
_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]    0.002962 
_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
C 2 AGS A 1 501 1 AGS AGS . 
D 2 AGS A 1 502 1 AGS AGS . 
E 3 MG B 1 501 1 MG MG . 
F 2 AGS B 1 502 1 AGS AGS . 
G 2 AGS B 1 503 1 AGS AGS . 
H 4 SO4 B 1 504 1 SO4 SO4 . 
I 3 MG B 1 505 1 MG MG . 
J 5 HOH A 1 601 2 HOH HOH . 
J 5 HOH A 2 602 14 HOH HOH . 
J 5 HOH A 3 603 15 HOH HOH . 
J 5 HOH A 4 604 17 HOH HOH . 
J 5 HOH A 5 605 18 HOH HOH . 
K 5 HOH B 1 601 1 HOH HOH . 
K 5 HOH B 2 602 3 HOH HOH . 
K 5 HOH B 3 603 4 HOH HOH . 
K 5 HOH B 4 604 8 HOH HOH . 
K 5 HOH B 5 605 20 HOH HOH . 
K 5 HOH B 6 606 21 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 . . . D 2 -38.327 -23.796 -24.658 1 139.97 ? PG AGS 502 A 1 
HETATM 2 S S1G AGS . . . D 2 -38.85 -21.913 -23.953 1 177.95 ? S1G AGS 502 A 1 
HETATM 3 O O2G AGS . . . D 2 -38.217 -24.85 -23.442 1 85.11 ? O2G AGS 502 A 1 
HETATM 4 O O3G AGS . . . D 2 -37.002 -23.725 -25.31 1 138.77 ? O3G AGS 502 A 1 
HETATM 5 P PB AGS . . . D 2 -39.663 -25.873 -25.888 1 286.57 ? PB AGS 502 A 1 
HETATM 6 O O1B AGS . . . D 2 -38.371 -26.473 -25.391 1 286.95 ? O1B AGS 502 A 1 
HETATM 7 O O2B AGS . . . D 2 -40.973 -26.208 -25.215 1 286.13 ? O2B AGS 502 A 1 
HETATM 8 O O3B AGS . . . D 2 -39.432 -24.29 -25.727 1 277.58 ? O3B AGS 502 A 1 
HETATM 9 P PA AGS . . . D 2 -39.514 -27.565 -28.165 1 164.53 ? PA AGS 502 A 1 
HETATM 10 O O1A AGS . . . D 2 -40.132 -28.674 -27.344 1 166.34 ? O1A AGS 502 A 1 
HETATM 11 O O2A AGS . . . D 2 -39.847 -27.451 -29.636 1 162.25 ? O2A AGS 502 A 1 
HETATM 12 O O3A AGS . . . D 2 -39.843 -26.139 -27.475 1 292.71 ? O3A AGS 502 A 1 
HETATM 13 O O5' AGS . . . D 2 -37.919 -27.558 -27.918 1 95.02 ? O5' AGS 502 A 1 
HETATM 14 C C5' AGS . . . D 2 -36.928 -28.071 -28.801 1 92.96 ? C5' AGS 502 A 1 
HETATM 15 C C4' AGS . . . D 2 -36.048 -26.878 -29.176 1 88.23 ? C4' AGS 502 A 1 
HETATM 16 O O4' AGS . . . D 2 -34.998 -27.244 -30.063 1 85.94 ? O4' AGS 502 A 1 
HETATM 17 C C3' AGS . . . D 2 -36.871 -25.861 -29.93 1 81.41 ? C3' AGS 502 A 1 
HETATM 18 O O3' AGS . . . D 2 -36.356 -24.551 -29.696 1 74.41 ? O3' AGS 502 A 1 
HETATM 19 C C2' AGS . . . D 2 -36.64 -26.151 -31.383 1 81.24 ? C2' AGS 502 A 1 
HETATM 20 O O2' AGS . . . D 2 -36.578 -24.888 -32.035 1 88.12 ? O2' AGS 502 A 1 
HETATM 21 C C1' AGS . . . D 2 -35.289 -26.827 -31.395 1 76.7 ? C1' AGS 502 A 1 
HETATM 22 N N9 AGS . . . D 2 -35.363 -28.051 -32.208 1 65.55 ? N9 AGS 502 A 1 
HETATM 23 C C8 AGS . . . D 2 -36.288 -29.01 -32.058 1 59.85 ? C8 AGS 502 A 1 
HETATM 24 N N7 AGS . . . D 2 -36.082 -30.017 -32.942 1 63.26 ? N7 AGS 502 A 1 
HETATM 25 C C5 AGS . . . D 2 -35 -29.701 -33.679 1 65.5 ? C5 AGS 502 A 1 
HETATM 26 C C6 AGS . . . D 2 -34.241 -30.331 -34.782 1 66.64 ? C6 AGS 502 A 1 
HETATM 27 N N6 AGS . . . D 2 -34.612 -31.532 -35.294 1 65.67 ? N6 AGS 502 A 1 
HETATM 28 N N1 AGS . . . D 2 -33.17 -29.661 -35.259 1 71.57 ? N1 AGS 502 A 1 
HETATM 29 C C2 AGS . . . D 2 -32.788 -28.469 -34.763 1 73.63 ? C2 AGS 502 A 1 
HETATM 30 N N3 AGS . . . D 2 -33.427 -27.836 -33.764 1 73.73 ? N3 AGS 502 A 1 
HETATM 31 C C4 AGS . . . D 2 -34.525 -28.395 -33.19 1 68.98 ? C4 AGS 502 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           431 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#