data_4UX3
#
_model_server_result.job_id            Ya0bn-grGceeWdi3124mjg 
_model_server_result.datetime_utc      '2024-11-22 22:38:29' 
_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          4ux3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":9999}' 
#
_entry.id    4UX3 
#
_exptl.entry_id    4UX3 
_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    1 
_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            4UX3 
_cell.length_a            73.151 
_cell.length_b            94.801 
_cell.length_c            284.768 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4UX3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 OG SER 40 A SER 39 1_555 C MG MG . A MG 8999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? 
metalc ? metalc2 C MG MG . A MG 8999 1_555 D O3G AGS . A AGS 9999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? 
#
_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                     4UX3 
_atom_sites.fract_transf_matrix[1][1]    0.01367 
_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]    0.010548 
_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]    0.003512 
_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 3 MG A 1 8999 8999 MG MG . 
D 4 AGS A 1 9999 9999 AGS AGS . 
#
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 4 -153.816 -55.541 598.415 1 150.72 ? PG AGS 9999 A 1 
HETATM 2 S S1G AGS . . . D 4 -155.151 -54.05 597.916 1 139.81 ? S1G AGS 9999 A 1 
HETATM 3 O O2G AGS . . . D 4 -152.612 -55.423 597.587 1 142.98 ? O2G AGS 9999 A 1 
HETATM 4 O O3G AGS . . . D 4 -153.381 -55.585 599.974 1 132.87 ? O3G AGS 9999 A 1 
HETATM 5 P PB AGS . . . D 4 -154.856 -57.841 599.193 1 143.42 ? PB AGS 9999 A 1 
HETATM 6 O O1B AGS . . . D 4 -154.269 -59.162 598.857 1 150.49 ? O1B AGS 9999 A 1 
HETATM 7 O O2B AGS . . . D 4 -154.407 -57.177 600.472 1 137.27 ? O2B AGS 9999 A 1 
HETATM 8 O O3B AGS . . . D 4 -154.608 -56.848 597.996 1 144.26 ? O3B AGS 9999 A 1 
HETATM 9 P PA AGS . . . D 4 -156.892 -58.474 600.553 1 139.1 ? PA AGS 9999 A 1 
HETATM 10 O O1A AGS . . . D 4 -156.533 -57.374 601.515 1 163.26 ? O1A AGS 9999 A 1 
HETATM 11 O O2A AGS . . . D 4 -156.225 -59.802 600.839 1 124.97 ? O2A AGS 9999 A 1 
HETATM 12 O O3A AGS . . . D 4 -156.43 -57.975 599.124 1 114.11 ? O3A AGS 9999 A 1 
HETATM 13 O O5' AGS . . . D 4 -158.487 -58.532 600.345 1 115.96 ? O5' AGS 9999 A 1 
HETATM 14 C C5' AGS . . . D 4 -159.299 -58.009 601.386 1 118.85 ? C5' AGS 9999 A 1 
HETATM 15 C C4' AGS . . . D 4 -160.634 -57.625 600.799 1 139.12 ? C4' AGS 9999 A 1 
HETATM 16 O O4' AGS . . . D 4 -161.432 -58.801 600.709 1 129.15 ? O4' AGS 9999 A 1 
HETATM 17 C C3' AGS . . . D 4 -161.353 -56.632 601.708 1 158.02 ? C3' AGS 9999 A 1 
HETATM 18 O O3' AGS . . . D 4 -161.293 -55.264 601.225 1 158.77 ? O3' AGS 9999 A 1 
HETATM 19 C C2' AGS . . . D 4 -162.767 -57.186 601.826 1 158.22 ? C2' AGS 9999 A 1 
HETATM 20 O O2' AGS . . . D 4 -163.663 -56.485 600.953 1 159.78 ? O2' AGS 9999 A 1 
HETATM 21 C C1' AGS . . . D 4 -162.68 -58.645 601.391 1 143.27 ? C1' AGS 9999 A 1 
HETATM 22 N N9 AGS . . . D 4 -162.696 -59.619 602.519 1 148.12 ? N9 AGS 9999 A 1 
HETATM 23 C C8 AGS . . . D 4 -161.69 -59.834 603.391 1 148.51 ? C8 AGS 9999 A 1 
HETATM 24 N N7 AGS . . . D 4 -161.997 -60.8 604.297 1 151.31 ? N7 AGS 9999 A 1 
HETATM 25 C C5 AGS . . . D 4 -163.228 -61.248 604 1 156.9 ? C5 AGS 9999 A 1 
HETATM 26 C C6 AGS . . . D 4 -164.157 -62.271 604.55 1 156.19 ? C6 AGS 9999 A 1 
HETATM 27 N N6 AGS . . . D 4 -163.82 -63.038 605.618 1 156.51 ? N6 AGS 9999 A 1 
HETATM 28 N N1 AGS . . . D 4 -165.354 -62.421 603.94 1 151.44 ? N1 AGS 9999 A 1 
HETATM 29 C C2 AGS . . . D 4 -165.708 -61.682 602.872 1 160.73 ? C2 AGS 9999 A 1 
HETATM 30 N N3 AGS . . . D 4 -164.916 -60.737 602.322 1 166.82 ? N3 AGS 9999 A 1 
HETATM 31 C C4 AGS . . . D 4 -163.684 -60.47 602.827 1 157.83 ? C4 AGS 9999 A 1 
#
_model_server_stats.io_time_ms              72 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#