data_2YB0
#
_model_server_result.job_id            IakmNTxlJr3IpVIdDRE94w 
_model_server_result.datetime_utc      '2024-11-24 01:53:23' 
_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          2yb0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1266}' 
#
_entry.id    2YB0 
#
_exptl.entry_id    2YB0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              228.202 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE" 
_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            2YB0 
_cell.length_a            109.186 
_cell.length_b            109.186 
_cell.length_c            308.882 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YB0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31 2 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 
#
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,I,J,K,R,S 1 1 
C,D,L,M,N,O,P,Q,T,U 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 I N N 
? 2 L N N 
? 2 O N N 
#
_chem_comp.formula           'C9 H12 N2 O5' 
_chem_comp.formula_weight    228.202 
_chem_comp.id                DUR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE" 
_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
N1 C2 DUR sing 83 n n 
N1 C6 DUR sing 84 n n 
N1 C1' DUR sing 85 n n 
C2 N3 DUR sing 86 n n 
C2 O2 DUR doub 87 n n 
N3 C4 DUR sing 88 n n 
N3 HN3 DUR sing 89 n n 
C4 C5 DUR sing 90 n n 
C4 O4 DUR doub 91 n n 
C5 C6 DUR doub 92 n n 
C5 H5 DUR sing 93 n n 
C6 H6 DUR sing 94 n n 
C1' C2' DUR sing 95 n n 
C1' O4' DUR sing 96 n n 
C1' H1' DUR sing 97 n n 
C2' C3' DUR sing 98 n n 
C2' "H2'1" DUR sing 99 n n 
C2' "H2'2" DUR sing 100 n n 
C3' C4' DUR sing 101 n n 
C3' O3' DUR sing 102 n n 
C3' H3' DUR sing 103 n n 
C4' O4' DUR sing 104 n n 
C4' C5' DUR sing 105 n n 
C4' H4' DUR sing 106 n n 
O3' HO3' DUR sing 107 n n 
C5' O5' DUR sing 108 n n 
C5' "H5'1" DUR sing 109 n n 
C5' "H5'2" DUR sing 110 n n 
O5' HO5' DUR sing 111 n n 
#
_atom_sites.entry_id                     2YB0 
_atom_sites.fract_transf_matrix[1][1]    0.009159 
_atom_sites.fract_transf_matrix[1][2]    0.005288 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010576 
_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]    0.003237 
_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 DUR A 1 1266 1266 DUR DUR . 
F 3 SO4 A 1 1267 1267 SO4 SO4 . 
G 3 SO4 A 1 1268 1268 SO4 SO4 . 
H 3 SO4 A 1 1269 1269 SO4 SO4 . 
I 2 DUR B 1 1266 1266 DUR DUR . 
J 3 SO4 B 1 1267 1267 SO4 SO4 . 
K 3 SO4 B 1 1268 1268 SO4 SO4 . 
L 2 DUR D 1 1266 1266 DUR DUR . 
M 3 SO4 D 1 1267 1267 SO4 SO4 . 
N 3 SO4 D 1 1268 1268 SO4 SO4 . 
O 2 DUR E 1 1266 1266 DUR DUR . 
P 3 SO4 E 1 1267 1267 SO4 SO4 . 
Q 3 SO4 E 1 1268 1268 SO4 SO4 . 
R 4 HOH A 1 2001 2001 HOH HOH . 
R 4 HOH A 2 2002 2002 HOH HOH . 
R 4 HOH A 3 2003 2003 HOH HOH . 
R 4 HOH A 4 2004 2004 HOH HOH . 
R 4 HOH A 5 2005 2005 HOH HOH . 
R 4 HOH A 6 2006 2006 HOH HOH . 
R 4 HOH A 7 2007 2007 HOH HOH . 
R 4 HOH A 8 2008 2008 HOH HOH . 
R 4 HOH A 9 2009 2009 HOH HOH . 
R 4 HOH A 10 2010 2010 HOH HOH . 
R 4 HOH A 11 2011 2011 HOH HOH . 
R 4 HOH A 12 2012 2012 HOH HOH . 
R 4 HOH A 13 2013 2013 HOH HOH . 
R 4 HOH A 14 2014 2014 HOH HOH . 
R 4 HOH A 15 2015 2015 HOH HOH . 
R 4 HOH A 16 2016 2016 HOH HOH . 
R 4 HOH A 17 2017 2017 HOH HOH . 
R 4 HOH A 18 2018 2018 HOH HOH . 
R 4 HOH A 19 2019 2019 HOH HOH . 
R 4 HOH A 20 2020 2020 HOH HOH . 
R 4 HOH A 21 2021 2021 HOH HOH . 
R 4 HOH A 22 2022 2022 HOH HOH . 
R 4 HOH A 23 2023 2023 HOH HOH . 
R 4 HOH A 24 2024 2024 HOH HOH . 
R 4 HOH A 25 2025 2025 HOH HOH . 
R 4 HOH A 26 2026 2026 HOH HOH . 
R 4 HOH A 27 2027 2027 HOH HOH . 
R 4 HOH A 28 2028 2028 HOH HOH . 
R 4 HOH A 29 2029 2029 HOH HOH . 
R 4 HOH A 30 2030 2030 HOH HOH . 
R 4 HOH A 31 2031 2031 HOH HOH . 
R 4 HOH A 32 2032 2032 HOH HOH . 
R 4 HOH A 33 2033 2033 HOH HOH . 
R 4 HOH A 34 2034 2034 HOH HOH . 
R 4 HOH A 35 2035 2035 HOH HOH . 
R 4 HOH A 36 2036 2036 HOH HOH . 
R 4 HOH A 37 2037 2037 HOH HOH . 
R 4 HOH A 38 2038 2038 HOH HOH . 
R 4 HOH A 39 2039 2039 HOH HOH . 
S 4 HOH B 1 2001 2001 HOH HOH . 
S 4 HOH B 2 2002 2002 HOH HOH . 
S 4 HOH B 3 2003 2003 HOH HOH . 
S 4 HOH B 4 2004 2004 HOH HOH . 
S 4 HOH B 5 2005 2005 HOH HOH . 
S 4 HOH B 6 2006 2006 HOH HOH . 
S 4 HOH B 7 2007 2007 HOH HOH . 
S 4 HOH B 8 2008 2008 HOH HOH . 
S 4 HOH B 9 2009 2009 HOH HOH . 
S 4 HOH B 10 2010 2010 HOH HOH . 
S 4 HOH B 11 2011 2011 HOH HOH . 
S 4 HOH B 12 2012 2012 HOH HOH . 
S 4 HOH B 13 2013 2013 HOH HOH . 
S 4 HOH B 14 2014 2014 HOH HOH . 
S 4 HOH B 15 2015 2015 HOH HOH . 
S 4 HOH B 16 2016 2016 HOH HOH . 
S 4 HOH B 17 2017 2017 HOH HOH . 
S 4 HOH B 18 2018 2018 HOH HOH . 
S 4 HOH B 19 2019 2019 HOH HOH . 
T 4 HOH D 1 2001 2001 HOH HOH . 
T 4 HOH D 2 2002 2002 HOH HOH . 
T 4 HOH D 3 2003 2003 HOH HOH . 
T 4 HOH D 4 2004 2004 HOH HOH . 
T 4 HOH D 5 2005 2005 HOH HOH . 
T 4 HOH D 6 2006 2006 HOH HOH . 
T 4 HOH D 7 2007 2007 HOH HOH . 
T 4 HOH D 8 2008 2008 HOH HOH . 
T 4 HOH D 9 2009 2009 HOH HOH . 
T 4 HOH D 10 2010 2010 HOH HOH . 
T 4 HOH D 11 2011 2011 HOH HOH . 
T 4 HOH D 12 2012 2012 HOH HOH . 
T 4 HOH D 13 2013 2013 HOH HOH . 
T 4 HOH D 14 2014 2014 HOH HOH . 
T 4 HOH D 15 2015 2015 HOH HOH . 
T 4 HOH D 16 2016 2016 HOH HOH . 
T 4 HOH D 17 2017 2017 HOH HOH . 
T 4 HOH D 18 2018 2018 HOH HOH . 
T 4 HOH D 19 2019 2019 HOH HOH . 
T 4 HOH D 20 2020 2020 HOH HOH . 
T 4 HOH D 21 2021 2021 HOH HOH . 
T 4 HOH D 22 2022 2022 HOH HOH . 
T 4 HOH D 23 2023 2023 HOH HOH . 
U 4 HOH E 1 2001 2001 HOH HOH . 
U 4 HOH E 2 2002 2002 HOH HOH . 
U 4 HOH E 3 2003 2003 HOH HOH . 
U 4 HOH E 4 2004 2004 HOH HOH . 
U 4 HOH E 5 2005 2005 HOH HOH . 
U 4 HOH E 6 2006 2006 HOH HOH . 
U 4 HOH E 7 2007 2007 HOH HOH . 
U 4 HOH E 8 2008 2008 HOH HOH . 
U 4 HOH E 9 2009 2009 HOH HOH . 
U 4 HOH E 10 2010 2010 HOH HOH . 
U 4 HOH E 11 2011 2011 HOH HOH . 
U 4 HOH E 12 2012 2012 HOH HOH . 
U 4 HOH E 13 2013 2013 HOH HOH . 
U 4 HOH E 14 2014 2014 HOH HOH . 
U 4 HOH E 15 2015 2015 HOH HOH . 
U 4 HOH E 16 2016 2016 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 N N1 DUR . . . E 2 -17.176 35.059 -7.703 1 41.87 ? N1 DUR 1266 A 1 
HETATM 2 C C2 DUR . . . E 2 -17.838 34.248 -6.75 1 44.42 ? C2 DUR 1266 A 1 
HETATM 3 N N3 DUR . . . E 2 -17.303 34.045 -5.552 1 41.07 ? N3 DUR 1266 A 1 
HETATM 4 C C4 DUR . . . E 2 -16.111 34.564 -5.25 1 43.37 ? C4 DUR 1266 A 1 
HETATM 5 C C5 DUR . . . E 2 -15.446 35.358 -6.161 1 36.4 ? C5 DUR 1266 A 1 
HETATM 6 C C6 DUR . . . E 2 -16 35.601 -7.402 1 47.66 ? C6 DUR 1266 A 1 
HETATM 7 O O2 DUR . . . E 2 -18.937 33.727 -6.992 1 43.19 ? O2 DUR 1266 A 1 
HETATM 8 O O4 DUR . . . E 2 -15.595 34.358 -4.134 1 32.99 ? O4 DUR 1266 A 1 
HETATM 9 C C1' DUR . . . E 2 -17.806 35.336 -8.985 1 34.68 ? C1' DUR 1266 A 1 
HETATM 10 C C2' DUR . . . E 2 -18.948 36.309 -8.759 1 31.53 ? C2' DUR 1266 A 1 
HETATM 11 C C3' DUR . . . E 2 -19.118 36.983 -10.104 1 39.76 ? C3' DUR 1266 A 1 
HETATM 12 C C4' DUR . . . E 2 -17.806 36.754 -10.822 1 39.76 ? C4' DUR 1266 A 1 
HETATM 13 O O3' DUR . . . E 2 -20.166 36.394 -10.881 1 36.13 ? O3' DUR 1266 A 1 
HETATM 14 O O4' DUR . . . E 2 -16.992 35.975 -9.957 1 41.07 ? O4' DUR 1266 A 1 
HETATM 15 C C5' DUR . . . E 2 -17.115 38.063 -11.207 1 57.29 ? C5' DUR 1266 A 1 
HETATM 16 O O5' DUR . . . E 2 -18.032 39.005 -11.806 1 53.25 ? O5' DUR 1266 A 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           727 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           16 
#