data_8DW6
#
_model_server_result.job_id            fkeeHldF-pR6D80d4orSeg 
_model_server_result.datetime_utc      '2024-11-09 23:18:07' 
_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          8dw6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":501}' 
#
_entry.id    8DW6 
#
_exptl.entry_id    8DW6 
_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    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            8DW6 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DW6 
_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    nonameric 
_pdbx_struct_assembly.oligomeric_count      9 
_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 
_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 J N N 
? 5 L N N 
? 5 N N N 
? 5 P N N 
? 5 R 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 B OG SER 204 B SER 204 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? 
metalc ? metalc2 B OE2 GLU 227 B GLU 227 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? 
metalc ? metalc3 J O3B AGS . B AGS 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc4 J O3A AGS . B AGS 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? 
metalc ? metalc5 C OG SER 204 C SER 204 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? 
metalc ? metalc6 C OE2 GLU 227 C GLU 227 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
metalc ? metalc7 L O3G AGS . C AGS 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? 
metalc ? metalc8 L O1B AGS . C AGS 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? 
metalc ? metalc9 N O2G AGS . D AGS 501 1_555 O MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? 
metalc ? metalc10 N O2B AGS . D AGS 501 1_555 O MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc11 P O2G AGS . E AGS 501 1_555 Q MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? 
metalc ? metalc12 P O2B AGS . E AGS 501 1_555 Q MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc13 F OG SER 204 F SER 204 1_555 S MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc14 R O3G AGS . F AGS 501 1_555 S MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? 
metalc ? metalc15 R O2B AGS . F AGS 501 1_555 S MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc16 H SG CYS 37 H CYS 37 1_555 T ZN ZN . H ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc17 H SG CYS 40 H CYS 40 1_555 T ZN ZN . H ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc18 H SG CYS 65 H CYS 65 1_555 T ZN ZN . H ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc19 H SG CYS 68 H CYS 68 1_555 T ZN ZN . H ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
#
_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                     8DW6 
_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
J 5 AGS B 1 501 501 AGS AGS . 
K 6 MG B 1 502 502 MG MG . 
L 5 AGS C 1 501 501 AGS AGS . 
M 6 MG C 1 502 502 MG MG . 
N 5 AGS D 1 501 501 AGS AGS . 
O 6 MG D 1 502 502 MG MG . 
P 5 AGS E 1 501 501 AGS AGS . 
Q 6 MG E 1 502 502 MG MG . 
R 5 AGS F 1 501 501 AGS AGS . 
S 6 MG F 1 502 502 MG MG . 
T 7 ZN H 1 401 401 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 . . . P 5 153.042 105.134 143.515 1 63.56 ? PG AGS 501 E 1 
HETATM 2 S S1G AGS . . . P 5 152.832 103.256 143.045 1 64.84 ? S1G AGS 501 E 1 
HETATM 3 O O2G AGS . . . P 5 152.962 106.008 142.23 1 54.19 ? O2G AGS 501 E 1 
HETATM 4 O O3G AGS . . . P 5 151.894 105.542 144.483 1 50.92 ? O3G AGS 501 E 1 
HETATM 5 P PB AGS . . . P 5 155.634 105.97 143.415 1 56.59 ? PB AGS 501 E 1 
HETATM 6 O O1B AGS . . . P 5 155.978 107.314 143.928 1 51.76 ? O1B AGS 501 E 1 
HETATM 7 O O2B AGS . . . P 5 155.216 105.995 141.943 1 58.24 ? O2B AGS 501 E 1 
HETATM 8 O O3B AGS . . . P 5 154.414 105.359 144.216 1 53.05 ? O3B AGS 501 E 1 
HETATM 9 P PA AGS . . . P 5 156.665 103.437 143.579 1 39.85 ? PA AGS 501 E 1 
HETATM 10 O O1A AGS . . . P 5 155.969 102.948 142.376 1 52.88 ? O1A AGS 501 E 1 
HETATM 11 O O2A AGS . . . P 5 155.929 103.154 144.89 1 53.08 ? O2A AGS 501 E 1 
HETATM 12 O O3A AGS . . . P 5 156.884 105.003 143.512 1 50.75 ? O3A AGS 501 E 1 
HETATM 13 O O5' AGS . . . P 5 158.114 102.813 143.581 1 51.85 ? O5' AGS 501 E 1 
HETATM 14 C C5' AGS . . . P 5 159.236 103.519 143.021 1 52.7 ? C5' AGS 501 E 1 
HETATM 15 C C4' AGS . . . P 5 160.294 102.522 142.624 1 48.19 ? C4' AGS 501 E 1 
HETATM 16 O O4' AGS . . . P 5 159.884 101.203 143.019 1 54.43 ? O4' AGS 501 E 1 
HETATM 17 C C3' AGS . . . P 5 160.544 102.402 141.128 1 52.54 ? C3' AGS 501 E 1 
HETATM 18 O O3' AGS . . . P 5 161.471 103.388 140.686 1 57.47 ? O3' AGS 501 E 1 
HETATM 19 C C2' AGS . . . P 5 161.115 100.985 140.988 1 55.33 ? C2' AGS 501 E 1 
HETATM 20 O O2' AGS . . . P 5 162.538 100.988 140.987 1 62.76 ? O2' AGS 501 E 1 
HETATM 21 C C1' AGS . . . P 5 160.577 100.255 142.229 1 53.74 ? C1' AGS 501 E 1 
HETATM 22 N N9 AGS . . . P 5 159.668 99.155 141.929 1 52.19 ? N9 AGS 501 E 1 
HETATM 23 C C8 AGS . . . P 5 158.324 99.237 141.671 1 53.17 ? C8 AGS 501 E 1 
HETATM 24 N N7 AGS . . . P 5 157.753 98.082 141.434 1 52.08 ? N7 AGS 501 E 1 
HETATM 25 C C5 AGS . . . P 5 158.796 97.173 141.545 1 53.04 ? C5 AGS 501 E 1 
HETATM 26 C C6 AGS . . . P 5 158.851 95.773 141.408 1 53.41 ? C6 AGS 501 E 1 
HETATM 27 N N6 AGS . . . P 5 157.793 95.014 141.117 1 53.3 ? N6 AGS 501 E 1 
HETATM 28 N N1 AGS . . . P 5 160.048 95.174 141.585 1 50.11 ? N1 AGS 501 E 1 
HETATM 29 C C2 AGS . . . P 5 161.111 95.929 141.877 1 49.22 ? C2 AGS 501 E 1 
HETATM 30 N N3 AGS . . . P 5 161.179 97.253 142.031 1 49.27 ? N3 AGS 501 E 1 
HETATM 31 C C4 AGS . . . P 5 159.979 97.821 141.851 1 52.24 ? C4 AGS 501 E 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    45 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#