data_9CDH
#
_model_server_result.job_id            FgHZp88xUQJfGT6RX_NQ2Q 
_model_server_result.datetime_utc      '2025-08-21 03:03:58' 
_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          9cdh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1102}' 
#
_entry.id    9CDH 
#
_exptl.entry_id    9CDH 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              506.196 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    2 
_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            9CDH 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9CDH 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 3 D N N 
? 3 G 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 ASN 39 A ASN 39 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.853 ? 
metalc ? metalc2 A SG CYS 499 A CYS 499 1_555 C ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? 
metalc ? metalc3 A SG CYS 502 A CYS 502 1_555 C ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc4 A SG CYS 525 A CYS 525 1_555 C ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc5 D O3G ANP . A ANP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.822 ? 
metalc ? metalc6 D O1B ANP . A ANP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc7 D O1A ANP . A ANP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? 
metalc ? metalc8 B OD1 ASN 39 B ASN 39 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? 
metalc ? metalc9 B SG CYS 499 B CYS 499 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc10 B SG CYS 502 B CYS 502 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc11 B SG CYS 525 B CYS 525 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc12 B SG CYS 536 B CYS 536 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc13 G O2G ANP . B ANP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? 
metalc ? metalc14 G O1B ANP . B ANP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc15 G O1A ANP . B ANP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? 
#
_chem_comp.formula           'C10 H17 N6 O12 P3' 
_chem_comp.formula_weight    506.196 
_chem_comp.id                ANP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' 
_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 ANP doub 13 n n 
PG O2G ANP sing 14 n n 
PG O3G ANP sing 15 n n 
PG N3B ANP sing 16 n n 
O2G HOG2 ANP sing 17 n n 
O3G HOG3 ANP sing 18 n n 
PB O1B ANP doub 19 n n 
PB O2B ANP sing 20 n n 
PB N3B ANP sing 21 n n 
PB O3A ANP sing 22 n n 
O2B HOB2 ANP sing 23 n n 
N3B HNB1 ANP sing 24 n n 
PA O1A ANP doub 25 n n 
PA O2A ANP sing 26 n n 
PA O3A ANP sing 27 n n 
PA O5' ANP sing 28 n n 
O2A HOA2 ANP sing 29 n n 
O5' C5' ANP sing 30 n n 
C5' C4' ANP sing 31 n n 
C5' "H5'1" ANP sing 32 n n 
C5' "H5'2" ANP sing 33 n n 
C4' O4' ANP sing 34 n n 
C4' C3' ANP sing 35 n n 
C4' H4' ANP sing 36 n n 
O4' C1' ANP sing 37 n n 
C3' O3' ANP sing 38 n n 
C3' C2' ANP sing 39 n n 
C3' H3' ANP sing 40 n n 
O3' HO3' ANP sing 41 n n 
C2' O2' ANP sing 42 n n 
C2' C1' ANP sing 43 n n 
C2' H2' ANP sing 44 n n 
O2' HO2' ANP sing 45 n n 
C1' N9 ANP sing 46 n n 
C1' H1' ANP sing 47 n n 
N9 C8 ANP sing 48 n y 
N9 C4 ANP sing 49 n y 
C8 N7 ANP doub 50 n y 
C8 H8 ANP sing 51 n n 
N7 C5 ANP sing 52 n y 
C5 C6 ANP sing 53 n y 
C5 C4 ANP doub 54 n y 
C6 N6 ANP sing 55 n n 
C6 N1 ANP doub 56 n y 
N6 HN61 ANP sing 57 n n 
N6 HN62 ANP sing 58 n n 
N1 C2 ANP sing 59 n y 
C2 N3 ANP doub 60 n y 
C2 H2 ANP sing 61 n n 
N3 C4 ANP sing 62 n y 
#
_atom_sites.entry_id                     9CDH 
_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
C 2 ZN A 1 1101 701 ZN ZN . 
D 3 ANP A 1 1102 702 ANP ANP . 
E 4 MG A 1 1103 703 MG MG . 
F 2 ZN B 1 1101 701 ZN ZN . 
G 3 ANP B 1 1102 702 ANP ANP . 
H 4 MG B 1 1103 703 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 P PG ANP . . . D 3 126.202 141.041 136.29 1 17.34 ? PG ANP 1102 A 1 
HETATM 2 O O1G ANP . . . D 3 127.025 139.887 136.853 1 26.11 ? O1G ANP 1102 A 1 
HETATM 3 O O2G ANP . . . D 3 125.191 140.618 135.232 1 22.95 ? O2G ANP 1102 A 1 
HETATM 4 O O3G ANP . . . D 3 127.014 142.285 135.945 1 29.59 ? O3G ANP 1102 A 1 
HETATM 5 P PB ANP . . . D 3 125.657 142.867 138.7 1 12.58 ? PB ANP 1102 A 1 
HETATM 6 O O1B ANP . . . D 3 126.28 143.996 137.94 1 18.34 ? O1B ANP 1102 A 1 
HETATM 7 O O2B ANP . . . D 3 124.636 143.123 139.773 1 22.07 ? O2B ANP 1102 A 1 
HETATM 8 N N3B ANP . . . D 3 125.237 141.634 137.672 1 17.11 ? N3B ANP 1102 A 1 
HETATM 9 P PA ANP . . . D 3 128.505 142.646 139.37 1 12.71 ? PA ANP 1102 A 1 
HETATM 10 O O1A ANP . . . D 3 128.776 143.309 138.064 1 20 ? O1A ANP 1102 A 1 
HETATM 11 O O2A ANP . . . D 3 129.429 141.56 139.877 1 23.73 ? O2A ANP 1102 A 1 
HETATM 12 O O3A ANP . . . D 3 126.978 142.156 139.489 1 20.53 ? O3A ANP 1102 A 1 
HETATM 13 O O5' ANP . . . D 3 128.463 143.849 140.495 1 18.26 ? O5' ANP 1102 A 1 
HETATM 14 C C5' ANP . . . D 3 127.968 143.6 141.787 1 20.32 ? C5' ANP 1102 A 1 
HETATM 15 C C4' ANP . . . D 3 127.166 144.762 142.325 1 18.55 ? C4' ANP 1102 A 1 
HETATM 16 O O4' ANP . . . D 3 128.025 145.816 142.758 1 20.39 ? O4' ANP 1102 A 1 
HETATM 17 C C3' ANP . . . D 3 126.23 145.427 141.316 1 21.14 ? C3' ANP 1102 A 1 
HETATM 18 O O3' ANP . . . D 3 125.061 144.721 141.091 1 24.41 ? O3' ANP 1102 A 1 
HETATM 19 C C2' ANP . . . D 3 126.053 146.813 141.913 1 20.35 ? C2' ANP 1102 A 1 
HETATM 20 O O2' ANP . . . D 3 125.109 146.76 142.941 1 25.14 ? O2' ANP 1102 A 1 
HETATM 21 C C1' ANP . . . D 3 127.458 147.059 142.494 1 15.67 ? C1' ANP 1102 A 1 
HETATM 22 N N9 ANP . . . D 3 128.336 147.78 141.58 1 14.97 ? N9 ANP 1102 A 1 
HETATM 23 C C8 ANP . . . D 3 129.316 147.274 140.775 1 17.99 ? C8 ANP 1102 A 1 
HETATM 24 N N7 ANP . . . D 3 129.93 148.183 140.082 1 14.29 ? N7 ANP 1102 A 1 
HETATM 25 C C5 ANP . . . D 3 129.324 149.355 140.439 1 12.79 ? C5 ANP 1102 A 1 
HETATM 26 C C6 ANP . . . D 3 129.517 150.69 140.053 1 13.83 ? C6 ANP 1102 A 1 
HETATM 27 N N6 ANP . . . D 3 130.44 151.057 139.158 1 13.93 ? N6 ANP 1102 A 1 
HETATM 28 N N1 ANP . . . D 3 128.741 151.621 140.609 1 15.49 ? N1 ANP 1102 A 1 
HETATM 29 C C2 ANP . . . D 3 127.826 151.253 141.5 1 11.38 ? C2 ANP 1102 A 1 
HETATM 30 N N3 ANP . . . D 3 127.549 150.041 141.938 1 9.73 ? N3 ANP 1102 A 1 
HETATM 31 C C4 ANP . . . D 3 128.33 149.125 141.373 1 12.28 ? C4 ANP 1102 A 1 
HETATM 32 H HNB1 ANP . . . D 3 124.362 141.608 137.51 1 21.11 ? HNB1 ANP 1102 A 1 
HETATM 33 H "H5'1" ANP . . . D 3 128.674 143.414 142.425 1 20.2 ? "H5'1" ANP 1102 A 1 
HETATM 34 H "H5'2" ANP . . . D 3 127.41 142.807 141.764 1 19.82 ? "H5'2" ANP 1102 A 1 
HETATM 35 H H4' ANP . . . D 3 126.655 144.433 143.081 1 19.84 ? H4' ANP 1102 A 1 
HETATM 36 H H3' ANP . . . D 3 126.717 145.564 140.489 1 19.89 ? H3' ANP 1102 A 1 
HETATM 37 H HO3' ANP . . . D 3 124.836 144.461 141.868 1 24.2 ? HO3' ANP 1102 A 1 
HETATM 38 H H2' ANP . . . D 3 125.827 147.48 141.246 1 21.12 ? H2' ANP 1102 A 1 
HETATM 39 H HO2' ANP . . . D 3 125.406 146.261 143.562 1 21.58 ? HO2' ANP 1102 A 1 
HETATM 40 H H1' ANP . . . D 3 127.407 147.587 143.303 1 17.8 ? H1' ANP 1102 A 1 
HETATM 41 H H8 ANP . . . D 3 129.507 146.364 140.746 1 18.35 ? H8 ANP 1102 A 1 
HETATM 42 H HN61 ANP . . . D 3 130.803 151.869 139.192 1 16.24 ? HN61 ANP 1102 A 1 
HETATM 43 H HN62 ANP . . . D 3 130.708 150.501 138.517 1 15.66 ? HN62 ANP 1102 A 1 
HETATM 44 H H2 ANP . . . D 3 127.312 151.943 141.853 1 15.52 ? H2 ANP 1102 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           264 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           44 
#