data_7TDG
#
_model_server_result.job_id            YcZrv2xzIVZRUIHcFc_JGQ 
_model_server_result.datetime_utc      '2025-07-31 04:15:20' 
_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          7tdg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Z","auth_seq_id":5104}' 
#
_entry.id    7TDG 
#
_exptl.entry_id    7TDG 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              505.208 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' 
_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            7TDG 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7TDG 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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
? 4 H N N 
? 4 N N N 
? 4 U N N 
? 4 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
disulf ? disulf1 A SG CYS 4876 A CYS 4876 1_555 A SG CYS 4882 A CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 B SG CYS 4876 C CYS 4876 1_555 B SG CYS 4882 C CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf3 C SG CYS 4876 D CYS 4876 1_555 C SG CYS 4882 D CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf4 D SG CYS 4876 B CYS 4876 1_555 D SG CYS 4882 B CYS 4882 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
metalc ? metalc1 A OE2 GLU 3893 A GLU 3893 1_555 F CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? 
metalc ? metalc2 A OE2 GLU 3967 A GLU 3967 1_555 F CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
metalc ? metalc3 A SG CYS 4958 A CYS 4958 1_555 E ZN ZN . A ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc4 A SG CYS 4961 A CYS 4961 1_555 E ZN ZN . A ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc5 A NE2 HIS 4978 A HIS 4978 1_555 E ZN ZN . A ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc6 A NE2 HIS 4983 A HIS 4983 1_555 E ZN ZN . A ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc7 A O THR 5001 A THR 5001 1_555 F CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc8 B OE2 GLU 3893 C GLU 3893 1_555 L CA CA . C CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? 
metalc ? metalc9 B OE2 GLU 3967 C GLU 3967 1_555 L CA CA . C CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc10 B SG CYS 4958 C CYS 4958 1_555 K ZN ZN . C ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc11 B SG CYS 4961 C CYS 4961 1_555 K ZN ZN . C ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc12 B NE2 HIS 4978 C HIS 4978 1_555 K ZN ZN . C ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc13 B NE2 HIS 4983 C HIS 4983 1_555 K ZN ZN . C ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc14 B O THR 5001 C THR 5001 1_555 L CA CA . C CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? 
metalc ? metalc15 C OE2 GLU 3893 D GLU 3893 1_555 S CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? 
metalc ? metalc16 C OE2 GLU 3967 D GLU 3967 1_555 S CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? 
metalc ? metalc17 C SG CYS 4958 D CYS 4958 1_555 R ZN ZN . D ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc18 C SG CYS 4961 D CYS 4961 1_555 R ZN ZN . D ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc19 C NE2 HIS 4978 D HIS 4978 1_555 R ZN ZN . D ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc20 C NE2 HIS 4983 D HIS 4983 1_555 R ZN ZN . D ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
metalc ? metalc21 C O THR 5001 D THR 5001 1_555 S CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? 
metalc ? metalc22 D OE2 GLU 3893 B GLU 3893 1_555 X CA CA . B CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? 
metalc ? metalc23 D OE2 GLU 3967 B GLU 3967 1_555 X CA CA . B CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc24 D SG CYS 4958 B CYS 4958 1_555 W ZN ZN . B ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc25 D SG CYS 4961 B CYS 4961 1_555 W ZN ZN . B ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc26 D NE2 HIS 4978 B HIS 4978 1_555 W ZN ZN . B ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc27 D NE2 HIS 4983 B HIS 4983 1_555 W ZN ZN . B ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc28 D O THR 5001 B THR 5001 1_555 X CA CA . B CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? 
#
_chem_comp.formula           'C11 H18 N5 O12 P3' 
_chem_comp.formula_weight    505.208 
_chem_comp.id                ACP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" 
#
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 ACP doub 1 n n 
PG O2G ACP sing 2 n n 
PG O3G ACP sing 3 n n 
PG C3B ACP sing 4 n n 
O2G HOG2 ACP sing 5 n n 
O3G HOG3 ACP sing 6 n n 
PB O1B ACP doub 7 n n 
PB O2B ACP sing 8 n n 
PB C3B ACP sing 9 n n 
PB O3A ACP sing 10 n n 
O2B HOB2 ACP sing 11 n n 
C3B H3B1 ACP sing 12 n n 
C3B H3B2 ACP sing 13 n n 
PA O1A ACP doub 14 n n 
PA O2A ACP sing 15 n n 
PA O3A ACP sing 16 n n 
PA O5' ACP sing 17 n n 
O2A HOA2 ACP sing 18 n n 
O5' C5' ACP sing 19 n n 
C5' C4' ACP sing 20 n n 
C5' "H5'1" ACP sing 21 n n 
C5' "H5'2" ACP sing 22 n n 
C4' O4' ACP sing 23 n n 
C4' C3' ACP sing 24 n n 
C4' H4' ACP sing 25 n n 
O4' C1' ACP sing 26 n n 
C3' O3' ACP sing 27 n n 
C3' C2' ACP sing 28 n n 
C3' H3' ACP sing 29 n n 
O3' HO3' ACP sing 30 n n 
C2' O2' ACP sing 31 n n 
C2' C1' ACP sing 32 n n 
C2' H2' ACP sing 33 n n 
O2' HO2' ACP sing 34 n n 
C1' N9 ACP sing 35 n n 
C1' H1' ACP sing 36 n n 
N9 C8 ACP sing 37 n y 
N9 C4 ACP sing 38 n y 
C8 N7 ACP doub 39 n y 
C8 H8 ACP sing 40 n n 
N7 C5 ACP sing 41 n y 
C5 C6 ACP sing 42 n y 
C5 C4 ACP doub 43 n y 
C6 N6 ACP sing 44 n n 
C6 N1 ACP doub 45 n y 
N6 HN61 ACP sing 46 n n 
N6 HN62 ACP sing 47 n n 
N1 C2 ACP sing 48 n y 
C2 N3 ACP doub 49 n y 
C2 H2 ACP sing 50 n n 
N3 C4 ACP sing 51 n y 
#
_atom_sites.entry_id                     7TDG 
_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
E 2 ZN A 1 5101 3 ZN ZN . 
F 3 CA A 1 5102 4 CA CA . 
G 3 CA A 1 5103 7 CA CA . 
H 4 ACP A 1 5104 3 ACP ACP . 
I 5 POV A 1 5105 2 POV LIG . 
J 5 POV A 1 5106 3 POV LIG . 
K 2 ZN C 1 5101 1 ZN ZN . 
L 3 CA C 1 5102 3 CA CA . 
M 3 CA C 1 5103 5 CA CA . 
N 4 ACP C 1 5104 2 ACP ACP . 
O 5 POV C 1 5105 6 POV LIG . 
P 5 POV C 1 5106 7 POV LIG . 
Q 5 POV C 1 5107 8 POV LIG . 
R 2 ZN D 1 5101 4 ZN ZN . 
S 3 CA D 1 5102 1 CA CA . 
T 3 CA D 1 5103 8 CA CA . 
U 4 ACP D 1 5104 4 ACP ACP . 
V 5 POV D 1 5105 1 POV LIG . 
W 2 ZN B 1 5101 2 ZN ZN . 
X 3 CA B 1 5102 2 CA CA . 
Y 3 CA B 1 5103 6 CA CA . 
Z 4 ACP B 1 5104 1 ACP ACP . 
AA 5 POV B 1 5105 4 POV LIG . 
BA 5 POV B 1 5106 5 POV LIG . 
#
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 ACP . . . Z 4 212.349 227.281 286.964 1 54.48 ? PG ACP 5104 B 1 
HETATM 2 O O1G ACP . . . Z 4 211.754 227.054 288.298 1 54.48 ? O1G ACP 5104 B 1 
HETATM 3 O O2G ACP . . . Z 4 211.328 226.77 285.831 1 54.48 ? O2G ACP 5104 B 1 
HETATM 4 O O3G ACP . . . Z 4 212.644 228.848 286.762 1 54.48 ? O3G ACP 5104 B 1 
HETATM 5 P PB ACP . . . Z 4 215.28 227.559 286.792 1 54.48 ? PB ACP 5104 B 1 
HETATM 6 O O1B ACP . . . Z 4 215.965 227.584 288.102 1 54.48 ? O1B ACP 5104 B 1 
HETATM 7 O O2B ACP . . . Z 4 214.707 229.026 286.456 1 54.48 ? O2B ACP 5104 B 1 
HETATM 8 C C3B ACP . . . Z 4 213.911 226.376 286.838 1 54.48 ? C3B ACP 5104 B 1 
HETATM 9 P PA ACP . . . Z 4 217.886 227.052 286.109 1 54.48 ? PA ACP 5104 B 1 
HETATM 10 O O1A ACP . . . Z 4 218.267 228.416 286.624 1 54.48 ? O1A ACP 5104 B 1 
HETATM 11 O O2A ACP . . . Z 4 218.051 225.836 286.98 1 54.48 ? O2A ACP 5104 B 1 
HETATM 12 O O3A ACP . . . Z 4 216.346 227.121 285.674 1 54.48 ? O3A ACP 5104 B 1 
HETATM 13 O O5' ACP . . . Z 4 218.659 226.797 284.728 1 54.48 ? O5' ACP 5104 B 1 
HETATM 14 C C5' ACP . . . Z 4 218.888 227.883 283.842 1 54.48 ? C5' ACP 5104 B 1 
HETATM 15 C C4' ACP . . . Z 4 220.382 228.033 283.616 1 54.48 ? C4' ACP 5104 B 1 
HETATM 16 O O4' ACP . . . Z 4 221.072 226.858 283.412 1 54.48 ? O4' ACP 5104 B 1 
HETATM 17 C C3' ACP . . . Z 4 220.68 228.971 282.462 1 54.48 ? C3' ACP 5104 B 1 
HETATM 18 O O3' ACP . . . Z 4 221.154 230.223 282.951 1 54.48 ? O3' ACP 5104 B 1 
HETATM 19 C C2' ACP . . . Z 4 221.717 228.261 281.615 1 54.48 ? C2' ACP 5104 B 1 
HETATM 20 O O2' ACP . . . Z 4 222.939 228.982 281.465 1 54.48 ? O2' ACP 5104 B 1 
HETATM 21 C C1' ACP . . . Z 4 221.985 226.95 282.32 1 54.48 ? C1' ACP 5104 B 1 
HETATM 22 N N9 ACP . . . Z 4 221.79 225.898 281.304 1 54.48 ? N9 ACP 5104 B 1 
HETATM 23 C C8 ACP . . . Z 4 221.012 224.804 281.377 1 54.48 ? C8 ACP 5104 B 1 
HETATM 24 N N7 ACP . . . Z 4 221.095 224.091 280.227 1 54.48 ? N7 ACP 5104 B 1 
HETATM 25 C C5 ACP . . . Z 4 221.929 224.744 279.41 1 54.48 ? C5 ACP 5104 B 1 
HETATM 26 C C6 ACP . . . Z 4 222.46 224.551 278.056 1 54.48 ? C6 ACP 5104 B 1 
HETATM 27 N N6 ACP . . . Z 4 222.098 223.479 277.324 1 54.48 ? N6 ACP 5104 B 1 
HETATM 28 N N1 ACP . . . Z 4 223.314 225.474 277.576 1 54.48 ? N1 ACP 5104 B 1 
HETATM 29 C C2 ACP . . . Z 4 223.688 226.547 278.29 1 54.48 ? C2 ACP 5104 B 1 
HETATM 30 N N3 ACP . . . Z 4 223.239 226.783 279.53 1 54.48 ? N3 ACP 5104 B 1 
HETATM 31 C C4 ACP . . . Z 4 222.38 225.933 280.122 1 54.48 ? C4 ACP 5104 B 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    151 
_model_server_stats.query_time_ms           356 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           31 
#