data_8T0Q
#
_model_server_result.job_id            HaEUK6FxciLWtZJcgs1O1Q 
_model_server_result.datetime_utc      '2025-01-07 08:07:51' 
_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          8t0q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":601}' 
#
_entry.id    8T0Q 
#
_exptl.entry_id    8T0Q 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              251.242 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-DEOXYADENOSINE" 
_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            8T0Q 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8T0Q 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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
? 5 I N N 
? 5 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
covale ? covale1 A NZ LYS 144 A LYS 144 1_555 F C4A PLP . A PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale2 B NZ LYS 144 B LYS 144 1_555 H C4A PLP . B PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.361 ? 
#
_chem_comp.formula           'C10 H13 N5 O3' 
_chem_comp.formula_weight    251.242 
_chem_comp.id                5AD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-DEOXYADENOSINE" 
_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
N1 C2 5AD doub 1 n y 
N1 C6 5AD sing 2 n y 
C2 N3 5AD sing 3 n y 
C2 H2 5AD sing 4 n n 
N3 C4 5AD doub 5 n y 
C4 N9 5AD sing 6 n y 
C4 C5 5AD sing 7 n y 
N9 C8 5AD sing 8 n y 
N9 C1' 5AD sing 9 n n 
C8 N7 5AD doub 10 n y 
C8 H8 5AD sing 11 n n 
N7 C5 5AD sing 12 n y 
C5 C6 5AD doub 13 n y 
C6 N6 5AD sing 14 n n 
N6 HN61 5AD sing 15 n n 
N6 HN62 5AD sing 16 n n 
C1' C2' 5AD sing 17 n n 
C1' O4' 5AD sing 18 n n 
C1' H1' 5AD sing 19 n n 
C2' C3' 5AD sing 20 n n 
C2' O2' 5AD sing 21 n n 
C2' H2' 5AD sing 22 n n 
C3' C4' 5AD sing 23 n n 
C3' O3' 5AD sing 24 n n 
C3' H3' 5AD sing 25 n n 
C4' C5' 5AD sing 26 n n 
C4' O4' 5AD sing 27 n n 
C4' H4' 5AD sing 28 n n 
C5' "H5'1" 5AD sing 29 n n 
C5' "H5'2" 5AD sing 30 n n 
C5' "H5'3" 5AD sing 31 n n 
O2' HO2' 5AD sing 32 n n 
O3' HO3' 5AD sing 33 n n 
#
_atom_sites.entry_id                     8T0Q 
_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
E 3 B12 A 1 401 401 B12 B12 . 
F 4 PLP A 1 402 601 PLP PLP . 
G 3 B12 B 1 401 401 B12 B12 . 
H 4 PLP B 1 402 601 PLP PLP . 
I 5 5AD C 1 601 302 5AD 5AD . 
J 5 5AD D 1 601 302 5AD 5AD . 
#
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 N N1 5AD . . . I 5 132.064 144.148 176.266 1 91.34 ? N1 5AD 601 C 1 
HETATM 2 C C2 5AD . . . I 5 131.489 144.279 175.116 1 96.07 ? C2 5AD 601 C 1 
HETATM 3 N N3 5AD . . . I 5 130.966 145.394 174.724 1 94.85 ? N3 5AD 601 C 1 
HETATM 4 C C4 5AD . . . I 5 131.02 146.426 175.48 1 92.73 ? C4 5AD 601 C 1 
HETATM 5 N N9 5AD . . . I 5 130.578 147.558 175.263 1 94.02 ? N9 5AD 601 C 1 
HETATM 6 C C8 5AD . . . I 5 130.831 148.32 176.308 1 95.32 ? C8 5AD 601 C 1 
HETATM 7 N N7 5AD . . . I 5 131.506 147.606 177.228 1 92.19 ? N7 5AD 601 C 1 
HETATM 8 C C5 5AD . . . I 5 131.636 146.407 176.735 1 91.97 ? C5 5AD 601 C 1 
HETATM 9 C C6 5AD . . . I 5 132.174 145.141 177.101 1 91.69 ? C6 5AD 601 C 1 
HETATM 10 N N6 5AD . . . I 5 132.787 144.938 178.257 1 94.47 ? N6 5AD 601 C 1 
HETATM 11 C C1' 5AD . . . I 5 129.938 147.708 173.979 1 92.03 ? C1' 5AD 601 C 1 
HETATM 12 C C2' 5AD . . . I 5 129.001 148.811 173.904 1 103.69 ? C2' 5AD 601 C 1 
HETATM 13 C C3' 5AD . . . I 5 129.817 150.023 173.92 1 103.87 ? C3' 5AD 601 C 1 
HETATM 14 C C4' 5AD . . . I 5 130.869 149.584 172.948 1 91.64 ? C4' 5AD 601 C 1 
HETATM 15 C C5' 5AD . . . I 5 132.239 150.306 173.085 1 93.55 ? C5' 5AD 601 C 1 
HETATM 16 O O4' 5AD . . . I 5 130.925 148.165 173.145 1 83.5 ? O4' 5AD 601 C 1 
HETATM 17 O O2' 5AD . . . I 5 128.417 148.712 172.618 1 103.12 ? O2' 5AD 601 C 1 
HETATM 18 O O3' 5AD . . . I 5 129.02 151.108 173.494 1 105.66 ? O3' 5AD 601 C 1 
HETATM 19 H H2 5AD . . . I 5 131.433 143.419 174.461 1 94.55 ? H2 5AD 601 C 1 
HETATM 20 H H8 5AD . . . I 5 130.578 149.369 176.393 1 94.49 ? H8 5AD 601 C 1 
HETATM 21 H HN61 5AD . . . I 5 133.161 144.025 178.477 1 94 ? HN61 5AD 601 C 1 
HETATM 22 H HN62 5AD . . . I 5 132.875 145.693 178.922 1 94.35 ? HN62 5AD 601 C 1 
HETATM 23 H H1' 5AD . . . I 5 129.489 146.773 173.616 1 93.19 ? H1' 5AD 601 C 1 
HETATM 24 H H2' 5AD . . . I 5 128.267 148.789 174.722 1 95.02 ? H2' 5AD 601 C 1 
HETATM 25 H H3' 5AD . . . I 5 130.249 150.218 174.908 1 95.53 ? H3' 5AD 601 C 1 
HETATM 26 H H4' 5AD . . . I 5 130.491 149.785 171.936 1 93.49 ? H4' 5AD 601 C 1 
HETATM 27 H "H5'1" 5AD . . . I 5 132.096 151.251 173.541 1 94.01 ? "H5'1" 5AD 601 C 1 
HETATM 28 H "H5'2" 5AD . . . I 5 132.888 149.72 173.682 1 94.41 ? "H5'2" 5AD 601 C 1 
HETATM 29 H HO2' 5AD . . . I 5 127.454 148.713 172.7 1 95.03 ? HO2' 5AD 601 C 1 
HETATM 30 H HO3' 5AD . . . I 5 129.481 151.938 173.68 1 94.53 ? HO3' 5AD 601 C 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           30 
#