data_1OSN
#
_model_server_result.job_id            GKdUxDBGcYZWHYNDPwvBog 
_model_server_result.datetime_utc      '2025-02-17 16:46:53' 
_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          1osn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":2500}' 
#
_entry.id    1OSN 
#
_exptl.entry_id    1OSN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              413.115 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "(E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94.8 
_cell.angle_gamma         90 
_cell.entry_id            1OSN 
_cell.length_a            99.7 
_cell.length_b            54.2 
_cell.length_c            167.8 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 1OSN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA tetrameric 4 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,M 1 1 
C,D,I,J,K,L 2 1 
A,B,C,D,E,F,G,H,I,J,K,L,M 3 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
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 L N N 
#
_chem_comp.formula           'C11 H14 Br N2 O8 P' 
_chem_comp.formula_weight    413.115 
_chem_comp.id                BVP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "(E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              'dna linking' 
_chem_comp.pdbx_synonyms     BVDU-MP 
#
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' BVP sing 114 n n 
O3' H3' BVP sing 115 n n 
C3' C2' BVP sing 116 n n 
C3' C4' BVP sing 117 n n 
C3' H1 BVP sing 118 n n 
C2' C1' BVP sing 119 n n 
C2' "H2'1" BVP sing 120 n n 
C2' "H2'2" BVP sing 121 n n 
C1' O4' BVP sing 122 n n 
C1' N1 BVP sing 123 n n 
C1' H1' BVP sing 124 n n 
O4' C4' BVP sing 125 n n 
C4' C5' BVP sing 126 n n 
C4' H4' BVP sing 127 n n 
C5' O5' BVP sing 128 n n 
C5' "H5'1" BVP sing 129 n n 
C5' "H5'2" BVP sing 130 n n 
O5' P BVP sing 131 n n 
P O1P BVP doub 132 n n 
P O2P BVP sing 133 n n 
P O3P BVP sing 134 n n 
O2P H2P BVP sing 135 n n 
O3P H3P BVP sing 136 n n 
N1 C6 BVP sing 137 n n 
N1 C2 BVP sing 138 n n 
C6 C5 BVP doub 139 n n 
C6 H6 BVP sing 140 n n 
C5 C5A BVP sing 141 n n 
C5 C4 BVP sing 142 n n 
C5A C5B BVP doub 143 e n 
C5A H5A BVP sing 144 n n 
C5B BR BVP sing 145 n n 
C5B H5B BVP sing 146 n n 
C4 O4 BVP doub 147 n n 
C4 N3 BVP sing 148 n n 
N3 C2 BVP sing 149 n n 
N3 HN3 BVP sing 150 n n 
C2 O2 BVP doub 151 n n 
#
_atom_sites.entry_id                     1OSN 
_atom_sites.fract_transf_matrix[1][1]    0.01003 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000842 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01845 
_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]    0.00598 
_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 2 ADP A 1 400 400 ADP ADP . 
F 3 BVP A 1 500 500 BVP BDP . 
G 2 ADP B 1 1400 400 ADP ADP . 
H 3 BVP B 1 1500 500 BVP BDP . 
I 2 ADP C 1 2400 400 ADP ADP . 
J 3 BVP C 1 2500 500 BVP BDP . 
K 2 ADP D 1 3400 400 ADP ADP . 
L 3 BVP D 1 3500 500 BVP BDP . 
M 4 HOH A 1 600 600 HOH HOH . 
M 4 HOH A 2 601 601 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 O O3' BVP . . . J 3 54.657 7.483 24.088 1 33.81 ? O3' BVP 2500 C 1 
HETATM 2 C C3' BVP . . . J 3 54.877 8.317 22.954 1 28.55 ? C3' BVP 2500 C 1 
HETATM 3 C C2' BVP . . . J 3 55.359 9.71 23.311 1 25.63 ? C2' BVP 2500 C 1 
HETATM 4 C C1' BVP . . . J 3 56.846 9.466 23.551 1 23.42 ? C1' BVP 2500 C 1 
HETATM 5 O O4' BVP . . . J 3 57.212 8.332 22.738 1 25.54 ? O4' BVP 2500 C 1 
HETATM 6 C C4' BVP . . . J 3 56.022 7.725 22.176 1 27.79 ? C4' BVP 2500 C 1 
HETATM 7 C C5' BVP . . . J 3 56.015 8.008 20.653 1 30.42 ? C5' BVP 2500 C 1 
HETATM 8 O O5' BVP . . . J 3 54.774 7.569 20.032 1 44.08 ? O5' BVP 2500 C 1 
HETATM 9 P P BVP . . . J 3 53.784 8.555 19.171 1 42.06 ? P BVP 2500 C 1 
HETATM 10 O O1P BVP . . . J 3 54.146 9.964 19.458 1 43.73 ? O1P BVP 2500 C 1 
HETATM 11 O O2P BVP . . . J 3 52.366 8.318 19.577 1 48.12 ? O2P BVP 2500 C 1 
HETATM 12 O O3P BVP . . . J 3 53.94 8.284 17.745 1 40.36 ? O3P BVP 2500 C 1 
HETATM 13 N N1 BVP . . . J 3 57.803 10.614 23.218 1 23.56 ? N1 BVP 2500 C 1 
HETATM 14 C C6 BVP . . . J 3 57.992 11.043 21.904 1 25.19 ? C6 BVP 2500 C 1 
HETATM 15 C C5 BVP . . . J 3 58.903 12.131 21.608 1 31.65 ? C5 BVP 2500 C 1 
HETATM 16 C C5A BVP . . . J 3 59.195 12.629 20.625 1 42.31 ? C5A BVP 2500 C 1 
HETATM 17 C C5B BVP . . . J 3 60.118 12.165 19.7 1 62.4 ? C5B BVP 2500 C 1 
HETATM 18 BR BR BVP . . . J 3 60.878 13.261 18.262 1 86.49 ? BR BVP 2500 C 1 
HETATM 19 C C4 BVP . . . J 3 59.6 12.741 22.738 1 35.83 ? C4 BVP 2500 C 1 
HETATM 20 O O4 BVP . . . J 3 60.417 13.693 22.632 1 50.13 ? O4 BVP 2500 C 1 
HETATM 21 N N3 BVP . . . J 3 59.344 12.244 24.007 1 26.37 ? N3 BVP 2500 C 1 
HETATM 22 C C2 BVP . . . J 3 58.483 11.218 24.27 1 27.95 ? C2 BVP 2500 C 1 
HETATM 23 O O2 BVP . . . J 3 58.336 10.865 25.429 1 36.33 ? O2 BVP 2500 C 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           23 
#