data_8YH5
#
_model_server_result.job_id            X7WzGhn2vcTRpUiLP99EYA 
_model_server_result.datetime_utc      '2024-11-28 08:40:30' 
_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          8yh5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":801}' 
#
_entry.id    8YH5 
#
_exptl.entry_id    8YH5 
_exptl.method      'ELECTRON MICROSCOPY' 
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_entity.details                     ? 
_entity.formula_weight              335.358 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-(3-methylbut-2-en-1-yl)adenosine 
_entity.pdbx_number_of_molecules    1 
_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            8YH5 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YH5 
_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    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
disulf ? disulf1 A SG CYS 108 B CYS 103 1_555 A SG CYS 119 B CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf2 C SG CYS 22 S CYS 22 1_555 C SG CYS 96 S CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf3 C SG CYS 159 S CYS 147 1_555 C SG CYS 229 S CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 E SG CYS 108 R CYS 83 1_555 E SG CYS 190 R CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_chem_comp.formula           'C15 H21 N5 O4' 
_chem_comp.formula_weight    335.358 
_chem_comp.id                ZIR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-(3-methylbut-2-en-1-yl)adenosine 
_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
C6 N1 ZIR doub 374 n y 
N1 C2 ZIR sing 375 n y 
N3 C2 ZIR doub 376 n y 
C2 H2 ZIR sing 377 n n 
C4 N3 ZIR sing 378 n y 
C5 C4 ZIR doub 379 n y 
N9 C4 ZIR sing 380 n y 
N7 C5 ZIR sing 381 n y 
C5 C6 ZIR sing 382 n y 
N10 C6 ZIR sing 383 n n 
N7 C8 ZIR doub 384 n y 
C8 N9 ZIR sing 385 n y 
C8 H8 ZIR sing 386 n n 
N9 C1' ZIR sing 387 n n 
C2' C1' ZIR sing 388 n n 
C1' O4' ZIR sing 389 n n 
C1' H1' ZIR sing 390 n n 
N10 C11 ZIR sing 391 n n 
N10 HN10 ZIR sing 392 n n 
C12 C11 ZIR sing 393 n n 
C11 H11 ZIR sing 394 n n 
C11 H11A ZIR sing 395 n n 
C12 C13 ZIR doub 396 n n 
C12 H12 ZIR sing 397 n n 
C14 C13 ZIR sing 398 n n 
C13 C15 ZIR sing 399 n n 
C14 H14 ZIR sing 400 n n 
C14 H14A ZIR sing 401 n n 
C14 H14B ZIR sing 402 n n 
C15 H15 ZIR sing 403 n n 
C15 H15A ZIR sing 404 n n 
C15 H15B ZIR sing 405 n n 
O2' C2' ZIR sing 406 n n 
C2' C3' ZIR sing 407 n n 
C2' H2' ZIR sing 408 n n 
O2' HO2' ZIR sing 409 n n 
C3' C4' ZIR sing 410 n n 
C3' O3' ZIR sing 411 n n 
C3' H3' ZIR sing 412 n n 
O3' HO3' ZIR sing 413 n n 
C5' C4' ZIR sing 414 n n 
C4' O4' ZIR sing 415 n n 
C4' H4' ZIR sing 416 n n 
C5' O5' ZIR sing 417 n n 
C5' H5' ZIR sing 418 n n 
C5' "H5'A" ZIR sing 419 n n 
O5' HO5' ZIR sing 420 n n 
#
_atom_sites.entry_id                     8YH5 
_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 
#
_pdbx_nonpoly_scheme.asym_id          F 
_pdbx_nonpoly_scheme.entity_id        5 
_pdbx_nonpoly_scheme.mon_id           ZIR 
_pdbx_nonpoly_scheme.pdb_strand_id    R 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      801 
_pdbx_nonpoly_scheme.auth_seq_num     301 
_pdbx_nonpoly_scheme.pdb_mon_id       ZIR 
_pdbx_nonpoly_scheme.auth_mon_id      i6a 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 ZIR . . . F 5 123.782 111.469 81.419 1 116.19 ? N1 ZIR 801 R 1 
HETATM 2 C C2 ZIR . . . F 5 124.575 111.307 82.484 1 116.19 ? C2 ZIR 801 R 1 
HETATM 3 N N3 ZIR . . . F 5 124.277 111.435 83.779 1 116.19 ? N3 ZIR 801 R 1 
HETATM 4 C C4 ZIR . . . F 5 122.997 111.769 83.946 1 116.19 ? C4 ZIR 801 R 1 
HETATM 5 C C5 ZIR . . . F 5 122.06 111.972 82.952 1 116.19 ? C5 ZIR 801 R 1 
HETATM 6 C C6 ZIR . . . F 5 122.499 111.803 81.629 1 116.19 ? C6 ZIR 801 R 1 
HETATM 7 N N7 ZIR . . . F 5 120.833 112.314 83.498 1 116.19 ? N7 ZIR 801 R 1 
HETATM 8 C C8 ZIR . . . F 5 121.055 112.31 84.786 1 116.19 ? C8 ZIR 801 R 1 
HETATM 9 N N9 ZIR . . . F 5 122.34 111.988 85.129 1 116.19 ? N9 ZIR 801 R 1 
HETATM 10 C C1' ZIR . . . F 5 122.858 111.844 86.473 1 116.19 ? C1' ZIR 801 R 1 
HETATM 11 N N10 ZIR . . . F 5 121.657 111.867 80.587 1 116.19 ? N10 ZIR 801 R 1 
HETATM 12 C C11 ZIR . . . F 5 120.233 111.941 80.749 1 116.19 ? C11 ZIR 801 R 1 
HETATM 13 C C12 ZIR . . . F 5 119.466 111.942 79.525 1 116.19 ? C12 ZIR 801 R 1 
HETATM 14 C C13 ZIR . . . F 5 118.324 111.314 79.312 1 116.19 ? C13 ZIR 801 R 1 
HETATM 15 C C14 ZIR . . . F 5 117.589 111.396 78.009 1 116.19 ? C14 ZIR 801 R 1 
HETATM 16 C C15 ZIR . . . F 5 117.691 110.414 80.333 1 116.19 ? C15 ZIR 801 R 1 
HETATM 17 C C2' ZIR . . . F 5 123.021 113.168 87.21 1 116.19 ? C2' ZIR 801 R 1 
HETATM 18 O O2' ZIR . . . F 5 124.1 113.041 88.121 1 116.19 ? O2' ZIR 801 R 1 
HETATM 19 C C3' ZIR . . . F 5 121.678 113.294 87.918 1 116.19 ? C3' ZIR 801 R 1 
HETATM 20 O O3' ZIR . . . F 5 121.772 114.068 89.105 1 116.19 ? O3' ZIR 801 R 1 
HETATM 21 C C4' ZIR . . . F 5 121.393 111.854 88.299 1 116.19 ? C4' ZIR 801 R 1 
HETATM 22 O O4' ZIR . . . F 5 121.921 111.078 87.206 1 116.19 ? O4' ZIR 801 R 1 
HETATM 23 C C5' ZIR . . . F 5 119.929 111.527 88.493 1 116.19 ? C5' ZIR 801 R 1 
HETATM 24 O O5' ZIR . . . F 5 119.142 111.843 87.353 1 116.19 ? O5' ZIR 801 R 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          16 
_model_server_stats.element_count           24 
#