data_9CDJ
#
_model_server_result.job_id            ImXwvTFAQxYTUnJPWfYIxQ 
_model_server_result.datetime_utc      '2025-08-21 03:04:05' 
_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          9cdj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":702}' 
#
_entry.id    9CDJ 
#
_exptl.entry_id    9CDJ 
_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            9CDJ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9CDJ 
_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 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? 
metalc ? metalc2 A SG CYS 499 A CYS 499 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc3 A SG CYS 502 A CYS 502 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc4 A SG CYS 525 A CYS 525 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc5 A SG CYS 536 A CYS 536 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc6 D O3G ANP . A ANP 702 1_555 E MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? 
metalc ? metalc7 D O1B ANP . A ANP 702 1_555 E MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? 
metalc ? metalc8 D O1A ANP . A ANP 702 1_555 E MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc9 B OD1 ASN 39 B ASN 39 1_555 H MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.872 ? 
metalc ? metalc10 B SG CYS 499 B CYS 499 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc11 B SG CYS 502 B CYS 502 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc12 B SG CYS 525 B CYS 525 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc13 B SG CYS 536 B CYS 536 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc14 G O2G ANP . B ANP 702 1_555 H MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? 
metalc ? metalc15 G O1B ANP . B ANP 702 1_555 H MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? 
metalc ? metalc16 G O1A ANP . B ANP 702 1_555 H MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
#
_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                     9CDJ 
_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 1 701 701 ZN ZN . 
D 3 ANP A 1 702 702 ANP ANP . 
E 4 MG A 1 703 703 MG MG . 
F 2 ZN B 1 701 701 ZN ZN . 
G 3 ANP B 1 702 702 ANP ANP . 
H 4 MG B 1 703 703 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 93.879 104.048 108.713 1 52.9 ? PG ANP 702 A 1 
HETATM 2 O O1G ANP . . . D 3 95.245 104.53 109.19 1 50.81 ? O1G ANP 702 A 1 
HETATM 3 O O2G ANP . . . D 3 93.958 102.901 107.708 1 49.75 ? O2G ANP 702 A 1 
HETATM 4 O O3G ANP . . . D 3 92.907 105.164 108.33 1 57.6 ? O3G ANP 702 A 1 
HETATM 5 P PB ANP . . . D 3 92.203 104.207 111.327 1 40.5 ? PB ANP 702 A 1 
HETATM 6 O O1B ANP . . . D 3 91.286 105.206 110.692 1 48.65 ? O1B ANP 702 A 1 
HETATM 7 O O2B ANP . . . D 3 91.718 103.319 112.442 1 49.67 ? O2B ANP 702 A 1 
HETATM 8 N N3B ANP . . . D 3 93.077 103.383 110.171 1 49.13 ? N3B ANP 702 A 1 
HETATM 9 P PA ANP . . . D 3 93.449 106.795 111.923 1 44.79 ? PA ANP 702 A 1 
HETATM 10 O O1A ANP . . . D 3 92.894 107.3 110.634 1 40.14 ? O1A ANP 702 A 1 
HETATM 11 O O2A ANP . . . D 3 94.798 107.293 112.402 1 53.5 ? O2A ANP 702 A 1 
HETATM 12 O O3A ANP . . . D 3 93.402 105.188 112.017 1 48.73 ? O3A ANP 702 A 1 
HETATM 13 O O5' ANP . . . D 3 92.323 107.17 113.07 1 44.78 ? O5' ANP 702 A 1 
HETATM 14 C C5' ANP . . . D 3 92.417 106.65 114.373 1 46.87 ? C5' ANP 702 A 1 
HETATM 15 C C4' ANP . . . D 3 91.065 106.281 114.944 1 46.51 ? C4' ANP 702 A 1 
HETATM 16 O O4' ANP . . . D 3 90.397 107.44 115.441 1 47.59 ? O4' ANP 702 A 1 
HETATM 17 C C3' ANP . . . D 3 90.074 105.671 113.951 1 50.09 ? C3' ANP 702 A 1 
HETATM 18 O O3' ANP . . . D 3 90.304 104.334 113.677 1 48.97 ? O3' ANP 702 A 1 
HETATM 19 C C2' ANP . . . D 3 88.738 105.977 114.605 1 47.07 ? C2' ANP 702 A 1 
HETATM 20 O O2' ANP . . . D 3 88.498 105.041 115.615 1 47.71 ? O2' ANP 702 A 1 
HETATM 21 C C1' ANP . . . D 3 89.028 107.365 115.202 1 48.63 ? C1' ANP 702 A 1 
HETATM 22 N N9 ANP . . . D 3 88.662 108.458 114.308 1 47.24 ? N9 ANP 702 A 1 
HETATM 23 C C8 ANP . . . D 3 89.484 109.236 113.541 1 41.83 ? C8 ANP 702 A 1 
HETATM 24 N N7 ANP . . . D 3 88.847 110.136 112.852 1 44.51 ? N7 ANP 702 A 1 
HETATM 25 C C5 ANP . . . D 3 87.531 109.947 113.179 1 38.2 ? C5 ANP 702 A 1 
HETATM 26 C C6 ANP . . . D 3 86.344 110.582 112.785 1 39.43 ? C6 ANP 702 A 1 
HETATM 27 N N6 ANP . . . D 3 86.318 111.6 111.916 1 49.18 ? N6 ANP 702 A 1 
HETATM 28 N N1 ANP . . . D 3 85.197 110.145 113.306 1 46.21 ? N1 ANP 702 A 1 
HETATM 29 C C2 ANP . . . D 3 85.218 109.134 114.17 1 46.31 ? C2 ANP 702 A 1 
HETATM 30 N N3 ANP . . . D 3 86.261 108.461 114.614 1 50.28 ? N3 ANP 702 A 1 
HETATM 31 C C4 ANP . . . D 3 87.397 108.909 114.086 1 45.09 ? C4 ANP 702 A 1 
HETATM 32 H HNB1 ANP . . . D 3 93.454 102.636 110.472 1 51.73 ? HNB1 ANP 702 A 1 
HETATM 33 H "H5'1" ANP . . . D 3 92.832 107.273 114.991 1 46.01 ? "H5'1" ANP 702 A 1 
HETATM 34 H "H5'2" ANP . . . D 3 92.987 105.866 114.36 1 47.58 ? "H5'2" ANP 702 A 1 
HETATM 35 H H4' ANP . . . D 3 91.222 105.664 115.675 1 47.69 ? H4' ANP 702 A 1 
HETATM 36 H H3' ANP . . . D 3 90.089 106.2 113.138 1 48.57 ? H3' ANP 702 A 1 
HETATM 37 H HO3' ANP . . . D 3 91.142 104.251 113.797 1 50.16 ? HO3' ANP 702 A 1 
HETATM 38 H H2' ANP . . . D 3 88.008 106.02 113.968 1 48.02 ? H2' ANP 702 A 1 
HETATM 39 H HO2' ANP . . . D 3 87.753 105.221 115.983 1 47.43 ? HO2' ANP 702 A 1 
HETATM 40 H H1' ANP . . . D 3 88.532 107.495 116.023 1 47.83 ? H1' ANP 702 A 1 
HETATM 41 H H8 ANP . . . D 3 90.406 109.113 113.529 1 43.42 ? H8 ANP 702 A 1 
HETATM 42 H HN61 ANP . . . D 3 87.036 112.114 111.801 1 46 ? HN61 ANP 702 A 1 
HETATM 43 H HN62 ANP . . . D 3 85.589 111.78 111.439 1 46.94 ? HN62 ANP 702 A 1 
HETATM 44 H H2 ANP . . . D 3 84.389 108.872 114.499 1 46.68 ? H2 ANP 702 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           44 
#