data_8GMS
#
_model_server_result.job_id            OcHsqQBvGwEYpW1z4s7Dyg 
_model_server_result.datetime_utc      '2024-11-26 22:17:14' 
_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          8gms 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":402}' 
#
_entry.id    8GMS 
#
_exptl.entry_id    8GMS 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          5 
_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            8GMS 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8GMS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I 
_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    ? 
_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
? 5 G N N 
? 5 I 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 C OG1 THR 74 F THR 73 1_555 F MG MG . F MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc2 F MG MG . F MG 401 1_555 G O2G AGS . F AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
metalc ? metalc3 D OG1 THR 74 G THR 73 1_555 H MG MG . G MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc4 H MG MG . G MG 401 1_555 I O2G AGS . G AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? 
metalc ? metalc5 H MG MG . G MG 401 1_555 I O1B AGS . G AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? 
#
_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                     8GMS 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
F 4 MG F 1 401 401 MG MG . 
G 5 AGS F 1 402 402 AGS AGS . 
H 4 MG G 1 401 401 MG MG . 
I 5 AGS G 1 402 402 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 . . . I 5 128.57 153.439 141.611 1 12.53 ? PG AGS 402 G 1 
HETATM 2 S S1G AGS . . . I 5 129.463 151.865 140.906 1 18.97 ? S1G AGS 402 G 1 
HETATM 3 O O2G AGS . . . I 5 128.528 153.371 143.163 1 15.81 ? O2G AGS 402 G 1 
HETATM 4 O O3G AGS . . . I 5 129.353 154.713 141.183 1 17.66 ? O3G AGS 402 G 1 
HETATM 5 P PB AGS . . . I 5 126.283 154.823 141.278 1 36.08 ? PB AGS 402 G 1 
HETATM 6 O O1B AGS . . . I 5 126.246 155.168 142.714 1 34.77 ? O1B AGS 402 G 1 
HETATM 7 O O2B AGS . . . I 5 124.908 154.546 140.674 1 23.52 ? O2B AGS 402 G 1 
HETATM 8 O O3B AGS . . . I 5 127.12 153.51 141.057 1 23.23 ? O3B AGS 402 G 1 
HETATM 9 P PA AGS . . . I 5 126.032 157.316 140.204 1 8.06 ? PA AGS 402 G 1 
HETATM 10 O O1A AGS . . . I 5 124.827 157.327 141.045 1 28.01 ? O1A AGS 402 G 1 
HETATM 11 O O2A AGS . . . I 5 126.964 158.509 140.421 1 14.79 ? O2A AGS 402 G 1 
HETATM 12 O O3A AGS . . . I 5 126.897 156.017 140.447 1 26.95 ? O3A AGS 402 G 1 
HETATM 13 O O5' AGS . . . I 5 125.556 157.217 138.708 1 22.44 ? O5' AGS 402 G 1 
HETATM 14 C C5' AGS . . . I 5 124.529 158.089 138.204 1 26.56 ? C5' AGS 402 G 1 
HETATM 15 C C4' AGS . . . I 5 124.86 158.472 136.784 1 29.99 ? C4' AGS 402 G 1 
HETATM 16 O O4' AGS . . . I 5 125.461 159.786 136.768 1 29.33 ? O4' AGS 402 G 1 
HETATM 17 C C3' AGS . . . I 5 125.836 157.544 136.062 1 24.86 ? C3' AGS 402 G 1 
HETATM 18 O O3' AGS . . . I 5 125.466 157.375 134.699 1 25.78 ? O3' AGS 402 G 1 
HETATM 19 C C2' AGS . . . I 5 127.175 158.269 136.21 1 18.68 ? C2' AGS 402 G 1 
HETATM 20 O O2' AGS . . . I 5 128.065 157.965 135.144 1 9.46 ? O2' AGS 402 G 1 
HETATM 21 C C1' AGS . . . I 5 126.739 159.732 136.168 1 22.48 ? C1' AGS 402 G 1 
HETATM 22 N N9 AGS . . . I 5 127.623 160.63 136.899 1 14.6 ? N9 AGS 402 G 1 
HETATM 23 C C8 AGS . . . I 5 128.385 160.327 137.997 1 18.61 ? C8 AGS 402 G 1 
HETATM 24 N N7 AGS . . . I 5 129.086 161.333 138.456 1 17.27 ? N7 AGS 402 G 1 
HETATM 25 C C5 AGS . . . I 5 128.759 162.377 137.603 1 14.46 ? C5 AGS 402 G 1 
HETATM 26 C C6 AGS . . . I 5 129.17 163.722 137.552 1 17.01 ? C6 AGS 402 G 1 
HETATM 27 N N6 AGS . . . I 5 130.031 164.269 138.411 1 24.51 ? N6 AGS 402 G 1 
HETATM 28 N N1 AGS . . . I 5 128.653 164.497 136.573 1 17.06 ? N1 AGS 402 G 1 
HETATM 29 C C2 AGS . . . I 5 127.79 163.954 135.71 1 22.08 ? C2 AGS 402 G 1 
HETATM 30 N N3 AGS . . . I 5 127.331 162.702 135.661 1 27.34 ? N3 AGS 402 G 1 
HETATM 31 C C4 AGS . . . I 5 127.858 161.958 136.642 1 16.05 ? C4 AGS 402 G 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           503 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#