data_5YZ8
#
_model_server_result.job_id            u1OyamK2qajmQOOKaVB4PQ 
_model_server_result.datetime_utc      '2024-11-24 12:07:55' 
_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          5yz8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":301}' 
#
_entry.id    5YZ8 
#
_exptl.entry_id    5YZ8 
_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    6 
_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         120 
_cell.entry_id            5YZ8 
_cell.length_a            108.072 
_cell.length_b            108.072 
_cell.length_c            224.069 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YZ8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,BA,CA,DA 
_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
? 2 G N N 
? 2 K N N 
? 2 N N N 
? 2 Q N N 
? 2 T N N 
? 2 W 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 OG1 THR 53 A THR 53 1_555 H MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc2 G O1G ANP . A ANP 301 1_555 H MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? 
metalc ? metalc3 G O1B ANP . A ANP 301 1_555 H MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc4 H MG MG . A MG 302 1_555 Y O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? 
metalc ? metalc5 H MG MG . A MG 302 1_555 Y O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc6 B OG1 THR 53 B THR 53 1_555 L MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc7 K O1G ANP . B ANP 301 1_555 L MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? 
metalc ? metalc8 K O1B ANP . B ANP 301 1_555 L MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? 
metalc ? metalc9 L MG MG . B MG 302 1_555 Z O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc10 L MG MG . B MG 302 1_555 Z O HOH . B HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc11 C OG1 THR 53 C THR 53 1_555 O MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc12 N O2G ANP . C ANP 301 1_555 O MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? 
metalc ? metalc13 N O2B ANP . C ANP 301 1_555 O MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc14 O MG MG . C MG 302 1_555 AA O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc15 O MG MG . C MG 302 1_555 AA O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc16 D OG1 THR 53 D THR 53 1_555 R MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? 
metalc ? metalc17 Q O3G ANP . D ANP 301 1_555 R MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? 
metalc ? metalc18 Q O2B ANP . D ANP 301 1_555 R MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc19 R MG MG . D MG 302 1_555 BA O HOH . D HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc20 R MG MG . D MG 302 1_555 BA O HOH . D HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
metalc ? metalc21 E OG1 THR 53 E THR 53 1_555 U MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc22 T O2G ANP . E ANP 301 1_555 U MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? 
metalc ? metalc23 T O2B ANP . E ANP 301 1_555 U MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? 
metalc ? metalc24 U MG MG . E MG 302 1_555 CA O HOH . E HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc25 U MG MG . E MG 302 1_555 CA O HOH . E HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc26 F OG1 THR 53 F THR 53 1_555 X MG MG . F MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? 
metalc ? metalc27 W O3G ANP . F ANP 301 1_555 X MG MG . F MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? 
metalc ? metalc28 W O1B ANP . F ANP 301 1_555 X MG MG . F MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? 
metalc ? metalc29 X MG MG . F MG 302 1_555 DA O HOH . F HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc30 X MG MG . F MG 302 1_555 DA O HOH . F HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? 
#
_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                     5YZ8 
_atom_sites.fract_transf_matrix[1][1]    0.009253 
_atom_sites.fract_transf_matrix[1][2]    0.005342 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010685 
_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]    0.004463 
_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
G 2 ANP A 1 301 301 ANP ANP . 
H 3 MG A 1 302 302 MG MG . 
I 4 CL A 1 303 303 CL CL . 
J 4 CL A 1 304 304 CL CL . 
K 2 ANP B 1 301 301 ANP ANP . 
L 3 MG B 1 302 302 MG MG . 
M 4 CL B 1 303 303 CL CL . 
N 2 ANP C 1 301 301 ANP ANP . 
O 3 MG C 1 302 302 MG MG . 
P 4 CL C 1 303 303 CL CL . 
Q 2 ANP D 1 301 301 ANP ANP . 
R 3 MG D 1 302 302 MG MG . 
S 4 CL D 1 303 303 CL CL . 
T 2 ANP E 1 301 301 ANP ANP . 
U 3 MG E 1 302 302 MG MG . 
V 4 CL E 1 303 303 CL CL . 
W 2 ANP F 1 301 301 ANP ANP . 
X 3 MG F 1 302 302 MG MG . 
Y 5 HOH A 1 401 401 HOH HOH . 
Y 5 HOH A 2 402 402 HOH HOH . 
Y 5 HOH A 3 403 403 HOH HOH . 
Y 5 HOH A 4 404 404 HOH HOH . 
Y 5 HOH A 5 405 405 HOH HOH . 
Y 5 HOH A 6 406 406 HOH HOH . 
Y 5 HOH A 7 407 407 HOH HOH . 
Z 5 HOH B 1 401 401 HOH HOH . 
Z 5 HOH B 2 402 402 HOH HOH . 
Z 5 HOH B 3 403 403 HOH HOH . 
Z 5 HOH B 4 404 404 HOH HOH . 
Z 5 HOH B 5 405 405 HOH HOH . 
Z 5 HOH B 6 406 406 HOH HOH . 
AA 5 HOH C 1 401 401 HOH HOH . 
AA 5 HOH C 2 402 402 HOH HOH . 
AA 5 HOH C 3 403 403 HOH HOH . 
AA 5 HOH C 4 404 404 HOH HOH . 
AA 5 HOH C 5 405 405 HOH HOH . 
AA 5 HOH C 6 406 406 HOH HOH . 
BA 5 HOH D 1 401 401 HOH HOH . 
BA 5 HOH D 2 402 402 HOH HOH . 
BA 5 HOH D 3 403 403 HOH HOH . 
BA 5 HOH D 4 404 404 HOH HOH . 
BA 5 HOH D 5 405 405 HOH HOH . 
BA 5 HOH D 6 406 406 HOH HOH . 
BA 5 HOH D 7 407 407 HOH HOH . 
CA 5 HOH E 1 401 401 HOH HOH . 
CA 5 HOH E 2 402 402 HOH HOH . 
CA 5 HOH E 3 403 403 HOH HOH . 
CA 5 HOH E 4 404 404 HOH HOH . 
CA 5 HOH E 5 405 405 HOH HOH . 
DA 5 HOH F 1 401 401 HOH HOH . 
DA 5 HOH F 2 402 402 HOH HOH . 
DA 5 HOH F 3 403 403 HOH HOH . 
DA 5 HOH F 4 404 404 HOH HOH . 
DA 5 HOH F 5 405 405 HOH HOH . 
DA 5 HOH F 6 406 406 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 . . . N 2 -5.703 17.373 -22.734 1 37.22 ? PG ANP 301 C 1 
HETATM 2 O O1G ANP . . . N 2 -6.571 17.685 -23.931 1 36.34 ? O1G ANP 301 C 1 
HETATM 3 O O2G ANP . . . N 2 -4.599 18.387 -22.515 1 36.95 ? O2G ANP 301 C 1 
HETATM 4 O O3G ANP . . . N 2 -6.478 17.029 -21.481 1 36.13 ? O3G ANP 301 C 1 
HETATM 5 P PB ANP . . . N 2 -3.919 15.846 -24.581 1 30.77 ? PB ANP 301 C 1 
HETATM 6 O O1B ANP . . . N 2 -4.827 15.659 -25.759 1 31.8 ? O1B ANP 301 C 1 
HETATM 7 O O2B ANP . . . N 2 -2.95 16.994 -24.563 1 31.27 ? O2B ANP 301 C 1 
HETATM 8 N N3B ANP . . . N 2 -4.849 15.904 -23.124 1 33.53 ? N3B ANP 301 C 1 
HETATM 9 P PA ANP . . . N 2 -1.684 14.399 -23.722 1 29.76 ? PA ANP 301 C 1 
HETATM 10 O O1A ANP . . . N 2 -0.536 14.372 -24.694 1 29.62 ? O1A ANP 301 C 1 
HETATM 11 O O2A ANP . . . N 2 -1.639 15.377 -22.583 1 30.43 ? O2A ANP 301 C 1 
HETATM 12 O O3A ANP . . . N 2 -3.034 14.526 -24.572 1 30.77 ? O3A ANP 301 C 1 
HETATM 13 O O5' ANP . . . N 2 -2.041 12.969 -23.106 1 29.81 ? O5' ANP 301 C 1 
HETATM 14 C C5' ANP . . . N 2 -1.155 11.884 -23.237 1 30.87 ? C5' ANP 301 C 1 
HETATM 15 C C4' ANP . . . N 2 -1.911 10.579 -23.092 1 31.4 ? C4' ANP 301 C 1 
HETATM 16 O O4' ANP . . . N 2 -0.986 9.591 -23.507 1 32.19 ? O4' ANP 301 C 1 
HETATM 17 C C3' ANP . . . N 2 -2.343 10.228 -21.675 1 31.84 ? C3' ANP 301 C 1 
HETATM 18 O O3' ANP . . . N 2 -3.769 10.256 -21.527 1 33.2 ? O3' ANP 301 C 1 
HETATM 19 C C2' ANP . . . N 2 -1.817 8.832 -21.452 1 32 ? C2' ANP 301 C 1 
HETATM 20 O O2' ANP . . . N 2 -2.845 7.856 -21.609 1 32.75 ? O2' ANP 301 C 1 
HETATM 21 C C1' ANP . . . N 2 -0.793 8.578 -22.537 1 32.94 ? C1' ANP 301 C 1 
HETATM 22 N N9 ANP . . . N 2 0.595 8.583 -22.003 1 34.36 ? N9 ANP 301 C 1 
HETATM 23 C C8 ANP . . . N 2 1.219 9.602 -21.375 1 35.29 ? C8 ANP 301 C 1 
HETATM 24 N N7 ANP . . . N 2 2.478 9.247 -21.009 1 36.11 ? N7 ANP 301 C 1 
HETATM 25 C C5 ANP . . . N 2 2.667 7.979 -21.411 1 36.68 ? C5 ANP 301 C 1 
HETATM 26 C C6 ANP . . . N 2 3.769 6.988 -21.351 1 38.25 ? C6 ANP 301 C 1 
HETATM 27 N N6 ANP . . . N 2 4.941 7.307 -20.772 1 40.39 ? N6 ANP 301 C 1 
HETATM 28 N N1 ANP . . . N 2 3.573 5.76 -21.892 1 38.24 ? N1 ANP 301 C 1 
HETATM 29 C C2 ANP . . . N 2 2.404 5.424 -22.482 1 37.14 ? C2 ANP 301 C 1 
HETATM 30 N N3 ANP . . . N 2 1.357 6.275 -22.571 1 35.79 ? N3 ANP 301 C 1 
HETATM 31 C C4 ANP . . . N 2 1.426 7.541 -22.068 1 35.47 ? C4 ANP 301 C 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           438 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           31 
#