data_5ARK
#
_model_server_result.job_id            yF1R96fairsR2qD-fQ4s_A 
_model_server_result.datetime_utc      '2024-11-24 21:30:15' 
_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          5ark 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1120}' 
#
_entry.id    5ARK 
#
_exptl.entry_id    5ARK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "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         90 
_cell.entry_id            5ARK 
_cell.length_a            76.19 
_cell.length_b            91.32 
_cell.length_c            93.43 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ARK 
_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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,K 1 1 
B,G,H,L 2 1 
C,I,M 3 1 
D,J,N 4 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 J 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
disulf ? disulf1 A SG CYS 40 A CYS 25 1_555 A SG CYS 96 A CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf2 A SG CYS 54 A CYS 39 1_555 A SG CYS 107 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf3 A SG CYS 72 A CYS 57 1_555 A SG CYS 122 A CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf4 A SG CYS 79 A CYS 64 1_555 A SG CYS 86 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf5 B SG CYS 40 B CYS 25 1_555 B SG CYS 96 B CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
disulf ? disulf6 B SG CYS 54 B CYS 39 1_555 B SG CYS 107 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf7 B SG CYS 72 B CYS 57 1_555 B SG CYS 122 B CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
disulf ? disulf8 B SG CYS 79 B CYS 64 1_555 B SG CYS 86 B CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf9 C SG CYS 40 C CYS 25 1_555 C SG CYS 96 C CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
disulf ? disulf10 C SG CYS 54 C CYS 39 1_555 C SG CYS 107 C CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf11 C SG CYS 72 C CYS 57 1_555 C SG CYS 122 C CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf12 C SG CYS 79 C CYS 64 1_555 C SG CYS 86 C CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf13 D SG CYS 40 D CYS 25 1_555 D SG CYS 96 D CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
disulf ? disulf14 D SG CYS 54 D CYS 39 1_555 D SG CYS 107 D CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf15 D SG CYS 72 D CYS 57 1_555 D SG CYS 122 D CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf16 D SG CYS 79 D CYS 64 1_555 D SG CYS 86 D CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DUMP 
#
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 UMP sing 362 n n 
N1 C6 UMP sing 363 n n 
N1 C1' UMP sing 364 n n 
C2 N3 UMP sing 365 n n 
C2 O2 UMP doub 366 n n 
N3 C4 UMP sing 367 n n 
N3 HN3 UMP sing 368 n n 
C4 C5 UMP sing 369 n n 
C4 O4 UMP doub 370 n n 
C5 C6 UMP doub 371 n n 
C5 H5 UMP sing 372 n n 
C6 H6 UMP sing 373 n n 
C1' C2' UMP sing 374 n n 
C1' O4' UMP sing 375 n n 
C1' H1' UMP sing 376 n n 
C2' C3' UMP sing 377 n n 
C2' H2' UMP sing 378 n n 
C2' "H2''" UMP sing 379 n n 
C3' C4' UMP sing 380 n n 
C3' O3' UMP sing 381 n n 
C3' H3' UMP sing 382 n n 
C4' O4' UMP sing 383 n n 
C4' C5' UMP sing 384 n n 
C4' H4' UMP sing 385 n n 
O3' HO3' UMP sing 386 n n 
C5' O5' UMP sing 387 n n 
C5' H5' UMP sing 388 n n 
C5' "H5''" UMP sing 389 n n 
O5' P UMP sing 390 n n 
P OP1 UMP doub 391 n n 
P OP2 UMP sing 392 n n 
P OP3 UMP sing 393 n n 
OP2 HOP2 UMP sing 394 n n 
OP3 HOP3 UMP sing 395 n n 
#
_atom_sites.entry_id                     5ARK 
_atom_sites.fract_transf_matrix[1][1]    0.013125 
_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]    0.010951 
_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]    0.010703 
_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 UMP A 1 1120 1120 UMP UMP . 
F 3 PO4 A 1 1121 1121 PO4 PO4 . 
G 2 UMP B 1 1120 1120 UMP UMP . 
H 3 PO4 B 1 1121 1121 PO4 PO4 . 
I 2 UMP C 1 1120 1120 UMP UMP . 
J 2 UMP D 1 1120 1120 UMP UMP . 
K 4 HOH A 1 2001 2001 HOH HOH . 
K 4 HOH A 2 2002 2002 HOH HOH . 
K 4 HOH A 3 2003 2003 HOH HOH . 
K 4 HOH A 4 2004 2004 HOH HOH . 
K 4 HOH A 5 2005 2005 HOH HOH . 
K 4 HOH A 6 2006 2006 HOH HOH . 
K 4 HOH A 7 2007 2007 HOH HOH . 
K 4 HOH A 8 2008 2008 HOH HOH . 
K 4 HOH A 9 2009 2009 HOH HOH . 
K 4 HOH A 10 2010 2010 HOH HOH . 
K 4 HOH A 11 2011 2011 HOH HOH . 
K 4 HOH A 12 2012 2012 HOH HOH . 
K 4 HOH A 13 2013 2013 HOH HOH . 
K 4 HOH A 14 2014 2014 HOH HOH . 
K 4 HOH A 15 2015 2015 HOH HOH . 
K 4 HOH A 16 2016 2016 HOH HOH . 
K 4 HOH A 17 2017 2017 HOH HOH . 
K 4 HOH A 18 2018 2018 HOH HOH . 
K 4 HOH A 19 2019 2019 HOH HOH . 
K 4 HOH A 20 2020 2020 HOH HOH . 
K 4 HOH A 21 2021 2021 HOH HOH . 
L 4 HOH B 1 2001 2001 HOH HOH . 
L 4 HOH B 2 2002 2002 HOH HOH . 
L 4 HOH B 3 2003 2003 HOH HOH . 
L 4 HOH B 4 2004 2004 HOH HOH . 
L 4 HOH B 5 2005 2005 HOH HOH . 
L 4 HOH B 6 2006 2006 HOH HOH . 
L 4 HOH B 7 2007 2007 HOH HOH . 
L 4 HOH B 8 2008 2008 HOH HOH . 
L 4 HOH B 9 2009 2009 HOH HOH . 
L 4 HOH B 10 2010 2010 HOH HOH . 
L 4 HOH B 11 2011 2011 HOH HOH . 
L 4 HOH B 12 2012 2012 HOH HOH . 
L 4 HOH B 13 2013 2013 HOH HOH . 
L 4 HOH B 14 2014 2014 HOH HOH . 
L 4 HOH B 15 2015 2015 HOH HOH . 
L 4 HOH B 16 2016 2016 HOH HOH . 
L 4 HOH B 17 2017 2017 HOH HOH . 
L 4 HOH B 18 2018 2018 HOH HOH . 
M 4 HOH C 1 2001 2001 HOH HOH . 
M 4 HOH C 2 2002 2002 HOH HOH . 
M 4 HOH C 3 2003 2003 HOH HOH . 
M 4 HOH C 4 2004 2004 HOH HOH . 
M 4 HOH C 5 2005 2005 HOH HOH . 
M 4 HOH C 6 2006 2006 HOH HOH . 
M 4 HOH C 7 2007 2007 HOH HOH . 
M 4 HOH C 8 2008 2008 HOH HOH . 
M 4 HOH C 9 2009 2009 HOH HOH . 
M 4 HOH C 10 2010 2010 HOH HOH . 
M 4 HOH C 11 2011 2011 HOH HOH . 
M 4 HOH C 12 2012 2012 HOH HOH . 
M 4 HOH C 13 2013 2013 HOH HOH . 
M 4 HOH C 14 2014 2014 HOH HOH . 
M 4 HOH C 15 2015 2015 HOH HOH . 
M 4 HOH C 16 2016 2016 HOH HOH . 
M 4 HOH C 17 2017 2017 HOH HOH . 
M 4 HOH C 18 2018 2018 HOH HOH . 
M 4 HOH C 19 2019 2019 HOH HOH . 
M 4 HOH C 20 2020 2020 HOH HOH . 
M 4 HOH C 21 2021 2021 HOH HOH . 
M 4 HOH C 22 2022 2022 HOH HOH . 
M 4 HOH C 23 2023 2023 HOH HOH . 
M 4 HOH C 24 2024 2024 HOH HOH . 
M 4 HOH C 25 2025 2025 HOH HOH . 
M 4 HOH C 26 2026 2026 HOH HOH . 
M 4 HOH C 27 2027 2027 HOH HOH . 
M 4 HOH C 28 2028 2028 HOH HOH . 
M 4 HOH C 29 2029 2029 HOH HOH . 
M 4 HOH C 30 2030 2030 HOH HOH . 
N 4 HOH D 1 2001 2001 HOH HOH . 
N 4 HOH D 2 2002 2002 HOH HOH . 
N 4 HOH D 3 2003 2003 HOH HOH . 
N 4 HOH D 4 2004 2004 HOH HOH . 
N 4 HOH D 5 2005 2005 HOH HOH . 
N 4 HOH D 6 2006 2006 HOH HOH . 
N 4 HOH D 7 2007 2007 HOH HOH . 
N 4 HOH D 8 2008 2008 HOH HOH . 
N 4 HOH D 9 2009 2009 HOH HOH . 
N 4 HOH D 10 2010 2010 HOH HOH . 
N 4 HOH D 11 2011 2011 HOH HOH . 
N 4 HOH D 12 2012 2012 HOH HOH . 
N 4 HOH D 13 2013 2013 HOH HOH . 
N 4 HOH D 14 2014 2014 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 UMP . . . G 2 9.438 -32.426 -49.994 0.5 57.95 ? N1 UMP 1120 B 1 
HETATM 2 C C2 UMP . . . G 2 9.439 -33.029 -51.293 0.5 56.25 ? C2 UMP 1120 B 1 
HETATM 3 N N3 UMP . . . G 2 9.199 -32.287 -52.384 0.5 59.59 ? N3 UMP 1120 B 1 
HETATM 4 C C4 UMP . . . G 2 8.938 -30.981 -52.289 0.5 57.18 ? C4 UMP 1120 B 1 
HETATM 5 C C5 UMP . . . G 2 8.916 -30.386 -51.043 0.5 58.44 ? C5 UMP 1120 B 1 
HETATM 6 C C6 UMP . . . G 2 9.153 -31.128 -49.901 0.5 57.3 ? C6 UMP 1120 B 1 
HETATM 7 O O2 UMP . . . G 2 9.671 -34.244 -51.492 0.5 48.29 ? O2 UMP 1120 B 1 
HETATM 8 O O4 UMP . . . G 2 8.713 -30.296 -53.309 0.5 51.71 ? O4 UMP 1120 B 1 
HETATM 9 C C1' UMP . . . G 2 9.663 -33.156 -48.716 0.5 58.34 ? C1' UMP 1120 B 1 
HETATM 10 C C2' UMP . . . G 2 10.557 -34.377 -48.788 0.6 56.14 ? C2' UMP 1120 B 1 
HETATM 11 C C3' UMP . . . G 2 10.758 -34.657 -47.314 0.6 57.49 ? C3' UMP 1120 B 1 
HETATM 12 C C4' UMP . . . G 2 10.681 -33.322 -46.612 0.6 56.68 ? C4' UMP 1120 B 1 
HETATM 13 O O3' UMP . . . G 2 9.676 -35.462 -46.855 0.6 57.92 ? O3' UMP 1120 B 1 
HETATM 14 O O4' UMP . . . G 2 10.258 -32.399 -47.639 0.6 59.49 ? O4' UMP 1120 B 1 
HETATM 15 C C5' UMP . . . G 2 12.012 -32.92 -46.005 0.6 55.21 ? C5' UMP 1120 B 1 
HETATM 16 O O5' UMP . . . G 2 12.266 -33.407 -44.67 0.6 53.76 ? O5' UMP 1120 B 1 
HETATM 17 P P UMP . . . G 2 13.084 -32.377 -43.72 1 48.86 ? P UMP 1120 B 1 
HETATM 18 O OP1 UMP . . . G 2 12.1 -31.249 -43.564 1 59.25 ? OP1 UMP 1120 B 1 
HETATM 19 O OP2 UMP . . . G 2 13.437 -33.043 -42.435 1 54.33 ? OP2 UMP 1120 B 1 
HETATM 20 O OP3 UMP . . . G 2 14.249 -32.017 -44.582 1 49.35 ? OP3 UMP 1120 B 1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#