data_9CDB
#
_model_server_result.job_id            Q474X3Zrujw7LQcPHfOJkg 
_model_server_result.datetime_utc      '2025-07-07 10:24:09' 
_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          9cdb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":701}' 
#
_entry.id    9CDB 
#
_exptl.entry_id    9CDB 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    12 
_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            9CDB 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9CDB 
_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_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,S,T,U,V,W,X,Y,Z,AA 
_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    x,y,z 
_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 J N N 
? 3 K N N 
? 3 M N N 
? 3 N N N 
? 3 P N N 
? 3 Q N N 
? 3 S N N 
? 3 T N N 
? 3 V N N 
? 3 W N N 
? 3 Y N N 
? 3 Z 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 OD1 ASP 533 A ASP 533 1_555 L MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc2 B OD1 ASP 533 B ASP 533 1_555 O MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc3 C OD1 ASP 533 C ASP 533 1_555 R MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? 
metalc ? metalc4 D OD1 ASP 533 D ASP 533 1_555 U MG MG . D MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc5 E OD1 ASP 533 E ASP 533 1_555 X MG MG . E MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? 
metalc ? metalc6 F OD1 ASP 533 F ASP 533 1_555 AA MG MG . F MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
#
_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 109 n n 
PG O2G ATP sing 110 n n 
PG O3G ATP sing 111 n n 
PG O3B ATP sing 112 n n 
O2G HOG2 ATP sing 113 n n 
O3G HOG3 ATP sing 114 n n 
PB O1B ATP doub 115 n n 
PB O2B ATP sing 116 n n 
PB O3B ATP sing 117 n n 
PB O3A ATP sing 118 n n 
O2B HOB2 ATP sing 119 n n 
PA O1A ATP doub 120 n n 
PA O2A ATP sing 121 n n 
PA O3A ATP sing 122 n n 
PA O5' ATP sing 123 n n 
O2A HOA2 ATP sing 124 n n 
O5' C5' ATP sing 125 n n 
C5' C4' ATP sing 126 n n 
C5' "H5'1" ATP sing 127 n n 
C5' "H5'2" ATP sing 128 n n 
C4' O4' ATP sing 129 n n 
C4' C3' ATP sing 130 n n 
C4' H4' ATP sing 131 n n 
O4' C1' ATP sing 132 n n 
C3' O3' ATP sing 133 n n 
C3' C2' ATP sing 134 n n 
C3' H3' ATP sing 135 n n 
O3' HO3' ATP sing 136 n n 
C2' O2' ATP sing 137 n n 
C2' C1' ATP sing 138 n n 
C2' H2' ATP sing 139 n n 
O2' HO2' ATP sing 140 n n 
C1' N9 ATP sing 141 n n 
C1' H1' ATP sing 142 n n 
N9 C8 ATP sing 143 n y 
N9 C4 ATP sing 144 n y 
C8 N7 ATP doub 145 n y 
C8 H8 ATP sing 146 n n 
N7 C5 ATP sing 147 n y 
C5 C6 ATP sing 148 n y 
C5 C4 ATP doub 149 n y 
C6 N6 ATP sing 150 n n 
C6 N1 ATP doub 151 n y 
N6 HN61 ATP sing 152 n n 
N6 HN62 ATP sing 153 n n 
N1 C2 ATP sing 154 n y 
C2 N3 ATP doub 155 n y 
C2 H2 ATP sing 156 n n 
N3 C4 ATP sing 157 n y 
#
_atom_sites.entry_id                     9CDB 
_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 3 ATP A 1 701 701 ATP LIG . 
K 3 ATP A 1 702 702 ATP LIG . 
L 4 MG A 1 703 1 MG MG . 
M 3 ATP B 1 701 3 ATP ATP . 
N 3 ATP B 1 702 7 ATP ATP . 
O 4 MG B 1 703 2 MG MG . 
P 3 ATP C 1 701 701 ATP LIG . 
Q 3 ATP C 1 702 702 ATP LIG . 
R 4 MG C 1 703 3 MG MG . 
S 3 ATP D 1 701 2 ATP ATP . 
T 3 ATP D 1 702 6 ATP ATP . 
U 4 MG D 1 703 4 MG MG . 
V 3 ATP E 1 701 701 ATP LIG . 
W 3 ATP E 1 702 4 ATP ATP . 
X 4 MG E 1 703 5 MG MG . 
Y 3 ATP F 1 701 1 ATP ATP . 
Z 3 ATP F 1 702 5 ATP ATP . 
AA 4 MG F 1 703 6 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 N N9 ATP . . . V 3 210.095 253.949 217.33 1 71.22 ? N9 ATP 701 E 1 
HETATM 2 C C8 ATP . . . V 3 208.954 253.41 216.761 1 71.22 ? C8 ATP 701 E 1 
HETATM 3 N N7 ATP . . . V 3 208.023 254.319 216.515 1 71.22 ? N7 ATP 701 E 1 
HETATM 4 C C5 ATP . . . V 3 208.573 255.509 216.939 1 71.22 ? C5 ATP 701 E 1 
HETATM 5 C C6 ATP . . . V 3 208.092 256.834 216.95 1 71.22 ? C6 ATP 701 E 1 
HETATM 6 N N6 ATP . . . V 3 206.891 257.19 216.498 1 71.22 ? N6 ATP 701 E 1 
HETATM 7 N N1 ATP . . . V 3 208.914 257.789 217.45 1 71.22 ? N1 ATP 701 E 1 
HETATM 8 C C2 ATP . . . V 3 210.122 257.429 217.902 1 71.22 ? C2 ATP 701 E 1 
HETATM 9 N N3 ATP . . . V 3 210.679 256.219 217.942 1 71.22 ? N3 ATP 701 E 1 
HETATM 10 C C4 ATP . . . V 3 209.843 255.299 217.441 1 71.22 ? C4 ATP 701 E 1 
#
_model_server_stats.io_time_ms              106 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           240 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           10 
#