data_7NFY
#
_model_server_result.job_id            0Www0Eh5G_lZ6bcNqBzY8A 
_model_server_result.datetime_utc      '2024-11-21 17:57:18' 
_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          7nfy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1001}' 
#
_entry.id    7NFY 
#
_exptl.entry_id    7NFY 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    5 
_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            7NFY 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7NFY 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 
_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
? 3 H N N 
? 3 J N N 
? 3 L N N 
? 3 N N N 
? 3 Q 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 OG1 THR 424 A THR 530 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc2 H O2G AGS . A AGS 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc3 H O1B AGS . A AGS 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc4 B OG1 THR 424 B THR 530 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
metalc ? metalc5 J O2G AGS . B AGS 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc6 J O1B AGS . B AGS 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc7 C OG1 THR 424 C THR 530 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc8 L O2G AGS . C AGS 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc9 L O1B AGS . C AGS 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc10 D OG1 THR 424 D THR 530 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc11 N O2G AGS . D AGS 1001 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc12 N O1B AGS . D AGS 1001 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
metalc ? metalc13 F OG1 THR 424 F THR 530 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc14 Q O2G AGS . F AGS 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc15 Q O1B AGS . F AGS 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
#
_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 45 n n 
PG O2G AGS sing 46 n n 
PG O3G AGS sing 47 n n 
PG O3B AGS sing 48 n n 
PB O1B AGS doub 49 n n 
PB O2B AGS sing 50 n n 
PB O3B AGS sing 51 n n 
PB O3A AGS sing 52 n n 
PA O1A AGS doub 53 n n 
PA O2A AGS sing 54 n n 
PA O3A AGS sing 55 n n 
PA O5' AGS sing 56 n n 
O5' C5' AGS sing 57 n n 
C5' C4' AGS sing 58 n n 
C4' O4' AGS sing 59 n n 
C4' C3' AGS sing 60 n n 
O4' C1' AGS sing 61 n n 
C3' O3' AGS sing 62 n n 
C3' C2' AGS sing 63 n n 
C2' O2' AGS sing 64 n n 
C2' C1' AGS sing 65 n n 
C1' N9 AGS sing 66 n n 
N9 C8 AGS sing 67 n y 
N9 C4 AGS sing 68 n y 
C8 N7 AGS doub 69 n y 
N7 C5 AGS sing 70 n y 
C5 C6 AGS sing 71 n y 
C5 C4 AGS doub 72 n y 
C6 N6 AGS sing 73 n n 
C6 N1 AGS doub 74 n y 
N1 C2 AGS sing 75 n y 
C2 N3 AGS doub 76 n y 
N3 C4 AGS sing 77 n y 
O2G HOG2 AGS sing 78 n n 
O3G H21 AGS sing 79 n n 
O2B HOB2 AGS sing 80 n n 
O2A HOA2 AGS sing 81 n n 
C5' "H5'1" AGS sing 82 n n 
C5' "H5'2" AGS sing 83 n n 
C4' H4' AGS sing 84 n n 
C3' H3' AGS sing 85 n n 
O3' HO3' AGS sing 86 n n 
C2' H2' AGS sing 87 n n 
O2' HO2' AGS sing 88 n n 
C1' H1' AGS sing 89 n n 
C8 H8 AGS sing 90 n n 
N6 HN61 AGS sing 91 n n 
N6 HN62 AGS sing 92 n n 
C2 H2 AGS sing 93 n n 
#
_atom_sites.entry_id                     7NFY 
_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
H 3 AGS A 1 1001 1001 AGS AGS . 
I 4 MG A 1 1002 1002 MG MG . 
J 3 AGS B 1 1001 1001 AGS AGS . 
K 4 MG B 1 1002 1002 MG MG . 
L 3 AGS C 1 1001 1001 AGS AGS . 
M 4 MG C 1 1002 1002 MG MG . 
N 3 AGS D 1 1001 1001 AGS AGS . 
O 4 MG D 1 1002 1002 MG MG . 
P 5 ADP E 1 1001 1001 ADP ADP . 
Q 3 AGS F 1 1001 1001 AGS AGS . 
R 4 MG F 1 1002 1002 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 . . . J 3 237.804 225.618 232.911 1 111.6 ? PG AGS 1001 B 1 
HETATM 2 S S1G AGS . . . J 3 238.204 223.749 232.693 1 111.6 ? S1G AGS 1001 B 1 
HETATM 3 O O2G AGS . . . J 3 237.618 226.226 231.515 1 111.6 ? O2G AGS 1001 B 1 
HETATM 4 O O3G AGS . . . J 3 236.526 225.753 233.761 1 111.6 ? O3G AGS 1001 B 1 
HETATM 5 P PB AGS . . . J 3 240.333 226.306 233.091 1 111.6 ? PB AGS 1001 B 1 
HETATM 6 O O1B AGS . . . J 3 240.463 225.582 231.825 1 111.6 ? O1B AGS 1001 B 1 
HETATM 7 O O2B AGS . . . J 3 241.023 225.719 234.31 1 111.6 ? O2B AGS 1001 B 1 
HETATM 8 O O3B AGS . . . J 3 238.899 226.412 233.618 1 111.6 ? O3B AGS 1001 B 1 
HETATM 9 P PA AGS . . . J 3 241.926 227.637 231.682 1 111.6 ? PA AGS 1001 B 1 
HETATM 10 O O1A AGS . . . J 3 241.094 227.826 230.517 1 111.6 ? O1A AGS 1001 B 1 
HETATM 11 O O2A AGS . . . J 3 242.724 226.341 231.814 1 111.6 ? O2A AGS 1001 B 1 
HETATM 12 O O3A AGS . . . J 3 241.021 227.656 232.91 1 111.6 ? O3A AGS 1001 B 1 
HETATM 13 O O5' AGS . . . J 3 242.855 228.873 231.77 1 111.6 ? O5' AGS 1001 B 1 
HETATM 14 C C5' AGS . . . J 3 242.197 230.102 231.868 1 111.6 ? C5' AGS 1001 B 1 
HETATM 15 C C4' AGS . . . J 3 243.104 231.142 232.432 1 111.6 ? C4' AGS 1001 B 1 
HETATM 16 O O4' AGS . . . J 3 243.945 230.566 233.441 1 111.6 ? O4' AGS 1001 B 1 
HETATM 17 C C3' AGS . . . J 3 244.031 231.807 231.419 1 111.6 ? C3' AGS 1001 B 1 
HETATM 18 O O3' AGS . . . J 3 243.763 233.2 231.375 1 111.6 ? O3' AGS 1001 B 1 
HETATM 19 C C2' AGS . . . J 3 245.427 231.591 231.992 1 111.6 ? C2' AGS 1001 B 1 
HETATM 20 O O2' AGS . . . J 3 246.157 232.793 231.816 1 111.6 ? O2' AGS 1001 B 1 
HETATM 21 C C1' AGS . . . J 3 245.123 231.326 233.455 1 111.6 ? C1' AGS 1001 B 1 
HETATM 22 N N9 AGS . . . J 3 246.144 230.591 234.177 1 111.6 ? N9 AGS 1001 B 1 
HETATM 23 C C8 AGS . . . J 3 245.974 229.501 234.982 1 111.6 ? C8 AGS 1001 B 1 
HETATM 24 N N7 AGS . . . J 3 247.083 229.045 235.502 1 111.6 ? N7 AGS 1001 B 1 
HETATM 25 C C5 AGS . . . J 3 248.051 229.884 234.989 1 111.6 ? C5 AGS 1001 B 1 
HETATM 26 C C6 AGS . . . J 3 249.444 229.928 235.148 1 111.6 ? C6 AGS 1001 B 1 
HETATM 27 N N6 AGS . . . J 3 250.132 229.08 235.91 1 111.6 ? N6 AGS 1001 B 1 
HETATM 28 N N1 AGS . . . J 3 250.115 230.891 234.495 1 111.6 ? N1 AGS 1001 B 1 
HETATM 29 C C2 AGS . . . J 3 249.432 231.744 233.731 1 111.6 ? C2 AGS 1001 B 1 
HETATM 30 N N3 AGS . . . J 3 248.124 231.803 233.511 1 111.6 ? N3 AGS 1001 B 1 
HETATM 31 C C4 AGS . . . J 3 247.487 230.837 234.168 1 111.6 ? C4 AGS 1001 B 1 
HETATM 32 H "H5'1" AGS . . . J 3 241.444 230.039 232.479 1 111.6 ? "H5'1" AGS 1001 B 1 
HETATM 33 H "H5'2" AGS . . . J 3 241.88 230.38 230.99 1 111.6 ? "H5'2" AGS 1001 B 1 
HETATM 34 H H4' AGS . . . J 3 242.559 231.831 232.846 1 111.6 ? H4' AGS 1001 B 1 
HETATM 35 H H3' AGS . . . J 3 243.95 231.401 230.541 1 111.6 ? H3' AGS 1001 B 1 
HETATM 36 H HO3' AGS . . . J 3 244.424 233.618 230.955 1 111.6 ? HO3' AGS 1001 B 1 
HETATM 37 H H2' AGS . . . J 3 245.871 230.835 231.575 1 111.6 ? H2' AGS 1001 B 1 
HETATM 38 H HO2' AGS . . . J 3 246.883 232.632 231.332 1 111.6 ? HO2' AGS 1001 B 1 
HETATM 39 H H1' AGS . . . J 3 244.955 232.172 233.906 1 111.6 ? H1' AGS 1001 B 1 
HETATM 40 H H8 AGS . . . J 3 245.107 229.114 235.173 1 111.6 ? H8 AGS 1001 B 1 
HETATM 41 H HN61 AGS . . . J 3 250.04 229.108 236.813 1 111.6 ? HN61 AGS 1001 B 1 
HETATM 42 H HN62 AGS . . . J 3 250.697 228.482 235.527 1 111.6 ? HN62 AGS 1001 B 1 
HETATM 43 H H2 AGS . . . J 3 249.944 232.425 233.268 1 111.6 ? H2 AGS 1001 B 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    103 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#