data_8U9P
#
_model_server_result.job_id            u67cqGgg1B91qQNaJ7Abyw 
_model_server_result.datetime_utc      '2024-11-07 05:43:40' 
_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          8u9p 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":901}' 
#
_entry.id    8U9P 
#
_exptl.entry_id    8U9P 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              492.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium' 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_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 
_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 H N N 
? 3 J N N 
? 3 L N N 
? 3 N N N 
? 3 P N N 
? 3 R N N 
? 3 T N N 
? 3 V 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 262 A THR 262 1_555 I MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? 
metalc ? metalc2 A OG1 THR 535 A THR 535 1_555 K MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.79 ? 
metalc ? metalc3 H O2B 08T . A 08T 901 1_555 I MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
metalc ? metalc4 J O2B 08T . A 08T 903 1_555 K MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? 
metalc ? metalc5 B OG1 THR 262 B THR 262 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc6 B OG1 THR 535 B THR 535 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc7 L O1B 08T . B 08T 901 1_555 M MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? 
metalc ? metalc8 N O1B 08T . B 08T 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? 
metalc ? metalc9 C OG1 THR 262 C THR 262 1_555 Q MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc10 C OG1 THR 535 C THR 535 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc11 P O2B 08T . C 08T 901 1_555 Q MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc12 R O2B 08T . C 08T 903 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? 
metalc ? metalc13 R O3A 08T . C 08T 903 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? 
metalc ? metalc14 R O3B 08T . C 08T 903 1_555 S MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? 
metalc ? metalc15 D OG1 THR 262 D THR 262 1_555 U MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.732 ? 
metalc ? metalc16 D OG1 THR 535 D THR 535 1_555 W MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? 
metalc ? metalc17 T O2B 08T . D 08T 901 1_555 U MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? 
metalc ? metalc18 V O2B 08T . D 08T 903 1_555 W MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
#
_chem_comp.formula           'C10 H14 Be F3 N5 O10 P2' 
_chem_comp.formula_weight    492.201 
_chem_comp.id                08T 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium' 
_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
O3' C3' 08T sing 1 n n 
O2' C2' 08T sing 2 n n 
C3' C4' 08T sing 3 n n 
C3' C2' 08T sing 4 n n 
C4' C5' 08T sing 5 n n 
C4' O4' 08T sing 6 n n 
C2' C1' 08T sing 7 n n 
C5' O5' 08T sing 8 n n 
O4' C1' 08T sing 9 n n 
C1' N9 08T sing 10 n n 
N3 C2 08T doub 11 n y 
N3 C4 08T sing 12 n y 
O2A PA 08T doub 13 n n 
C2 N1 08T sing 14 n y 
O5' PA 08T sing 15 n n 
C4 N9 08T sing 16 n y 
C4 C5 08T doub 17 n y 
N9 C8 08T sing 18 n y 
PA O1A 08T sing 19 n n 
PA O3A 08T sing 20 n n 
N1 C6 08T doub 21 n y 
C5 C6 08T sing 22 n y 
C5 N7 08T sing 23 n y 
O3A PB 08T sing 24 n n 
C8 N7 08T doub 25 n y 
C6 N6 08T sing 26 n n 
O1B PB 08T doub 27 n n 
PB O3B 08T sing 28 n n 
PB O2B 08T sing 29 n n 
F1 BE 08T sing 30 n n 
BE F3 08T sing 31 n n 
O3B BE 08T sing 32 n n 
BE F2 08T sing 33 n n 
C5' H1 08T sing 34 n n 
C5' H2 08T sing 35 n n 
C4' H3 08T sing 36 n n 
C3' H4 08T sing 37 n n 
O3' H5 08T sing 38 n n 
C2' H6 08T sing 39 n n 
O2' H7 08T sing 40 n n 
C1' H8 08T sing 41 n n 
O1A H9 08T sing 42 n n 
C2 H10 08T sing 43 n n 
O2B H11 08T sing 44 n n 
N6 H12 08T sing 45 n n 
N6 H13 08T sing 46 n n 
C8 H14 08T sing 47 n n 
#
_atom_sites.entry_id                     8U9P 
_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
H 3 08T A 1 901 901 08T ADP . 
I 4 MG A 1 902 903 MG MG . 
J 3 08T A 1 903 904 08T ADP . 
K 4 MG A 1 904 906 MG MG . 
L 3 08T B 1 901 901 08T ADP . 
M 4 MG B 1 902 903 MG MG . 
N 3 08T B 1 903 904 08T ADP . 
O 4 MG B 1 904 906 MG MG . 
P 3 08T C 1 901 901 08T ADP . 
Q 4 MG C 1 902 903 MG MG . 
R 3 08T C 1 903 904 08T ADP . 
S 4 MG C 1 904 906 MG MG . 
T 3 08T D 1 901 901 08T ADP . 
U 4 MG D 1 902 903 MG MG . 
V 3 08T D 1 903 904 08T ADP . 
W 4 MG D 1 904 906 MG MG . 
X 5 ADP E 1 901 901 ADP ADP . 
Y 5 ADP E 1 902 904 ADP ADP . 
#
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 PA 08T . . . L 3 147.339 145.164 190.908 1 95.22 ? PA 08T 901 B 1 
HETATM 2 P PB 08T . . . L 3 148.769 147.026 189.134 1 85.14 ? PB 08T 901 B 1 
HETATM 3 BE BE 08T . . . L 3 147.987 147.656 186.616 1 97.1 ? BE 08T 901 B 1 
HETATM 4 C C5' 08T . . . L 3 147.23 142.54 191.073 1 95.93 ? C5' 08T 901 B 1 
HETATM 5 O O5' 08T . . . L 3 147.937 143.769 191.337 1 92.5 ? O5' 08T 901 B 1 
HETATM 6 C C4' 08T . . . L 3 147.654 141.521 192.097 1 89.73 ? C4' 08T 901 B 1 
HETATM 7 O O4' 08T . . . L 3 149.091 141.499 192.183 1 84.5 ? O4' 08T 901 B 1 
HETATM 8 C C3' 08T . . . L 3 147.175 141.805 193.512 1 96.2 ? C3' 08T 901 B 1 
HETATM 9 O O3' 08T . . . L 3 145.879 141.252 193.716 1 102.53 ? O3' 08T 901 B 1 
HETATM 10 C C2' 08T . . . L 3 148.234 141.109 194.367 1 100.83 ? C2' 08T 901 B 1 
HETATM 11 O O2' 08T . . . L 3 147.891 139.75 194.612 1 112 ? O2' 08T 901 B 1 
HETATM 12 C C1' 08T . . . L 3 149.501 141.253 193.516 1 93.5 ? C1' 08T 901 B 1 
HETATM 13 N N1 08T . . . L 3 152.077 143.569 197.34 1 92.75 ? N1 08T 901 B 1 
HETATM 14 O O1A 08T . . . L 3 147.298 146.147 192.001 1 92.97 ? O1A 08T 901 B 1 
HETATM 15 O O1B 08T . . . L 3 147.688 148.027 189.527 1 95.19 ? O1B 08T 901 B 1 
HETATM 16 F F1 08T . . . L 3 146.608 148.035 187.17 1 98.03 ? F1 08T 901 B 1 
HETATM 17 C C2 08T . . . L 3 151.296 142.486 197.324 1 96.59 ? C2 08T 901 B 1 
HETATM 18 O O2A 08T . . . L 3 146.004 144.96 190.207 1 99.73 ? O2A 08T 901 B 1 
HETATM 19 O O2B 08T . . . L 3 150.138 147.381 189.561 1 94.96 ? O2B 08T 901 B 1 
HETATM 20 F F2 08T . . . L 3 148.843 148.925 186.321 1 103.27 ? F2 08T 901 B 1 
HETATM 21 N N3 08T . . . L 3 150.652 141.934 196.293 1 93.78 ? N3 08T 901 B 1 
HETATM 22 O O3A 08T . . . L 3 148.334 145.678 189.816 1 86.6 ? O3A 08T 901 B 1 
HETATM 23 O O3B 08T . . . L 3 148.758 146.731 187.661 1 88.63 ? O3B 08T 901 B 1 
HETATM 24 F F3 08T . . . L 3 147.807 146.92 185.269 1 106.71 ? F3 08T 901 B 1 
HETATM 25 C C4 08T . . . L 3 150.865 142.62 195.167 1 87.18 ? C4 08T 901 B 1 
HETATM 26 C C5 08T . . . L 3 151.647 143.755 195.026 1 89 ? C5 08T 901 B 1 
HETATM 27 C C6 08T . . . L 3 152.278 144.241 196.187 1 91.73 ? C6 08T 901 B 1 
HETATM 28 N N6 08T . . . L 3 153.059 145.325 196.211 1 95.9 ? N6 08T 901 B 1 
HETATM 29 N N7 08T . . . L 3 151.641 144.193 193.712 1 95.75 ? N7 08T 901 B 1 
HETATM 30 C C8 08T . . . L 3 150.873 143.326 193.1 1 93.42 ? C8 08T 901 B 1 
HETATM 31 N N9 08T . . . L 3 150.37 142.35 193.915 1 90.41 ? N9 08T 901 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           31 
#