data_4XSC
#
_model_server_result.job_id            zFBSfrAvmJgD3zQ26eeVpA 
_model_server_result.datetime_utc      '2024-11-13 11:48:52' 
_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          4xsc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1001}' 
#
_entry.id    4XSC 
#
_exptl.entry_id    4XSC 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              413.115 
_entity.id                          2 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            4XSC 
_cell.length_a            149.515 
_cell.length_b            149.515 
_cell.length_c            88.971 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XSC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32' 
#
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 
#
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,N 1 1 
C,D,I,J,K,L,O,P 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 E N N 
? 2 G N N 
? 2 I N N 
? 2 K 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 107 n n 
O3' H3' BVP sing 108 n n 
C3' C2' BVP sing 109 n n 
C3' C4' BVP sing 110 n n 
C3' H1 BVP sing 111 n n 
C2' C1' BVP sing 112 n n 
C2' "H2'1" BVP sing 113 n n 
C2' "H2'2" BVP sing 114 n n 
C1' O4' BVP sing 115 n n 
C1' N1 BVP sing 116 n n 
C1' H1' BVP sing 117 n n 
O4' C4' BVP sing 118 n n 
C4' C5' BVP sing 119 n n 
C4' H4' BVP sing 120 n n 
C5' O5' BVP sing 121 n n 
C5' "H5'1" BVP sing 122 n n 
C5' "H5'2" BVP sing 123 n n 
O5' P BVP sing 124 n n 
P O1P BVP doub 125 n n 
P O2P BVP sing 126 n n 
P O3P BVP sing 127 n n 
O2P H2P BVP sing 128 n n 
O3P H3P BVP sing 129 n n 
N1 C6 BVP sing 130 n n 
N1 C2 BVP sing 131 n n 
C6 C5 BVP doub 132 n n 
C6 H6 BVP sing 133 n n 
C5 C5A BVP sing 134 n n 
C5 C4 BVP sing 135 n n 
C5A C5B BVP doub 136 e n 
C5A H5A BVP sing 137 n n 
C5B BR BVP sing 138 n n 
C5B H5B BVP sing 139 n n 
C4 O4 BVP doub 140 n n 
C4 N3 BVP sing 141 n n 
N3 C2 BVP sing 142 n n 
N3 HN3 BVP sing 143 n n 
C2 O2 BVP doub 144 n n 
#
_atom_sites.entry_id                     4XSC 
_atom_sites.fract_transf_matrix[1][1]    0.006688 
_atom_sites.fract_transf_matrix[1][2]    0.003861 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007723 
_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]    0.01124 
_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 BVP A 1 1001 1001 BVP BVP . 
F 3 1PE A 1 1002 2001 1PE 1PE . 
G 2 BVP B 1 1001 1001 BVP BVP . 
H 3 1PE B 1 1002 2001 1PE 1PE . 
I 2 BVP C 1 1001 1001 BVP BVP . 
J 3 1PE C 1 1002 2001 1PE 1PE . 
K 2 BVP D 1 1001 1001 BVP BVP . 
L 3 1PE D 1 1002 2001 1PE 1PE . 
M 4 HOH A 1 1101 18 HOH HOH . 
M 4 HOH A 2 1102 19 HOH HOH . 
M 4 HOH A 3 1103 30 HOH HOH . 
M 4 HOH A 4 1104 29 HOH HOH . 
M 4 HOH A 5 1105 22 HOH HOH . 
M 4 HOH A 6 1106 23 HOH HOH . 
M 4 HOH A 7 1107 20 HOH HOH . 
M 4 HOH A 8 1108 21 HOH HOH . 
N 4 HOH B 1 1101 34 HOH HOH . 
N 4 HOH B 2 1102 32 HOH HOH . 
N 4 HOH B 3 1103 31 HOH HOH . 
N 4 HOH B 4 1104 33 HOH HOH . 
O 4 HOH C 1 1101 10 HOH HOH . 
O 4 HOH C 2 1102 15 HOH HOH . 
O 4 HOH C 3 1103 12 HOH HOH . 
O 4 HOH C 4 1104 27 HOH HOH . 
O 4 HOH C 5 1105 14 HOH HOH . 
O 4 HOH C 6 1106 26 HOH HOH . 
O 4 HOH C 7 1107 11 HOH HOH . 
O 4 HOH C 8 1108 16 HOH HOH . 
O 4 HOH C 9 1109 25 HOH HOH . 
P 4 HOH D 1 1101 17 HOH HOH . 
P 4 HOH D 2 1102 6 HOH HOH . 
P 4 HOH D 3 1103 28 HOH HOH . 
P 4 HOH D 4 1104 5 HOH HOH . 
P 4 HOH D 5 1105 4 HOH HOH . 
P 4 HOH D 6 1106 13 HOH HOH . 
P 4 HOH D 7 1107 24 HOH HOH . 
P 4 HOH D 8 1108 3 HOH HOH . 
P 4 HOH D 9 1109 8 HOH HOH . 
P 4 HOH D 10 1110 1 HOH HOH . 
P 4 HOH D 11 1111 7 HOH HOH . 
P 4 HOH D 12 1112 9 HOH HOH . 
P 4 HOH D 13 1113 2 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 . . . E 2 -11.049 -2.198 -78.999 1 45.61 ? O3' BVP 1001 A 1 
HETATM 2 C C3' BVP . . . E 2 -12.328 -2.691 -79.225 1 42.6 ? C3' BVP 1001 A 1 
HETATM 3 C C2' BVP . . . E 2 -12.365 -4.177 -79.133 1 36.43 ? C2' BVP 1001 A 1 
HETATM 4 C C1' BVP . . . E 2 -12.416 -4.429 -77.831 1 34.88 ? C1' BVP 1001 A 1 
HETATM 5 O O4' BVP . . . E 2 -13.167 -3.166 -77.173 1 51.04 ? O4' BVP 1001 A 1 
HETATM 6 C C4' BVP . . . E 2 -13.278 -2.235 -78.056 1 45.22 ? C4' BVP 1001 A 1 
HETATM 7 C C5' BVP . . . E 2 -14.702 -2.102 -78.552 1 46.08 ? C5' BVP 1001 A 1 
HETATM 8 O O5' BVP . . . E 2 -14.988 -0.746 -78.934 1 25.48 ? O5' BVP 1001 A 1 
HETATM 9 P P BVP . . . E 2 -15.709 -0.471 -80.372 1 36.46 ? P BVP 1001 A 1 
HETATM 10 O O1P BVP . . . E 2 -15.136 -1.408 -81.415 1 23.8 ? O1P BVP 1001 A 1 
HETATM 11 O O2P BVP . . . E 2 -17.193 -0.702 -80.238 1 32.7 ? O2P BVP 1001 A 1 
HETATM 12 O O3P BVP . . . E 2 -15.461 0.972 -80.808 1 28.3 ? O3P BVP 1001 A 1 
HETATM 13 N N1 BVP . . . E 2 -13.135 -5.607 -77.561 1 31.12 ? N1 BVP 1001 A 1 
HETATM 14 C C6 BVP . . . E 2 -14.356 -5.495 -76.895 1 41.18 ? C6 BVP 1001 A 1 
HETATM 15 C C5 BVP . . . E 2 -15.159 -6.681 -76.581 1 44.51 ? C5 BVP 1001 A 1 
HETATM 16 C C5A BVP . . . E 2 -16.475 -6.514 -75.864 1 61.38 ? C5A BVP 1001 A 1 
HETATM 17 C C5B BVP . . . E 2 -17.624 -6.183 -76.599 1 71.92 ? C5B BVP 1001 A 1 
HETATM 18 BR BR BVP . . . E 2 -19.326 -5.966 -75.674 1 146.23 ? BR BVP 1001 A 1 
HETATM 19 C C4 BVP . . . E 2 -14.696 -8.017 -76.953 1 40.52 ? C4 BVP 1001 A 1 
HETATM 20 O O4 BVP . . . E 2 -15.386 -9.025 -76.679 1 37.6 ? O4 BVP 1001 A 1 
HETATM 21 N N3 BVP . . . E 2 -13.452 -8.155 -77.627 1 45.33 ? N3 BVP 1001 A 1 
HETATM 22 C C2 BVP . . . E 2 -12.645 -6.966 -77.946 1 33.6 ? C2 BVP 1001 A 1 
HETATM 23 O O2 BVP . . . E 2 -11.604 -7.122 -78.514 1 34.93 ? O2 BVP 1001 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           23 
#