data_3EUK
#
_model_server_result.job_id            xO0BgGPcmii4jPpcU2UZlQ 
_model_server_result.datetime_utc      '2024-11-22 17:40:00' 
_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          3euk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":2004}' 
#
_entry.id    3EUK 
#
_exptl.entry_id    3EUK 
_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 
_cell.angle_gamma         120 
_cell.entry_id            3EUK 
_cell.length_a            172.414 
_cell.length_b            172.414 
_cell.length_c            491.587 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EUK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
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_and_software_defined_assembly 1 
PISA pentameric 5 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,I,J,K,L 1 1 
D,E,F,G,H,M,N,O,P 2 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 I N N 
? 4 L N N 
? 4 M N N 
? 4 O N N 
#
_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                     3EUK 
_atom_sites.fract_transf_matrix[1][1]    0.0058 
_atom_sites.fract_transf_matrix[1][2]    0.003349 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006697 
_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]    0.002034 
_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
I 4 AGS A 1 2001 2001 AGS ATG . 
J 5 MG A 1 2011 2011 MG MG . 
K 5 MG A 1 2012 2012 MG MG . 
L 4 AGS C 1 2002 2002 AGS ATG . 
M 4 AGS F 1 2003 2003 AGS ATG . 
N 5 MG F 1 2013 2013 MG MG . 
O 4 AGS H 1 2004 2004 AGS ATG . 
P 5 MG H 1 2014 2014 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 . . . O 4 -50.982 22.705 -13.069 1 98.93 ? PG AGS 2004 H 1 
HETATM 2 S S1G AGS . . . O 4 -51.086 22.923 -11.299 1 103.64 ? S1G AGS 2004 H 1 
HETATM 3 O O2G AGS . . . O 4 -50.496 24.014 -13.617 1 99.17 ? O2G AGS 2004 H 1 
HETATM 4 O O3G AGS . . . O 4 -50.239 21.518 -13.499 1 98.72 ? O3G AGS 2004 H 1 
HETATM 5 P PB AGS . . . O 4 -53.796 23.034 -13.583 1 99.55 ? PB AGS 2004 H 1 
HETATM 6 O O1B AGS . . . O 4 -53.749 24.394 -14.172 1 99.48 ? O1B AGS 2004 H 1 
HETATM 7 O O2B AGS . . . O 4 -54.213 22.941 -12.164 1 98.78 ? O2B AGS 2004 H 1 
HETATM 8 O O3B AGS . . . O 4 -52.385 22.338 -13.735 1 99.63 ? O3B AGS 2004 H 1 
HETATM 9 P PA AGS . . . O 4 -55.903 22.669 -15.507 1 101.83 ? PA AGS 2004 H 1 
HETATM 10 O O1A AGS . . . O 4 -54.974 22.933 -16.643 1 101.45 ? O1A AGS 2004 H 1 
HETATM 11 O O2A AGS . . . O 4 -56.901 23.656 -15.076 1 103.28 ? O2A AGS 2004 H 1 
HETATM 12 O O3A AGS . . . O 4 -54.905 22.218 -14.28 1 101.5 ? O3A AGS 2004 H 1 
HETATM 13 O O5' AGS . . . O 4 -56.708 21.3 -15.614 1 100.97 ? O5' AGS 2004 H 1 
HETATM 14 C C5' AGS . . . O 4 -56.13 20.099 -16.057 1 100.34 ? C5' AGS 2004 H 1 
HETATM 15 C C4' AGS . . . O 4 -57.279 19.07 -16.019 1 100.36 ? C4' AGS 2004 H 1 
HETATM 16 O O4' AGS . . . O 4 -58.298 19.498 -16.871 1 100.96 ? O4' AGS 2004 H 1 
HETATM 17 C C3' AGS . . . O 4 -56.89 17.657 -16.476 1 100.65 ? C3' AGS 2004 H 1 
HETATM 18 O O3' AGS . . . O 4 -57.136 16.696 -15.46 1 99.41 ? O3' AGS 2004 H 1 
HETATM 19 C C2' AGS . . . O 4 -57.693 17.373 -17.759 1 101.78 ? C2' AGS 2004 H 1 
HETATM 20 O O2' AGS . . . O 4 -58.516 16.162 -17.711 1 102.21 ? O2' AGS 2004 H 1 
HETATM 21 C C1' AGS . . . O 4 -58.547 18.64 -17.932 1 102.47 ? C1' AGS 2004 H 1 
HETATM 22 N N9 AGS . . . O 4 -58.251 19.37 -19.225 1 103.63 ? N9 AGS 2004 H 1 
HETATM 23 C C8 AGS . . . O 4 -57.552 20.553 -19.523 1 104.15 ? C8 AGS 2004 H 1 
HETATM 24 N N7 AGS . . . O 4 -57.458 20.954 -20.792 1 103.86 ? N7 AGS 2004 H 1 
HETATM 25 C C5 AGS . . . O 4 -58.164 19.953 -21.4 1 104.39 ? C5 AGS 2004 H 1 
HETATM 26 C C6 AGS . . . O 4 -58.497 19.676 -22.768 1 105.01 ? C6 AGS 2004 H 1 
HETATM 27 N N6 AGS . . . O 4 -58.077 20.577 -23.83 1 105.81 ? N6 AGS 2004 H 1 
HETATM 28 N N1 AGS . . . O 4 -59.248 18.537 -23.081 1 105.49 ? N1 AGS 2004 H 1 
HETATM 29 C C2 AGS . . . O 4 -59.672 17.649 -22.088 1 105.27 ? C2 AGS 2004 H 1 
HETATM 30 N N3 AGS . . . O 4 -59.423 17.789 -20.749 1 104.71 ? N3 AGS 2004 H 1 
HETATM 31 C C4 AGS . . . O 4 -58.656 18.954 -20.46 1 104.13 ? C4 AGS 2004 H 1 
#
_model_server_stats.io_time_ms              70 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#