data_8GAO
#
_model_server_result.job_id            -mFphNgKmlZLXyHFpU0wAQ 
_model_server_result.datetime_utc      '2024-10-25 20:27:15' 
_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          8gao 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":501}' 
#
_entry.id    8GAO 
#
_exptl.entry_id    8GAO 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          6 
_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            8GAO 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8GAO 
_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    decameric 
_pdbx_struct_assembly.oligomeric_count      10 
_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,J,K,L,M,N,O,P,Q,R,S,T,U 
_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
? 6 K N N 
? 6 M N N 
? 6 O N N 
? 6 Q N N 
? 6 S 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
covale ? covale1 I O3' GTP 1 P GTP 1 1_555 I P C 2 P C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? 
metalc ? metalc1 B OE1 GLN 227 B GLN 227 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc2 K O2G AGS . B AGS 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? 
metalc ? metalc3 K O3G AGS . B AGS 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc4 K O3B AGS . B AGS 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? 
metalc ? metalc5 C OE1 GLN 227 C GLN 227 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc6 M O3G AGS . C AGS 501 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? 
metalc ? metalc7 M O1B AGS . C AGS 501 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc8 O O2G AGS . D AGS 501 1_555 P MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? 
metalc ? metalc9 O O2B AGS . D AGS 501 1_555 P MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? 
metalc ? metalc10 Q O3G AGS . E AGS 501 1_555 R MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? 
metalc ? metalc11 Q O1B AGS . E AGS 501 1_555 R MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc12 S O3G AGS . F AGS 501 1_555 T MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? 
metalc ? metalc13 S O2B AGS . F AGS 501 1_555 T MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc14 S O3B AGS . F AGS 501 1_555 T MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? 
metalc ? metalc15 S O2A AGS . F AGS 501 1_555 T MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? 
metalc ? metalc16 G SG CYS 35 G CYS 37 1_555 U ZN ZN . G ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc17 G SG CYS 38 G CYS 40 1_555 U ZN ZN . G ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc18 G SG CYS 63 G CYS 65 1_555 U ZN ZN . G ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc19 G SG CYS 66 G CYS 68 1_555 U ZN ZN . G ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
hydrog WATSON-CRICK hydrog1 I N1 GTP 1 P GTP 1 1_555 J N3 DC 40 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 I N2 GTP 1 P GTP 1 1_555 J O2 DC 40 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 I O6 GTP 1 P GTP 1 1_555 J N4 DC 40 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 I N3 C 2 P C 2 1_555 J N1 DG 39 T DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 I N4 C 2 P C 2 1_555 J O6 DG 39 T DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 I O2 C 2 P C 2 1_555 J N2 DG 39 T DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 I N3 C 3 P C 3 1_555 J N1 DG 38 T DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 I N4 C 3 P C 3 1_555 J O6 DG 38 T DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 I O2 C 3 P C 3 1_555 J N2 DG 38 T DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 I N1 G 4 P G 4 1_555 J N3 DC 37 T DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 I N2 G 4 P G 4 1_555 J O2 DC 37 T DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 I O6 G 4 P G 4 1_555 J N4 DC 37 T DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 I N1 A 5 P A 5 1_555 J N3 DT 36 T DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 I N6 A 5 P A 5 1_555 J O4 DT 36 T DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 40 n n 
PG O2G AGS sing 41 n n 
PG O3G AGS sing 42 n n 
PG O3B AGS sing 43 n n 
PB O1B AGS doub 44 n n 
PB O2B AGS sing 45 n n 
PB O3B AGS sing 46 n n 
PB O3A AGS sing 47 n n 
PA O1A AGS doub 48 n n 
PA O2A AGS sing 49 n n 
PA O3A AGS sing 50 n n 
PA O5' AGS sing 51 n n 
O5' C5' AGS sing 52 n n 
C5' C4' AGS sing 53 n n 
C4' O4' AGS sing 54 n n 
C4' C3' AGS sing 55 n n 
O4' C1' AGS sing 56 n n 
C3' O3' AGS sing 57 n n 
C3' C2' AGS sing 58 n n 
C2' O2' AGS sing 59 n n 
C2' C1' AGS sing 60 n n 
C1' N9 AGS sing 61 n n 
N9 C8 AGS sing 62 n y 
N9 C4 AGS sing 63 n y 
C8 N7 AGS doub 64 n y 
N7 C5 AGS sing 65 n y 
C5 C6 AGS sing 66 n y 
C5 C4 AGS doub 67 n y 
C6 N6 AGS sing 68 n n 
C6 N1 AGS doub 69 n y 
N1 C2 AGS sing 70 n y 
C2 N3 AGS doub 71 n y 
N3 C4 AGS sing 72 n y 
O2G HOG2 AGS sing 73 n n 
O3G H21 AGS sing 74 n n 
O2B HOB2 AGS sing 75 n n 
O2A HOA2 AGS sing 76 n n 
C5' "H5'1" AGS sing 77 n n 
C5' "H5'2" AGS sing 78 n n 
C4' H4' AGS sing 79 n n 
C3' H3' AGS sing 80 n n 
O3' HO3' AGS sing 81 n n 
C2' H2' AGS sing 82 n n 
O2' HO2' AGS sing 83 n n 
C1' H1' AGS sing 84 n n 
C8 H8 AGS sing 85 n n 
N6 HN61 AGS sing 86 n n 
N6 HN62 AGS sing 87 n n 
C2 H2 AGS sing 88 n n 
#
_atom_sites.entry_id                     8GAO 
_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
K 6 AGS B 1 501 501 AGS AGS . 
L 7 MG B 1 502 502 MG MG . 
M 6 AGS C 1 501 501 AGS AGS . 
N 7 MG C 1 502 502 MG MG . 
O 6 AGS D 1 501 501 AGS AGS . 
P 7 MG D 1 502 502 MG MG . 
Q 6 AGS E 1 501 501 AGS AGS . 
R 7 MG E 1 502 502 MG MG . 
S 6 AGS F 1 501 501 AGS AGS . 
T 7 MG F 1 502 502 MG MG . 
U 8 ZN G 1 401 525 ZN ZN . 
#
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 . . . Q 6 91.435 70.982 97.03 1 63.56 ? PG AGS 501 E 1 
HETATM 2 S S1G AGS . . . Q 6 90.596 70.358 95.39 1 64.84 ? S1G AGS 501 E 1 
HETATM 3 O O2G AGS . . . Q 6 92.721 71.781 96.682 1 54.19 ? O2G AGS 501 E 1 
HETATM 4 O O3G AGS . . . Q 6 90.445 71.905 97.797 1 50.92 ? O3G AGS 501 E 1 
HETATM 5 P PB AGS . . . Q 6 90.664 68.854 98.513 1 56.59 ? PB AGS 501 E 1 
HETATM 6 O O1B AGS . . . Q 6 89.751 69.658 99.355 1 51.76 ? O1B AGS 501 E 1 
HETATM 7 O O2B AGS . . . Q 6 91.369 67.717 99.253 1 58.24 ? O2B AGS 501 E 1 
HETATM 8 O O3B AGS . . . Q 6 91.81 69.767 97.925 1 53.05 ? O3B AGS 501 E 1 
HETATM 9 P PA AGS . . . Q 6 89.044 66.853 97.586 1 39.85 ? PA AGS 501 E 1 
HETATM 10 O O1A AGS . . . Q 6 87.602 67.153 97.693 1 52.88 ? O1A AGS 501 E 1 
HETATM 11 O O2A AGS . . . Q 6 89.661 66.189 98.819 1 53.08 ? O2A AGS 501 E 1 
HETATM 12 O O3A AGS . . . Q 6 89.868 68.172 97.335 1 50.75 ? O3A AGS 501 E 1 
HETATM 13 O O5' AGS . . . Q 6 89.277 65.988 96.287 1 51.85 ? O5' AGS 501 E 1 
HETATM 14 C C5' AGS . . . Q 6 90.603 65.816 95.748 1 52.7 ? C5' AGS 501 E 1 
HETATM 15 C C4' AGS . . . Q 6 90.742 64.394 95.272 1 48.19 ? C4' AGS 501 E 1 
HETATM 16 O O4' AGS . . . Q 6 89.486 63.706 95.455 1 54.43 ? O4' AGS 501 E 1 
HETATM 17 C C3' AGS . . . Q 6 91.092 64.236 93.796 1 52.54 ? C3' AGS 501 E 1 
HETATM 18 O O3' AGS . . . Q 6 91.888 63.075 93.587 1 57.47 ? O3' AGS 501 E 1 
HETATM 19 C C2' AGS . . . Q 6 89.717 64.114 93.139 1 55.33 ? C2' AGS 501 E 1 
HETATM 20 O O2' AGS . . . Q 6 89.775 63.364 91.932 1 62.76 ? O2' AGS 501 E 1 
HETATM 21 C C1' AGS . . . Q 6 88.935 63.346 94.203 1 53.74 ? C1' AGS 501 E 1 
HETATM 22 N N9 AGS . . . Q 6 87.51 63.653 94.224 1 52.19 ? N9 AGS 501 E 1 
HETATM 23 C C8 AGS . . . Q 6 86.903 64.721 94.829 1 53.17 ? C8 AGS 501 E 1 
HETATM 24 N N7 AGS . . . Q 6 85.6 64.747 94.686 1 52.08 ? N7 AGS 501 E 1 
HETATM 25 C C5 AGS . . . Q 6 85.331 63.616 93.931 1 53.04 ? C5 AGS 501 E 1 
HETATM 26 C C6 AGS . . . Q 6 84.131 63.071 93.435 1 53.41 ? C6 AGS 501 E 1 
HETATM 27 N N6 AGS . . . Q 6 82.929 63.615 93.636 1 53.3 ? N6 AGS 501 E 1 
HETATM 28 N N1 AGS . . . Q 6 84.211 61.929 92.716 1 50.11 ? N1 AGS 501 E 1 
HETATM 29 C C2 AGS . . . Q 6 85.413 61.379 92.514 1 49.22 ? C2 AGS 501 E 1 
HETATM 30 N N3 AGS . . . Q 6 86.609 61.802 92.93 1 49.27 ? N3 AGS 501 E 1 
HETATM 31 C C4 AGS . . . Q 6 86.498 62.933 93.638 1 52.24 ? C4 AGS 501 E 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    40 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#