data_2XY3
#
_model_server_result.job_id            MueUAamsSl_P-EXPBgXf5w 
_model_server_result.datetime_utc      '2025-07-27 22:23:44' 
_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          2xy3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":1130}' 
#
_entry.id    2XY3 
#
_exptl.entry_id    2XY3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              467.157 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    6 
_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            2XY3 
_cell.length_a            98.474 
_cell.length_b            98.4 
_cell.length_c            97.993 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2XY3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 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,C,G,H,I,J,P,Q,R 1 1 
D,E,F,K,L,M,N,O,S,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 G N N 
? 2 H N N 
? 2 I N N 
? 2 K N N 
? 2 L N N 
? 2 N N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 I O1A DUP . C DUP 1129 1_555 J MG MG . C MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc2 I O1B DUP . C DUP 1129 1_555 J MG MG . C MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc3 I O2G DUP . C DUP 1129 1_555 J MG MG . C MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
metalc ? metalc4 L O1A DUP . E DUP 1130 1_555 M MG MG . E MG 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc5 L O1B DUP . E DUP 1130 1_555 M MG MG . E MG 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc6 L O2G DUP . E DUP 1130 1_555 M MG MG . E MG 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc7 N O1B DUP . F DUP 1129 1_555 O MG MG . F MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc8 N O2G DUP . F DUP 1129 1_555 O MG MG . F MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc9 N O1A DUP . F DUP 1129 1_555 O MG MG . F MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
#
_chem_comp.formula           'C9 H16 N3 O13 P3' 
_chem_comp.formula_weight    467.157 
_chem_comp.id                DUP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" 
_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
O4 C4 DUP doub 83 n n 
C4 C5 DUP sing 84 n y 
C4 N3 DUP sing 85 n y 
C5 C6 DUP doub 86 n y 
C5 H5 DUP sing 87 n n 
C6 N1 DUP sing 88 n y 
C6 H6 DUP sing 89 n n 
N3 C2 DUP sing 90 n y 
N3 HN3 DUP sing 91 n n 
C2 O2 DUP doub 92 n n 
C2 N1 DUP sing 93 n y 
N1 C1' DUP sing 94 n n 
C1' C2' DUP sing 95 n n 
C1' O4' DUP sing 96 n n 
C1' H1' DUP sing 97 n n 
C2' C3' DUP sing 98 n n 
C2' "H2'1" DUP sing 99 n n 
C2' "H2'2" DUP sing 100 n n 
C3' O3' DUP sing 101 n n 
C3' C4' DUP sing 102 n n 
C3' H1 DUP sing 103 n n 
O3' H3' DUP sing 104 n n 
O4' C4' DUP sing 105 n n 
C4' C5' DUP sing 106 n n 
C4' H4' DUP sing 107 n n 
C5' O5' DUP sing 108 n n 
C5' "H5'1" DUP sing 109 n n 
C5' "H5'2" DUP sing 110 n n 
O5' PA DUP sing 111 n n 
PA O1A DUP doub 112 n n 
PA O2A DUP sing 113 n n 
PA N3A DUP sing 114 n n 
O2A H2A DUP sing 115 n n 
N3A PB DUP sing 116 n n 
N3A H3A DUP sing 117 n n 
PB O1B DUP doub 118 n n 
PB O2B DUP sing 119 n n 
PB O3B DUP sing 120 n n 
O2B H2B DUP sing 121 n n 
O3B PG DUP sing 122 n n 
PG O2G DUP doub 123 n n 
PG O1G DUP sing 124 n n 
PG O3G DUP sing 125 n n 
O1G H1G DUP sing 126 n n 
O3G H3G DUP sing 127 n n 
#
_atom_sites.entry_id                     2XY3 
_atom_sites.fract_transf_matrix[1][1]    0.010155 
_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]    0.010163 
_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]    0.010205 
_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
G 2 DUP A 1 1130 1130 DUP DUP . 
H 2 DUP B 1 1129 1129 DUP DUP . 
I 2 DUP C 1 1129 1129 DUP DUP . 
J 3 MG C 1 1130 1130 MG MG . 
K 2 DUP D 1 1130 1130 DUP DUP . 
L 2 DUP E 1 1130 1130 DUP DUP . 
M 3 MG E 1 1131 1131 MG MG . 
N 2 DUP F 1 1129 1129 DUP DUP . 
O 3 MG F 1 1130 1130 MG MG . 
P 4 HOH A 1 2001 2001 HOH HOH . 
P 4 HOH A 2 2002 2002 HOH HOH . 
P 4 HOH A 3 2003 2003 HOH HOH . 
P 4 HOH A 4 2004 2004 HOH HOH . 
P 4 HOH A 5 2005 2005 HOH HOH . 
P 4 HOH A 6 2006 2006 HOH HOH . 
P 4 HOH A 7 2007 2007 HOH HOH . 
P 4 HOH A 8 2008 2008 HOH HOH . 
P 4 HOH A 9 2009 2009 HOH HOH . 
P 4 HOH A 10 2010 2010 HOH HOH . 
P 4 HOH A 11 2011 2011 HOH HOH . 
P 4 HOH A 12 2012 2012 HOH HOH . 
P 4 HOH A 13 2013 2013 HOH HOH . 
P 4 HOH A 14 2014 2014 HOH HOH . 
P 4 HOH A 15 2015 2015 HOH HOH . 
P 4 HOH A 16 2016 2016 HOH HOH . 
P 4 HOH A 17 2017 2017 HOH HOH . 
P 4 HOH A 18 2018 2018 HOH HOH . 
P 4 HOH A 19 2019 2019 HOH HOH . 
P 4 HOH A 20 2020 2020 HOH HOH . 
P 4 HOH A 21 2021 2021 HOH HOH . 
P 4 HOH A 22 2022 2022 HOH HOH . 
Q 4 HOH B 1 2001 2001 HOH HOH . 
Q 4 HOH B 2 2002 2002 HOH HOH . 
Q 4 HOH B 3 2003 2003 HOH HOH . 
Q 4 HOH B 4 2004 2004 HOH HOH . 
Q 4 HOH B 5 2005 2005 HOH HOH . 
Q 4 HOH B 6 2006 2006 HOH HOH . 
Q 4 HOH B 7 2007 2007 HOH HOH . 
Q 4 HOH B 8 2008 2008 HOH HOH . 
Q 4 HOH B 9 2009 2009 HOH HOH . 
Q 4 HOH B 10 2010 2010 HOH HOH . 
Q 4 HOH B 11 2011 2011 HOH HOH . 
Q 4 HOH B 12 2012 2012 HOH HOH . 
R 4 HOH C 1 2001 2001 HOH HOH . 
R 4 HOH C 2 2002 2002 HOH HOH . 
R 4 HOH C 3 2003 2003 HOH HOH . 
R 4 HOH C 4 2004 2004 HOH HOH . 
R 4 HOH C 5 2005 2005 HOH HOH . 
R 4 HOH C 6 2006 2006 HOH HOH . 
R 4 HOH C 7 2007 2007 HOH HOH . 
R 4 HOH C 8 2008 2008 HOH HOH . 
R 4 HOH C 9 2009 2009 HOH HOH . 
R 4 HOH C 10 2010 2010 HOH HOH . 
R 4 HOH C 11 2011 2011 HOH HOH . 
R 4 HOH C 12 2012 2012 HOH HOH . 
R 4 HOH C 13 2013 2013 HOH HOH . 
R 4 HOH C 14 2014 2014 HOH HOH . 
R 4 HOH C 15 2015 2015 HOH HOH . 
R 4 HOH C 16 2016 2016 HOH HOH . 
R 4 HOH C 17 2017 2017 HOH HOH . 
R 4 HOH C 18 2018 2018 HOH HOH . 
R 4 HOH C 19 2019 2019 HOH HOH . 
R 4 HOH C 20 2020 2020 HOH HOH . 
S 4 HOH D 1 2001 2001 HOH HOH . 
S 4 HOH D 2 2002 2002 HOH HOH . 
S 4 HOH D 3 2003 2003 HOH HOH . 
S 4 HOH D 4 2004 2004 HOH HOH . 
S 4 HOH D 5 2005 2005 HOH HOH . 
S 4 HOH D 6 2006 2006 HOH HOH . 
S 4 HOH D 7 2007 2007 HOH HOH . 
S 4 HOH D 8 2008 2008 HOH HOH . 
S 4 HOH D 9 2009 2009 HOH HOH . 
S 4 HOH D 10 2010 2010 HOH HOH . 
S 4 HOH D 11 2011 2011 HOH HOH . 
S 4 HOH D 12 2012 2012 HOH HOH . 
S 4 HOH D 13 2013 2013 HOH HOH . 
S 4 HOH D 14 2014 2014 HOH HOH . 
S 4 HOH D 15 2015 2015 HOH HOH . 
S 4 HOH D 16 2016 2016 HOH HOH . 
S 4 HOH D 17 2017 2017 HOH HOH . 
S 4 HOH D 18 2018 2018 HOH HOH . 
S 4 HOH D 19 2019 2019 HOH HOH . 
S 4 HOH D 20 2020 2020 HOH HOH . 
S 4 HOH D 21 2021 2021 HOH HOH . 
S 4 HOH D 22 2022 2022 HOH HOH . 
T 4 HOH E 1 2001 2001 HOH HOH . 
T 4 HOH E 2 2002 2002 HOH HOH . 
T 4 HOH E 3 2003 2003 HOH HOH . 
T 4 HOH E 4 2004 2004 HOH HOH . 
T 4 HOH E 5 2005 2005 HOH HOH . 
T 4 HOH E 6 2006 2006 HOH HOH . 
T 4 HOH E 7 2007 2007 HOH HOH . 
T 4 HOH E 8 2008 2008 HOH HOH . 
T 4 HOH E 9 2009 2009 HOH HOH . 
T 4 HOH E 10 2010 2010 HOH HOH . 
T 4 HOH E 11 2011 2011 HOH HOH . 
T 4 HOH E 12 2012 2012 HOH HOH . 
T 4 HOH E 13 2013 2013 HOH HOH . 
T 4 HOH E 14 2014 2014 HOH HOH . 
T 4 HOH E 15 2015 2015 HOH HOH . 
T 4 HOH E 16 2016 2016 HOH HOH . 
T 4 HOH E 17 2017 2017 HOH HOH . 
T 4 HOH E 18 2018 2018 HOH HOH . 
T 4 HOH E 19 2019 2019 HOH HOH . 
T 4 HOH E 20 2020 2020 HOH HOH . 
U 4 HOH F 1 2001 2001 HOH HOH . 
U 4 HOH F 2 2002 2002 HOH HOH . 
U 4 HOH F 3 2003 2003 HOH HOH . 
U 4 HOH F 4 2004 2004 HOH HOH . 
U 4 HOH F 5 2005 2005 HOH HOH . 
U 4 HOH F 6 2006 2006 HOH HOH . 
U 4 HOH F 7 2007 2007 HOH HOH . 
U 4 HOH F 8 2008 2008 HOH HOH . 
U 4 HOH F 9 2009 2009 HOH HOH . 
U 4 HOH F 10 2010 2010 HOH HOH . 
U 4 HOH F 11 2011 2011 HOH HOH . 
U 4 HOH F 12 2012 2012 HOH HOH . 
U 4 HOH F 13 2013 2013 HOH HOH . 
U 4 HOH F 14 2014 2014 HOH HOH . 
U 4 HOH F 15 2015 2015 HOH HOH . 
U 4 HOH F 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 O O4 DUP . . . L 2 9.409 51.922 -40.379 1 38.5 ? O4 DUP 1130 E 1 
HETATM 2 C C4 DUP . . . L 2 9.014 52.919 -39.768 1 37.56 ? C4 DUP 1130 E 1 
HETATM 3 C C5 DUP . . . L 2 7.711 52.978 -39.314 1 37.64 ? C5 DUP 1130 E 1 
HETATM 4 C C6 DUP . . . L 2 7.289 54.119 -38.624 1 37.97 ? C6 DUP 1130 E 1 
HETATM 5 N N3 DUP . . . L 2 9.856 53.93 -39.521 1 36.23 ? N3 DUP 1130 E 1 
HETATM 6 C C2 DUP . . . L 2 9.42 55.01 -38.865 1 36.75 ? C2 DUP 1130 E 1 
HETATM 7 O O2 DUP . . . L 2 10.248 55.909 -38.699 1 36.38 ? O2 DUP 1130 E 1 
HETATM 8 N N1 DUP . . . L 2 8.145 55.121 -38.41 1 37.63 ? N1 DUP 1130 E 1 
HETATM 9 C C1' DUP . . . L 2 7.7 56.293 -37.616 1 38.3 ? C1' DUP 1130 E 1 
HETATM 10 C C2' DUP . . . L 2 6.703 57.176 -38.351 1 37.22 ? C2' DUP 1130 E 1 
HETATM 11 C C3' DUP . . . L 2 5.414 56.886 -37.619 1 37.37 ? C3' DUP 1130 E 1 
HETATM 12 O O3' DUP . . . L 2 4.568 58.021 -37.597 1 36.3 ? O3' DUP 1130 E 1 
HETATM 13 O O4' DUP . . . L 2 7.117 55.863 -36.341 1 37.6 ? O4' DUP 1130 E 1 
HETATM 14 C C4' DUP . . . L 2 5.836 56.489 -36.222 1 37.42 ? C4' DUP 1130 E 1 
HETATM 15 C C5' DUP . . . L 2 4.808 55.584 -35.587 1 38.15 ? C5' DUP 1130 E 1 
HETATM 16 O O5' DUP . . . L 2 4.539 54.472 -36.417 1 41 ? O5' DUP 1130 E 1 
HETATM 17 P PA DUP . . . L 2 3.5 53.316 -35.938 1 42.63 ? PA DUP 1130 E 1 
HETATM 18 O O1A DUP . . . L 2 2.163 53.996 -35.644 1 40.04 ? O1A DUP 1130 E 1 
HETATM 19 O O2A DUP . . . L 2 3.672 52.174 -36.898 1 39.45 ? O2A DUP 1130 E 1 
HETATM 20 N N3A DUP . . . L 2 4.144 52.842 -34.492 1 42.5 ? N3A DUP 1130 E 1 
HETATM 21 P PB DUP . . . L 2 3.394 53.319 -33.084 1 41.61 ? PB DUP 1130 E 1 
HETATM 22 O O1B DUP . . . L 2 1.896 53.026 -33.264 1 40.01 ? O1B DUP 1130 E 1 
HETATM 23 O O2B DUP . . . L 2 4.184 52.577 -32.009 1 40.33 ? O2B DUP 1130 E 1 
HETATM 24 O O3B DUP . . . L 2 3.57 54.889 -32.891 1 41.21 ? O3B DUP 1130 E 1 
HETATM 25 P PG DUP . . . L 2 2.261 55.839 -32.674 1 43.83 ? PG DUP 1130 E 1 
HETATM 26 O O2G DUP . . . L 2 1.378 55.514 -33.877 1 45.25 ? O2G DUP 1130 E 1 
HETATM 27 O O1G DUP . . . L 2 1.824 55.421 -31.283 1 40.9 ? O1G DUP 1130 E 1 
HETATM 28 O O3G DUP . . . L 2 2.837 57.233 -32.767 1 46.07 ? O3G DUP 1130 E 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#