data_3EIH
#
_model_server_result.job_id            wFUuLkgnyiQP_ffdozTZYg 
_model_server_result.datetime_utc      '2024-10-19 08:21:42' 
_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          3eih 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    3EIH 
#
_exptl.entry_id    3EIH 
_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    2 
_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            3EIH 
_cell.length_a            76.956 
_cell.length_b            119.804 
_cell.length_c            156.831 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EIH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E 1 1 
B,F,G 2 1 
C,H,I 3 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
? 2 D N N 
? 2 F 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 OG SER 83 A SER 180 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc2 A OD1 ASP 135 A ASP 232 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? 
metalc ? metalc3 B OG SER 83 B SER 180 1_555 G MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
metalc ? metalc4 B OD1 ASP 135 B ASP 232 1_555 G MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.135 ? 
metalc ? metalc5 C OG SER 83 C SER 180 1_555 I MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
#
_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                     3EIH 
_atom_sites.fract_transf_matrix[1][1]    0.012994 
_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]    0.008347 
_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]    0.006376 
_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
D 2 AGS A 1 501 1 AGS ATG . 
E 3 MG A 1 502 438 MG MG . 
F 2 AGS B 1 501 1 AGS ATG . 
G 3 MG B 1 502 438 MG MG . 
H 4 EDO C 1 501 1 EDO EDO . 
I 3 MG C 1 502 438 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 . . . D 2 -1.324 -36.964 -18.386 1 81.87 ? PG AGS 501 A 1 
HETATM 2 S S1G AGS . . . D 2 -1.468 -38.36 -16.872 1 82.17 ? S1G AGS 501 A 1 
HETATM 3 O O2G AGS . . . D 2 -0.806 -37.62 -19.661 1 82.19 ? O2G AGS 501 A 1 
HETATM 4 O O3G AGS . . . D 2 -2.654 -36.203 -18.378 1 81.97 ? O3G AGS 501 A 1 
HETATM 5 P PB AGS . . . D 2 1.293 -36.806 -17.644 1 74.87 ? PB AGS 501 A 1 
HETATM 6 O O1B AGS . . . D 2 1.738 -36.659 -16.21 1 73.91 ? O1B AGS 501 A 1 
HETATM 7 O O2B AGS . . . D 2 1.318 -38.171 -18.288 1 74.94 ? O2B AGS 501 A 1 
HETATM 8 O O3B AGS . . . D 2 -0.11 -36.066 -17.872 1 77.67 ? O3B AGS 501 A 1 
HETATM 9 P PA AGS . . . D 2 1.767 -35.209 -19.985 1 71.89 ? PA AGS 501 A 1 
HETATM 10 O O1A AGS . . . D 2 3.088 -34.793 -20.593 1 70.19 ? O1A AGS 501 A 1 
HETATM 11 O O2A AGS . . . D 2 0.845 -36.201 -20.665 1 72 ? O2A AGS 501 A 1 
HETATM 12 O O3A AGS . . . D 2 2.188 -35.812 -18.545 1 74.52 ? O3A AGS 501 A 1 
HETATM 13 O O5' AGS . . . D 2 0.877 -33.906 -19.695 1 69.59 ? O5' AGS 501 A 1 
HETATM 14 C C5' AGS . . . D 2 -0.077 -33.465 -20.655 1 68.09 ? C5' AGS 501 A 1 
HETATM 15 C C4' AGS . . . D 2 0.395 -32.148 -21.276 1 67.91 ? C4' AGS 501 A 1 
HETATM 16 O O4' AGS . . . D 2 0.54 -31.125 -20.292 1 65.47 ? O4' AGS 501 A 1 
HETATM 17 C C3' AGS . . . D 2 1.776 -32.192 -21.942 1 68.87 ? C3' AGS 501 A 1 
HETATM 18 O O3' AGS . . . D 2 1.853 -32.806 -23.247 1 71.59 ? O3' AGS 501 A 1 
HETATM 19 C C2' AGS . . . D 2 2.159 -30.735 -21.98 1 67.21 ? C2' AGS 501 A 1 
HETATM 20 O O2' AGS . . . D 2 1.416 -30.067 -23.006 1 66.25 ? O2' AGS 501 A 1 
HETATM 21 C C1' AGS . . . D 2 1.647 -30.278 -20.632 1 66.39 ? C1' AGS 501 A 1 
HETATM 22 N N9 AGS . . . D 2 2.721 -30.353 -19.597 1 66.14 ? N9 AGS 501 A 1 
HETATM 23 C C8 AGS . . . D 2 2.626 -31.044 -18.445 1 66 ? C8 AGS 501 A 1 
HETATM 24 N N7 AGS . . . D 2 3.743 -30.921 -17.686 1 65.25 ? N7 AGS 501 A 1 
HETATM 25 C C5 AGS . . . D 2 4.584 -30.127 -18.355 1 65.15 ? C5 AGS 501 A 1 
HETATM 26 C C6 AGS . . . D 2 5.936 -29.603 -18.1 1 65.5 ? C6 AGS 501 A 1 
HETATM 27 N N6 AGS . . . D 2 6.584 -29.94 -16.961 1 64.19 ? N6 AGS 501 A 1 
HETATM 28 N N1 AGS . . . D 2 6.489 -28.805 -19.046 1 66.91 ? N1 AGS 501 A 1 
HETATM 29 C C2 AGS . . . D 2 5.825 -28.5 -20.186 1 67.47 ? C2 AGS 501 A 1 
HETATM 30 N N3 AGS . . . D 2 4.587 -28.948 -20.479 1 66.62 ? N3 AGS 501 A 1 
HETATM 31 C C4 AGS . . . D 2 3.921 -29.751 -19.616 1 65.8 ? C4 AGS 501 A 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           99 
_model_server_stats.create_model_time_ms    79 
_model_server_stats.query_time_ms           384 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           31 
#