data_9J8E
#
_model_server_result.job_id            ojKdFe-KMtX1anl2krE2VA 
_model_server_result.datetime_utc      '2024-10-18 23:29:40' 
_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          9j8e 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    9J8E 
#
_exptl.entry_id    9J8E 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              573.517 
_entity.id                          2 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            BIOTINYL-5-AMP 
_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            9J8E 
_cell.length_a            55.58 
_cell.length_b            55.58 
_cell.length_c            201.924 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9J8E 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 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 C N N 
? 2 D N N 
#
_chem_comp.formula           'C20 H28 N7 O9 P S' 
_chem_comp.formula_weight    573.517 
_chem_comp.id                BT5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              BIOTINYL-5-AMP 
_chem_comp.type              'rna linking' 
_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
CBB OBB BT5 sing 70 n n 
CBB OCB BT5 doub 71 n n 
CBB CAB BT5 sing 72 n n 
OBB P BT5 sing 73 n n 
CAB C9B BT5 sing 74 n n 
CAB H101 BT5 sing 75 n n 
CAB H102 BT5 sing 76 n n 
C9B C8B BT5 sing 77 n n 
C9B H9B1 BT5 sing 78 n n 
C9B H9B2 BT5 sing 79 n n 
C8B C7B BT5 sing 80 n n 
C8B H8B1 BT5 sing 81 n n 
C8B H8B2 BT5 sing 82 n n 
C7B C2B BT5 sing 83 n n 
C7B H7B1 BT5 sing 84 n n 
C7B H7B2 BT5 sing 85 n n 
C2B S1B BT5 sing 86 n n 
C2B C4B BT5 sing 87 n n 
C2B H2B BT5 sing 88 n n 
S1B C6B BT5 sing 89 n n 
C6B C5B BT5 sing 90 n n 
C6B H6B1 BT5 sing 91 n n 
C6B H6B2 BT5 sing 92 n n 
C5B N1B BT5 sing 93 n n 
C5B C4B BT5 sing 94 n n 
C5B H5B BT5 sing 95 n n 
N1B C3B BT5 sing 96 n n 
N1B H1B BT5 sing 97 n n 
C3B O3B BT5 doub 98 n n 
C3B N2B BT5 sing 99 n n 
N2B C4B BT5 sing 100 n n 
N2B H4 BT5 sing 101 n n 
C4B H4B BT5 sing 102 n n 
P OP1 BT5 doub 103 n n 
P OP2 BT5 sing 104 n n 
P O5' BT5 sing 105 n n 
OP2 H2P BT5 sing 106 n n 
O5' C5' BT5 sing 107 n n 
C5' C4' BT5 sing 108 n n 
C5' H5' BT5 sing 109 n n 
C5' "H5''" BT5 sing 110 n n 
C4' O4' BT5 sing 111 n n 
C4' C3' BT5 sing 112 n n 
C4' H4' BT5 sing 113 n n 
O4' C1' BT5 sing 114 n n 
C3' O3' BT5 sing 115 n n 
C3' C2' BT5 sing 116 n n 
C3' H3' BT5 sing 117 n n 
O3' H2 BT5 sing 118 n n 
C2' O2' BT5 sing 119 n n 
C2' C1' BT5 sing 120 n n 
C2' H1 BT5 sing 121 n n 
O2' H2' BT5 sing 122 n n 
C1' N9 BT5 sing 123 n n 
C1' H1' BT5 sing 124 n n 
N9 C8 BT5 sing 125 n y 
N9 C4 BT5 sing 126 n y 
C8 N7 BT5 doub 127 n y 
C8 H8 BT5 sing 128 n n 
N7 C5 BT5 sing 129 n y 
C5 C6 BT5 doub 130 n y 
C5 C4 BT5 sing 131 n y 
C6 N6 BT5 sing 132 n n 
C6 N1 BT5 sing 133 n y 
N6 HN61 BT5 sing 134 n n 
N6 HN62 BT5 sing 135 n n 
N1 C2 BT5 doub 136 n y 
C2 N3 BT5 sing 137 n y 
C2 H3 BT5 sing 138 n n 
N3 C4 BT5 doub 139 n y 
#
_atom_sites.entry_id                     9J8E 
_atom_sites.fract_transf_matrix[1][1]    0.017992 
_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]    0.017992 
_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]    0.004952 
_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
C 2 BT5 A 1 401 1 BT5 LIG . 
D 2 BT5 B 1 401 1 BT5 LIG . 
E 3 HOH A 1 501 59 HOH HOH . 
E 3 HOH A 2 502 22 HOH HOH . 
E 3 HOH A 3 503 15 HOH HOH . 
E 3 HOH A 4 504 27 HOH HOH . 
E 3 HOH A 5 505 45 HOH HOH . 
E 3 HOH A 6 506 60 HOH HOH . 
E 3 HOH A 7 507 54 HOH HOH . 
E 3 HOH A 8 508 57 HOH HOH . 
E 3 HOH A 9 509 18 HOH HOH . 
E 3 HOH A 10 510 1 HOH HOH . 
E 3 HOH A 11 511 39 HOH HOH . 
E 3 HOH A 12 512 17 HOH HOH . 
E 3 HOH A 13 513 20 HOH HOH . 
E 3 HOH A 14 514 43 HOH HOH . 
E 3 HOH A 15 515 53 HOH HOH . 
E 3 HOH A 16 516 16 HOH HOH . 
E 3 HOH A 17 517 38 HOH HOH . 
E 3 HOH A 18 518 26 HOH HOH . 
E 3 HOH A 19 519 8 HOH HOH . 
E 3 HOH A 20 520 42 HOH HOH . 
E 3 HOH A 21 521 19 HOH HOH . 
E 3 HOH A 22 522 61 HOH HOH . 
E 3 HOH A 23 523 30 HOH HOH . 
E 3 HOH A 24 524 3 HOH HOH . 
E 3 HOH A 25 525 14 HOH HOH . 
E 3 HOH A 26 526 50 HOH HOH . 
E 3 HOH A 27 527 44 HOH HOH . 
F 3 HOH B 1 501 13 HOH HOH . 
F 3 HOH B 2 502 23 HOH HOH . 
F 3 HOH B 3 503 56 HOH HOH . 
F 3 HOH B 4 504 35 HOH HOH . 
F 3 HOH B 5 505 10 HOH HOH . 
F 3 HOH B 6 506 48 HOH HOH . 
F 3 HOH B 7 507 46 HOH HOH . 
F 3 HOH B 8 508 40 HOH HOH . 
F 3 HOH B 9 509 12 HOH HOH . 
F 3 HOH B 10 510 31 HOH HOH . 
F 3 HOH B 11 511 41 HOH HOH . 
F 3 HOH B 12 512 9 HOH HOH . 
F 3 HOH B 13 513 32 HOH HOH . 
F 3 HOH B 14 514 7 HOH HOH . 
F 3 HOH B 15 515 25 HOH HOH . 
F 3 HOH B 16 516 55 HOH HOH . 
F 3 HOH B 17 517 4 HOH HOH . 
F 3 HOH B 18 518 34 HOH HOH . 
F 3 HOH B 19 519 58 HOH HOH . 
F 3 HOH B 20 520 62 HOH HOH . 
F 3 HOH B 21 521 49 HOH HOH . 
F 3 HOH B 22 522 37 HOH HOH . 
F 3 HOH B 23 523 63 HOH HOH . 
F 3 HOH B 24 524 2 HOH HOH . 
F 3 HOH B 25 525 47 HOH HOH . 
F 3 HOH B 26 526 24 HOH HOH . 
F 3 HOH B 27 527 6 HOH HOH . 
F 3 HOH B 28 528 28 HOH HOH . 
F 3 HOH B 29 529 5 HOH HOH . 
F 3 HOH B 30 530 52 HOH HOH . 
F 3 HOH B 31 531 36 HOH HOH . 
F 3 HOH B 32 532 29 HOH HOH . 
F 3 HOH B 33 533 11 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 C CBB BT5 . . . D 2 5.69 -32.37 11.159 1 43.6 ? CBB BT5 401 B 1 
HETATM 2 O OBB BT5 . . . D 2 5.939 -33.759 11.138 1 43.46 ? OBB BT5 401 B 1 
HETATM 3 O OCB BT5 . . . D 2 6.103 -31.652 10.3 1 47.2 ? OCB BT5 401 B 1 
HETATM 4 C CAB BT5 . . . D 2 4.873 -31.76 12.297 1 40.33 ? CAB BT5 401 B 1 
HETATM 5 C C9B BT5 . . . D 2 5.742 -31.228 13.456 1 34.03 ? C9B BT5 401 B 1 
HETATM 6 C C8B BT5 . . . D 2 5.028 -29.996 14.039 1 33.22 ? C8B BT5 401 B 1 
HETATM 7 C C7B BT5 . . . D 2 5.918 -29.05 14.86 1 28.75 ? C7B BT5 401 B 1 
HETATM 8 C C2B BT5 . . . D 2 5.809 -29.372 16.356 1 26.57 ? C2B BT5 401 B 1 
HETATM 9 S S1B BT5 . . . D 2 6.062 -28.154 17.222 1 27.34 ? S1B BT5 401 B 1 
HETATM 10 C C6B BT5 . . . D 2 4.783 -28.103 18.422 1 25.58 ? C6B BT5 401 B 1 
HETATM 11 C C5B BT5 . . . D 2 3.608 -29.213 17.852 1 25.87 ? C5B BT5 401 B 1 
HETATM 12 N N1B BT5 . . . D 2 3.951 -29.822 19.149 1 20.69 ? N1B BT5 401 B 1 
HETATM 13 C C3B BT5 . . . D 2 4.711 -31.057 18.859 1 20.72 ? C3B BT5 401 B 1 
HETATM 14 O O3B BT5 . . . D 2 5.149 -31.854 19.625 1 23.27 ? O3B BT5 401 B 1 
HETATM 15 N N2B BT5 . . . D 2 4.85 -31.209 17.415 1 23.38 ? N2B BT5 401 B 1 
HETATM 16 C C4B BT5 . . . D 2 4.252 -30.073 16.766 1 24.77 ? C4B BT5 401 B 1 
HETATM 17 P P BT5 . . . D 2 6.279 -34.469 9.681 1 48.53 ? P BT5 401 B 1 
HETATM 18 O OP1 BT5 . . . D 2 6.035 -35.955 9.795 1 39.15 ? OP1 BT5 401 B 1 
HETATM 19 O OP2 BT5 . . . D 2 5.474 -33.792 8.554 1 31.3 -1 OP2 BT5 401 B 1 
HETATM 20 O O5' BT5 . . . D 2 7.899 -34.325 9.5 1 36.4 ? O5' BT5 401 B 1 
HETATM 21 C C5' BT5 . . . D 2 8.595 -34.983 10.516 1 35.44 ? C5' BT5 401 B 1 
HETATM 22 C C4' BT5 . . . D 2 10.014 -35.079 9.945 1 40.91 ? C4' BT5 401 B 1 
HETATM 23 O O4' BT5 . . . D 2 10.626 -33.66 9.868 1 40.95 ? O4' BT5 401 B 1 
HETATM 24 C C3' BT5 . . . D 2 10.891 -35.707 10.725 1 46.96 ? C3' BT5 401 B 1 
HETATM 25 O O3' BT5 . . . D 2 10.807 -37.119 10.776 1 48.22 ? O3' BT5 401 B 1 
HETATM 26 C C2' BT5 . . . D 2 12.199 -35.326 9.91 1 47.09 ? C2' BT5 401 B 1 
HETATM 27 O O2' BT5 . . . D 2 13.318 -35.87 10.566 1 51.16 ? O2' BT5 401 B 1 
HETATM 28 C C1' BT5 . . . D 2 12.147 -33.982 9.886 1 45.35 ? C1' BT5 401 B 1 
HETATM 29 N N9 BT5 . . . D 2 12.425 -32.901 10.887 1 40.24 ? N9 BT5 401 B 1 
HETATM 30 C C8 BT5 . . . D 2 12.672 -33.054 12.189 1 38.17 ? C8 BT5 401 B 1 
HETATM 31 N N7 BT5 . . . D 2 12.908 -31.869 12.75 1 33.65 ? N7 BT5 401 B 1 
HETATM 32 C C5 BT5 . . . D 2 12.834 -30.93 11.789 1 27.47 ? C5 BT5 401 B 1 
HETATM 33 C C6 BT5 . . . D 2 12.971 -29.533 11.753 1 26.33 ? C6 BT5 401 B 1 
HETATM 34 N N6 BT5 . . . D 2 13.274 -28.779 12.956 1 24.83 ? N6 BT5 401 B 1 
HETATM 35 N N1 BT5 . . . D 2 12.813 -28.889 10.612 1 29.73 ? N1 BT5 401 B 1 
HETATM 36 C C2 BT5 . . . D 2 12.527 -29.556 9.498 1 34.15 ? C2 BT5 401 B 1 
HETATM 37 N N3 BT5 . . . D 2 12.371 -30.871 9.5 1 32.48 ? N3 BT5 401 B 1 
HETATM 38 C C4 BT5 . . . D 2 12.52 -31.585 10.617 1 28.06 ? C4 BT5 401 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           38 
#