data_8DBU
#
_model_server_result.job_id            JFG30-1ZkREg-wcOAAumAw 
_model_server_result.datetime_utc      '2024-12-21 18:54:30' 
_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          8dbu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":600}' 
#
_entry.id    8DBU 
#
_exptl.entry_id    8DBU 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          9 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_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            8DBU 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DBU 
_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    22-meric 
_pdbx_struct_assembly.oligomeric_count      22 
_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,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA 
_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
? 9 W N N 
? 9 Y N N 
? 9 AA N N 
? 9 DA 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 176 A THR 176 1_555 X MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc2 W O2G ATP . A ATP 600 1_555 X MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc3 W O2B ATP . A ATP 600 1_555 X MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
metalc ? metalc4 B OG1 THR 176 B THR 176 1_555 Z MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc5 Y O2G ATP . B ATP 600 1_555 Z MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc6 Y O2B ATP . B ATP 600 1_555 Z MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc7 C OG1 THR 176 C THR 176 1_555 BA MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc8 AA O2G ATP . C ATP 600 1_555 BA MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc9 AA O2B ATP . C ATP 600 1_555 BA MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? 
metalc ? metalc10 D OG1 THR 157 D THR 156 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc11 CA MG MG . D MG 501 1_555 DA O1G ATP . D ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? 
metalc ? metalc12 CA MG MG . D MG 501 1_555 DA O3B ATP . D ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? 
metalc ? metalc13 CA MG MG . D MG 501 1_555 DA O1B ATP . D ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc14 E OG1 THR 157 E THR 156 1_555 FA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? 
metalc ? metalc15 EA O1B ADP . E ADP 501 1_555 FA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc16 EA O2B ADP . E ADP 501 1_555 FA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                ATP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "ADENOSINE-5'-TRIPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 O1G ATP doub 114 n n 
PG O2G ATP sing 115 n n 
PG O3G ATP sing 116 n n 
PG O3B ATP sing 117 n n 
O2G HOG2 ATP sing 118 n n 
O3G HOG3 ATP sing 119 n n 
PB O1B ATP doub 120 n n 
PB O2B ATP sing 121 n n 
PB O3B ATP sing 122 n n 
PB O3A ATP sing 123 n n 
O2B HOB2 ATP sing 124 n n 
PA O1A ATP doub 125 n n 
PA O2A ATP sing 126 n n 
PA O3A ATP sing 127 n n 
PA O5' ATP sing 128 n n 
O2A HOA2 ATP sing 129 n n 
O5' C5' ATP sing 130 n n 
C5' C4' ATP sing 131 n n 
C5' "H5'1" ATP sing 132 n n 
C5' "H5'2" ATP sing 133 n n 
C4' O4' ATP sing 134 n n 
C4' C3' ATP sing 135 n n 
C4' H4' ATP sing 136 n n 
O4' C1' ATP sing 137 n n 
C3' O3' ATP sing 138 n n 
C3' C2' ATP sing 139 n n 
C3' H3' ATP sing 140 n n 
O3' HO3' ATP sing 141 n n 
C2' O2' ATP sing 142 n n 
C2' C1' ATP sing 143 n n 
C2' H2' ATP sing 144 n n 
O2' HO2' ATP sing 145 n n 
C1' N9 ATP sing 146 n n 
C1' H1' ATP sing 147 n n 
N9 C8 ATP sing 148 n y 
N9 C4 ATP sing 149 n y 
C8 N7 ATP doub 150 n y 
C8 H8 ATP sing 151 n n 
N7 C5 ATP sing 152 n y 
C5 C6 ATP sing 153 n y 
C5 C4 ATP doub 154 n y 
C6 N6 ATP sing 155 n n 
C6 N1 ATP doub 156 n y 
N6 HN61 ATP sing 157 n n 
N6 HN62 ATP sing 158 n n 
N1 C2 ATP sing 159 n y 
C2 N3 ATP doub 160 n y 
C2 H2 ATP sing 161 n n 
N3 C4 ATP sing 162 n y 
#
_atom_sites.entry_id                     8DBU 
_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
W 9 ATP A 1 600 600 ATP ATP . 
X 10 MG A 1 601 601 MG MG . 
Y 9 ATP B 1 600 600 ATP ATP . 
Z 10 MG B 1 601 601 MG MG . 
AA 9 ATP C 1 600 600 ATP ATP . 
BA 10 MG C 1 601 601 MG MG . 
CA 10 MG D 1 501 501 MG MG . 
DA 9 ATP D 1 502 601 ATP ATP . 
EA 11 ADP E 1 501 500 ADP ADP . 
FA 10 MG E 1 502 502 MG MG . 
GA 11 ADP F 1 500 500 ADP ADP . 
#
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 ATP . . . W 9 155.31 140.661 205.915 1 52.9 ? PG ATP 600 A 1 
HETATM 2 O O1G ATP . . . W 9 156.513 139.839 206.289 1 52.9 ? O1G ATP 600 A 1 
HETATM 3 O O2G ATP . . . W 9 153.999 139.906 206.165 1 52.9 ? O2G ATP 600 A 1 
HETATM 4 O O3G ATP . . . W 9 155.398 141.196 204.516 1 52.9 ? O3G ATP 600 A 1 
HETATM 5 P PB ATP . . . W 9 154.23 143.22 207.104 1 52.9 ? PB ATP 600 A 1 
HETATM 6 O O1B ATP . . . W 9 154.235 144.228 205.992 1 52.9 ? O1B ATP 600 A 1 
HETATM 7 O O2B ATP . . . W 9 152.823 142.735 207.449 1 52.9 ? O2B ATP 600 A 1 
HETATM 8 O O3B ATP . . . W 9 155.194 141.959 206.853 1 52.9 ? O3B ATP 600 A 1 
HETATM 9 P PA ATP . . . W 9 154.776 143.484 210.014 1 52.9 ? PA ATP 600 A 1 
HETATM 10 O O1A ATP . . . W 9 155.293 142.146 210.374 1 52.9 ? O1A ATP 600 A 1 
HETATM 11 O O2A ATP . . . W 9 153.368 143.803 210.483 1 52.9 ? O2A ATP 600 A 1 
HETATM 12 O O3A ATP . . . W 9 154.856 143.807 208.432 1 52.9 ? O3A ATP 600 A 1 
HETATM 13 O O5' ATP . . . W 9 155.724 144.579 210.649 1 52.9 ? O5' ATP 600 A 1 
HETATM 14 C C5' ATP . . . W 9 157.135 144.634 210.332 1 52.9 ? C5' ATP 600 A 1 
HETATM 15 C C4' ATP . . . W 9 157.885 145.081 211.566 1 52.9 ? C4' ATP 600 A 1 
HETATM 16 O O4' ATP . . . W 9 157.598 146.467 211.848 1 52.9 ? O4' ATP 600 A 1 
HETATM 17 C C3' ATP . . . W 9 157.569 144.302 212.846 1 52.9 ? C3' ATP 600 A 1 
HETATM 18 O O3' ATP . . . W 9 158.766 143.977 213.545 1 52.9 ? O3' ATP 600 A 1 
HETATM 19 C C2' ATP . . . W 9 156.665 145.253 213.625 1 52.9 ? C2' ATP 600 A 1 
HETATM 20 O O2' ATP . . . W 9 156.804 145.09 215.029 1 52.9 ? O2' ATP 600 A 1 
HETATM 21 C C1' ATP . . . W 9 157.222 146.608 213.2 1 52.9 ? C1' ATP 600 A 1 
HETATM 22 N N9 ATP . . . W 9 156.275 147.716 213.315 1 52.9 ? N9 ATP 600 A 1 
HETATM 23 C C8 ATP . . . W 9 155.025 147.829 212.751 1 52.9 ? C8 ATP 600 A 1 
HETATM 24 N N7 ATP . . . W 9 154.399 148.935 213.038 1 52.9 ? N7 ATP 600 A 1 
HETATM 25 C C5 ATP . . . W 9 155.279 149.619 213.861 1 52.9 ? C5 ATP 600 A 1 
HETATM 26 C C6 ATP . . . W 9 155.223 150.853 214.509 1 52.9 ? C6 ATP 600 A 1 
HETATM 27 N N6 ATP . . . W 9 154.165 151.694 214.43 1 52.9 ? N6 ATP 600 A 1 
HETATM 28 N N1 ATP . . . W 9 156.272 151.245 215.258 1 52.9 ? N1 ATP 600 A 1 
HETATM 29 C C2 ATP . . . W 9 157.327 150.424 215.345 1 52.9 ? C2 ATP 600 A 1 
HETATM 30 N N3 ATP . . . W 9 157.499 149.228 214.778 1 52.9 ? N3 ATP 600 A 1 
HETATM 31 C C4 ATP . . . W 9 156.439 148.878 214.046 1 52.9 ? C4 ATP 600 A 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    117 
_model_server_stats.query_time_ms           345 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           31 
#