data_5YT3
#
_model_server_result.job_id            Kl0UYCt3M6K9MaU1mNrUkw 
_model_server_result.datetime_utc      '2024-11-08 09:11:50' 
_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          5yt3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    5YT3 
#
_exptl.entry_id    5YT3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              506.196 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC 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            5YT3 
_cell.length_a            132.17 
_cell.length_b            132.55 
_cell.length_c            91.21 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YT3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,K,L 1 1 
C,D,H,I,J,M,N 2 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
? 2 E N N 
? 2 G N N 
? 2 H N N 
? 2 J 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 157 A ASN 195 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc2 A OD2 ASP 170 A ASP 208 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc3 E O2G ANP . A ANP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? 
metalc ? metalc4 E O1B ANP . A ANP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc5 E O1A ANP . A ANP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.855 ? 
metalc ? metalc6 C OD1 ASN 157 C ASN 195 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
metalc ? metalc7 C OD2 ASP 170 C ASP 208 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? 
metalc ? metalc8 H O2G ANP . C ANP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? 
metalc ? metalc9 H O1B ANP . C ANP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc10 H O1A ANP . C ANP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? 
#
_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                     5YT3 
_atom_sites.fract_transf_matrix[1][1]    0.007566 
_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]    0.007544 
_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]    0.010964 
_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 ANP A 1 401 1 ANP ANP . 
F 3 MG A 1 402 1 MG MG . 
G 2 ANP B 1 401 2 ANP ANP . 
H 2 ANP C 1 401 3 ANP ANP . 
I 3 MG C 1 402 2 MG MG . 
J 2 ANP D 1 401 4 ANP ANP . 
K 4 HOH A 1 501 24 HOH HOH . 
K 4 HOH A 2 502 12 HOH HOH . 
K 4 HOH A 3 503 4 HOH HOH . 
K 4 HOH A 4 504 23 HOH HOH . 
K 4 HOH A 5 505 9 HOH HOH . 
L 4 HOH B 1 501 25 HOH HOH . 
L 4 HOH B 2 502 26 HOH HOH . 
M 4 HOH C 1 501 6 HOH HOH . 
M 4 HOH C 2 502 18 HOH HOH . 
M 4 HOH C 3 503 1 HOH HOH . 
M 4 HOH C 4 504 28 HOH HOH . 
N 4 HOH D 1 501 21 HOH HOH . 
N 4 HOH D 2 502 22 HOH HOH . 
N 4 HOH D 3 503 29 HOH HOH . 
#
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 . . . H 2 -13.524 -17.296 6.955 1 51.84 ? PG ANP 401 C 1 
HETATM 2 O O1G ANP . . . H 2 -12.789 -18.017 5.847 1 52.19 ? O1G ANP 401 C 1 
HETATM 3 O O2G ANP . . . H 2 -14.2 -15.981 6.599 1 41.51 ? O2G ANP 401 C 1 
HETATM 4 O O3G ANP . . . H 2 -12.719 -17.193 8.236 1 51.92 ? O3G ANP 401 C 1 
HETATM 5 P PB ANP . . . H 2 -16.303 -17.985 7.748 1 38.58 ? PB ANP 401 C 1 
HETATM 6 O O1B ANP . . . H 2 -16.735 -16.917 6.805 1 35.62 ? O1B ANP 401 C 1 
HETATM 7 O O2B ANP . . . H 2 -17.158 -19.208 7.917 1 50.96 ? O2B ANP 401 C 1 
HETATM 8 N N3B ANP . . . H 2 -14.722 -18.522 7.291 1 43.79 ? N3B ANP 401 C 1 
HETATM 9 P PA ANP . . . H 2 -16.262 -15.997 9.831 1 50.3 ? PA ANP 401 C 1 
HETATM 10 O O1A ANP . . . H 2 -15.688 -15.047 8.802 1 49.49 ? O1A ANP 401 C 1 
HETATM 11 O O2A ANP . . . H 2 -15.582 -16.32 11.155 1 50.47 ? O2A ANP 401 C 1 
HETATM 12 O O3A ANP . . . H 2 -16.273 -17.5 9.278 1 45.62 ? O3A ANP 401 C 1 
HETATM 13 O O5' ANP . . . H 2 -17.804 -15.507 10 1 48.01 ? O5' ANP 401 C 1 
HETATM 14 C C5' ANP . . . H 2 -18.709 -16.288 10.814 1 48.03 ? C5' ANP 401 C 1 
HETATM 15 C C4' ANP . . . H 2 -20.144 -15.786 10.687 1 44.96 ? C4' ANP 401 C 1 
HETATM 16 O O4' ANP . . . H 2 -20.107 -14.439 11.098 1 40.7 ? O4' ANP 401 C 1 
HETATM 17 C C3' ANP . . . H 2 -20.643 -15.751 9.25 1 46.47 ? C3' ANP 401 C 1 
HETATM 18 O O3' ANP . . . H 2 -21.728 -16.652 8.994 1 55.45 ? O3' ANP 401 C 1 
HETATM 19 C C2' ANP . . . H 2 -21.079 -14.335 9.051 1 40.93 ? C2' ANP 401 C 1 
HETATM 20 O O2' ANP . . . H 2 -22.305 -14.299 8.349 1 36.85 ? O2' ANP 401 C 1 
HETATM 21 C C1' ANP . . . H 2 -21.074 -13.697 10.426 1 40.81 ? C1' ANP 401 C 1 
HETATM 22 N N9 ANP . . . H 2 -20.574 -12.326 10.195 1 48 ? N9 ANP 401 C 1 
HETATM 23 C C8 ANP . . . H 2 -19.308 -11.981 9.893 1 52.05 ? C8 ANP 401 C 1 
HETATM 24 N N7 ANP . . . H 2 -19.199 -10.652 9.654 1 51.24 ? N7 ANP 401 C 1 
HETATM 25 C C5 ANP . . . H 2 -20.399 -10.13 9.826 1 52.71 ? C5 ANP 401 C 1 
HETATM 26 C C6 ANP . . . H 2 -20.972 -8.788 9.746 1 63.34 ? C6 ANP 401 C 1 
HETATM 27 N N6 ANP . . . H 2 -20.165 -7.759 9.432 1 75.27 ? N6 ANP 401 C 1 
HETATM 28 N N1 ANP . . . H 2 -22.291 -8.616 9.992 1 64.58 ? N1 ANP 401 C 1 
HETATM 29 C C2 ANP . . . H 2 -23.071 -9.654 10.322 1 59.66 ? C2 ANP 401 C 1 
HETATM 30 N N3 ANP . . . H 2 -22.606 -10.908 10.418 1 56.79 ? N3 ANP 401 C 1 
HETATM 31 C C4 ANP . . . H 2 -21.307 -11.213 10.176 1 52.11 ? C4 ANP 401 C 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#