data_9J8E
#
_model_server_result.job_id            m1uli-t_z_0tG0i94e2ZPA 
_model_server_result.datetime_utc      '2024-10-18 23:26:02' 
_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":"C","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 . . . C 2 22.086 -4.594 4.244 1 42.78 ? CBB BT5 401 A 1 
HETATM 2 O OBB BT5 . . . C 2 22.009 -6.008 4.273 1 45.94 ? OBB BT5 401 A 1 
HETATM 3 O OCB BT5 . . . C 2 21.503 -3.954 5.059 1 48.59 ? OCB BT5 401 A 1 
HETATM 4 C CAB BT5 . . . C 2 22.902 -3.856 3.174 1 36.94 ? CAB BT5 401 A 1 
HETATM 5 C C9B BT5 . . . C 2 22.075 -3.584 1.895 1 30.7 ? C9B BT5 401 A 1 
HETATM 6 C C8B BT5 . . . C 2 22.476 -2.205 1.337 1 29.72 ? C8B BT5 401 A 1 
HETATM 7 C C7B BT5 . . . C 2 21.596 -1.695 0.184 1 21.69 ? C7B BT5 401 A 1 
HETATM 8 C C2B BT5 . . . C 2 22.398 -0.81 -0.768 1 20 ? C2B BT5 401 A 1 
HETATM 9 S S1B BT5 . . . C 2 21.514 -0.516 -1.96 1 25.04 ? S1B BT5 401 A 1 
HETATM 10 C C6B BT5 . . . C 2 22.683 -0.065 -3.195 1 18.94 ? C6B BT5 401 A 1 
HETATM 11 C C5B BT5 . . . C 2 24.12 -0.878 -2.731 1 24.02 ? C5B BT5 401 A 1 
HETATM 12 N N1B BT5 . . . C 2 23.69 -1.706 -3.872 1 19.92 ? N1B BT5 401 A 1 
HETATM 13 C C3B BT5 . . . C 2 23.137 -2.967 -3.307 1 19.19 ? C3B BT5 401 A 1 
HETATM 14 O O3B BT5 . . . C 2 22.675 -3.884 -3.909 1 18.88 ? O3B BT5 401 A 1 
HETATM 15 N N2B BT5 . . . C 2 23.198 -2.919 -1.84 1 18.03 ? N2B BT5 401 A 1 
HETATM 16 C C4B BT5 . . . C 2 23.773 -1.649 -1.45 1 23.18 ? C4B BT5 401 A 1 
HETATM 17 P P BT5 . . . C 2 21.535 -6.723 5.694 1 49.43 ? P BT5 401 A 1 
HETATM 18 O OP1 BT5 . . . C 2 22.352 -6.12 6.855 1 30.93 -1 OP1 BT5 401 A 1 
HETATM 19 O OP2 BT5 . . . C 2 21.65 -8.222 5.548 1 41.31 ? OP2 BT5 401 A 1 
HETATM 20 O O5' BT5 . . . C 2 19.917 -6.496 5.829 1 38.87 ? O5' BT5 401 A 1 
HETATM 21 C C5' BT5 . . . C 2 19.214 -7.187 4.84 1 36.5 ? C5' BT5 401 A 1 
HETATM 22 C C4' BT5 . . . C 2 17.785 -7.283 5.389 1 39.89 ? C4' BT5 401 A 1 
HETATM 23 O O4' BT5 . . . C 2 17.173 -5.867 5.489 1 39.31 ? O4' BT5 401 A 1 
HETATM 24 C C3' BT5 . . . C 2 16.936 -7.89 4.562 1 45.67 ? C3' BT5 401 A 1 
HETATM 25 O O3' BT5 . . . C 2 17.045 -9.3 4.451 1 46.39 ? O3' BT5 401 A 1 
HETATM 26 C C2' BT5 . . . C 2 15.581 -7.526 5.307 1 43.93 ? C2' BT5 401 A 1 
HETATM 27 O O2' BT5 . . . C 2 14.506 -7.968 4.518 1 47.09 ? O2' BT5 401 A 1 
HETATM 28 C C1' BT5 . . . C 2 15.651 -6.19 5.416 1 44.52 ? C1' BT5 401 A 1 
HETATM 29 N N9 BT5 . . . C 2 15.387 -5.061 4.47 1 39.72 ? N9 BT5 401 A 1 
HETATM 30 C C8 BT5 . . . C 2 15.144 -5.184 3.165 1 38.53 ? C8 BT5 401 A 1 
HETATM 31 N N7 BT5 . . . C 2 14.92 -3.984 2.64 1 34.88 ? N7 BT5 401 A 1 
HETATM 32 C C5 BT5 . . . C 2 15.002 -3.07 3.619 1 26.28 ? C5 BT5 401 A 1 
HETATM 33 C C6 BT5 . . . C 2 14.874 -1.675 3.667 1 25.13 ? C6 BT5 401 A 1 
HETATM 34 N N6 BT5 . . . C 2 14.577 -0.928 2.459 1 21.25 ? N6 BT5 401 A 1 
HETATM 35 N N1 BT5 . . . C 2 15.021 -1.046 4.824 1 29.16 ? N1 BT5 401 A 1 
HETATM 36 C C2 BT5 . . . C 2 15.293 -1.73 5.935 1 34.25 ? C2 BT5 401 A 1 
HETATM 37 N N3 BT5 . . . C 2 15.443 -3.054 5.917 1 33.93 ? N3 BT5 401 A 1 
HETATM 38 C C4 BT5 . . . C 2 15.301 -3.75 4.782 1 27.67 ? C4 BT5 401 A 1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           38 
#