data_3EUK
#
_model_server_result.job_id            oshPgmJmQkARRvGyqBxGYQ 
_model_server_result.datetime_utc      '2024-11-26 03:06:35' 
_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":"M","auth_seq_id":2003}' 
#
_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 . . . M 4 -34.267 29.662 -10.648 1 87.91 ? PG AGS 2003 F 1 
HETATM 2 S S1G AGS . . . M 4 -35.134 29.873 -9.094 1 88.13 ? S1G AGS 2003 F 1 
HETATM 3 O O2G AGS . . . M 4 -34.167 28.177 -10.85 1 87.16 ? O2G AGS 2003 F 1 
HETATM 4 O O3G AGS . . . M 4 -34.809 30.415 -11.774 1 88.79 ? O3G AGS 2003 F 1 
HETATM 5 P PB AGS . . . M 4 -31.419 29.576 -10.432 1 90.24 ? PB AGS 2003 F 1 
HETATM 6 O O1B AGS . . . M 4 -31.445 28.228 -11.054 1 91.72 ? O1B AGS 2003 F 1 
HETATM 7 O O2B AGS . . . M 4 -31.116 29.618 -8.98 1 91.54 ? O2B AGS 2003 F 1 
HETATM 8 O O3B AGS . . . M 4 -32.797 30.301 -10.648 1 89.11 ? O3B AGS 2003 F 1 
HETATM 9 P PA AGS . . . M 4 -29.145 29.757 -12.086 1 87.85 ? PA AGS 2003 F 1 
HETATM 10 O O1A AGS . . . M 4 -29.977 29.459 -13.283 1 88.3 ? O1A AGS 2003 F 1 
HETATM 11 O O2A AGS . . . M 4 -28.233 28.768 -11.508 1 89.32 ? O2A AGS 2003 F 1 
HETATM 12 O O3A AGS . . . M 4 -30.221 30.325 -10.996 1 88.84 ? O3A AGS 2003 F 1 
HETATM 13 O O5' AGS . . . M 4 -28.288 31.069 -12.161 1 89.38 ? O5' AGS 2003 F 1 
HETATM 14 C C5' AGS . . . M 4 -28.856 32.295 -12.494 1 91.87 ? C5' AGS 2003 F 1 
HETATM 15 C C4' AGS . . . M 4 -27.693 33.273 -12.469 1 93.75 ? C4' AGS 2003 F 1 
HETATM 16 O O4' AGS . . . M 4 -26.729 32.884 -13.401 1 95.78 ? O4' AGS 2003 F 1 
HETATM 17 C C3' AGS . . . M 4 -28.076 34.716 -12.809 1 95.18 ? C3' AGS 2003 F 1 
HETATM 18 O O3' AGS . . . M 4 -28.139 35.446 -11.591 1 93.9 ? O3' AGS 2003 F 1 
HETATM 19 C C2' AGS . . . M 4 -26.969 35.221 -13.748 1 97.09 ? C2' AGS 2003 F 1 
HETATM 20 O O2' AGS . . . M 4 -26.159 36.338 -13.271 1 99.46 ? O2' AGS 2003 F 1 
HETATM 21 C C1' AGS . . . M 4 -26.155 33.951 -14.059 1 97.46 ? C1' AGS 2003 F 1 
HETATM 22 N N9 AGS . . . M 4 -26.107 33.682 -15.527 1 98.41 ? N9 AGS 2003 F 1 
HETATM 23 C C8 AGS . . . M 4 -26.918 32.959 -16.4 1 99.01 ? C8 AGS 2003 F 1 
HETATM 24 N N7 AGS . . . M 4 -26.595 32.917 -17.694 1 100.61 ? N7 AGS 2003 F 1 
HETATM 25 C C5 AGS . . . M 4 -25.46 33.684 -17.68 1 100.88 ? C5 AGS 2003 F 1 
HETATM 26 C C6 AGS . . . M 4 -24.528 34.115 -18.698 1 101.82 ? C6 AGS 2003 F 1 
HETATM 27 N N6 AGS . . . M 4 -24.694 33.724 -20.094 1 100.88 ? N6 AGS 2003 F 1 
HETATM 28 N N1 AGS . . . M 4 -23.442 34.92 -18.341 1 103.01 ? N1 AGS 2003 F 1 
HETATM 29 C C2 AGS . . . M 4 -23.241 35.322 -17.014 1 102.78 ? C2 AGS 2003 F 1 
HETATM 30 N N3 AGS . . . M 4 -24.046 34.987 -15.958 1 101.1 ? N3 AGS 2003 F 1 
HETATM 31 C C4 AGS . . . M 4 -25.141 34.171 -16.35 1 100.09 ? C4 AGS 2003 F 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           261 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#