data_2VSN
#
_model_server_result.job_id            KQdju0EgPUryV3At0HsoMQ 
_model_server_result.datetime_utc      '2024-11-09 02:51:00' 
_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          2vsn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":900}' 
#
_entry.id    2VSN 
#
_exptl.entry_id    2VSN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            2VSN 
_cell.length_a            86.691 
_cell.length_b            105.692 
_cell.length_c            151.036 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2VSN 
_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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 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 C N N 
? 2 D N N 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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 UDP sing 358 n n 
N1 C6 UDP sing 359 n n 
N1 C1' UDP sing 360 n n 
C2 N3 UDP sing 361 n n 
C2 O2 UDP doub 362 n n 
N3 C4 UDP sing 363 n n 
N3 HN3 UDP sing 364 n n 
C4 C5 UDP sing 365 n n 
C4 O4 UDP doub 366 n n 
C5 C6 UDP doub 367 n n 
C5 H5 UDP sing 368 n n 
C6 H6 UDP sing 369 n n 
C1' C2' UDP sing 370 n n 
C1' O4' UDP sing 371 n n 
C1' H1' UDP sing 372 n n 
C2' O2' UDP sing 373 n n 
C2' C3' UDP sing 374 n n 
C2' H2' UDP sing 375 n n 
O2' HO2' UDP sing 376 n n 
C3' C4' UDP sing 377 n n 
C3' O3' UDP sing 378 n n 
C3' H3' UDP sing 379 n n 
C4' O4' UDP sing 380 n n 
C4' C5' UDP sing 381 n n 
C4' H4' UDP sing 382 n n 
O3' HO3' UDP sing 383 n n 
C5' O5' UDP sing 384 n n 
C5' "H5'1" UDP sing 385 n n 
C5' "H5'2" UDP sing 386 n n 
O5' PA UDP sing 387 n n 
PA O1A UDP doub 388 n n 
PA O2A UDP sing 389 n n 
PA O3A UDP sing 390 n n 
O2A HOA2 UDP sing 391 n n 
O3A PB UDP sing 392 n n 
PB O1B UDP doub 393 n n 
PB O2B UDP sing 394 n n 
PB O3B UDP sing 395 n n 
O2B HOB2 UDP sing 396 n n 
O3B HOB3 UDP sing 397 n n 
#
_atom_sites.entry_id                     2VSN 
_atom_sites.fract_transf_matrix[1][1]    0.011535 
_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]    0.009461 
_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]    0.006621 
_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
C 2 UDP A 1 900 900 UDP UDP . 
D 2 UDP B 1 900 900 UDP UDP . 
E 3 HOH A 1 2001 2001 HOH HOH . 
E 3 HOH A 2 2002 2002 HOH HOH . 
E 3 HOH A 3 2003 2003 HOH HOH . 
E 3 HOH A 4 2004 2004 HOH HOH . 
E 3 HOH A 5 2005 2005 HOH HOH . 
E 3 HOH A 6 2006 2006 HOH HOH . 
E 3 HOH A 7 2007 2007 HOH HOH . 
E 3 HOH A 8 2008 2008 HOH HOH . 
E 3 HOH A 9 2009 2009 HOH HOH . 
E 3 HOH A 10 2010 2010 HOH HOH . 
E 3 HOH A 11 2011 2011 HOH HOH . 
E 3 HOH A 12 2012 2012 HOH HOH . 
E 3 HOH A 13 2013 2013 HOH HOH . 
E 3 HOH A 14 2014 2014 HOH HOH . 
E 3 HOH A 15 2015 2015 HOH HOH . 
E 3 HOH A 16 2016 2016 HOH HOH . 
E 3 HOH A 17 2017 2017 HOH HOH . 
E 3 HOH A 18 2018 2018 HOH HOH . 
E 3 HOH A 19 2019 2019 HOH HOH . 
E 3 HOH A 20 2020 2020 HOH HOH . 
E 3 HOH A 21 2021 2021 HOH HOH . 
E 3 HOH A 22 2022 2022 HOH HOH . 
E 3 HOH A 23 2023 2023 HOH HOH . 
E 3 HOH A 24 2024 2024 HOH HOH . 
E 3 HOH A 25 2025 2025 HOH HOH . 
E 3 HOH A 26 2026 2026 HOH HOH . 
E 3 HOH A 27 2027 2027 HOH HOH . 
E 3 HOH A 28 2028 2028 HOH HOH . 
E 3 HOH A 29 2029 2029 HOH HOH . 
E 3 HOH A 30 2030 2030 HOH HOH . 
E 3 HOH A 31 2031 2031 HOH HOH . 
E 3 HOH A 32 2032 2032 HOH HOH . 
E 3 HOH A 33 2033 2033 HOH HOH . 
E 3 HOH A 34 2034 2034 HOH HOH . 
E 3 HOH A 35 2035 2035 HOH HOH . 
E 3 HOH A 36 2036 2036 HOH HOH . 
E 3 HOH A 37 2037 2037 HOH HOH . 
E 3 HOH A 38 2038 2038 HOH HOH . 
E 3 HOH A 39 2039 2039 HOH HOH . 
E 3 HOH A 40 2040 2040 HOH HOH . 
E 3 HOH A 41 2041 2041 HOH HOH . 
F 3 HOH B 1 2001 2001 HOH HOH . 
F 3 HOH B 2 2002 2002 HOH HOH . 
F 3 HOH B 3 2003 2003 HOH HOH . 
F 3 HOH B 4 2004 2004 HOH HOH . 
F 3 HOH B 5 2005 2005 HOH HOH . 
F 3 HOH B 6 2006 2006 HOH HOH . 
F 3 HOH B 7 2007 2007 HOH HOH . 
F 3 HOH B 8 2008 2008 HOH HOH . 
F 3 HOH B 9 2009 2009 HOH HOH . 
F 3 HOH B 10 2010 2010 HOH HOH . 
F 3 HOH B 11 2011 2011 HOH HOH . 
F 3 HOH B 12 2012 2012 HOH HOH . 
F 3 HOH B 13 2013 2013 HOH HOH . 
F 3 HOH B 14 2014 2014 HOH HOH . 
F 3 HOH B 15 2015 2015 HOH HOH . 
F 3 HOH B 16 2016 2016 HOH HOH . 
F 3 HOH B 17 2017 2017 HOH HOH . 
F 3 HOH B 18 2018 2018 HOH HOH . 
F 3 HOH B 19 2019 2019 HOH HOH . 
F 3 HOH B 20 2020 2020 HOH HOH . 
F 3 HOH B 21 2021 2021 HOH HOH . 
F 3 HOH B 22 2022 2022 HOH HOH . 
F 3 HOH B 23 2023 2023 HOH HOH . 
F 3 HOH B 24 2024 2024 HOH HOH . 
F 3 HOH B 25 2025 2025 HOH HOH . 
F 3 HOH B 26 2026 2026 HOH HOH . 
F 3 HOH B 27 2027 2027 HOH HOH . 
F 3 HOH B 28 2028 2028 HOH HOH . 
F 3 HOH B 29 2029 2029 HOH HOH . 
F 3 HOH B 30 2030 2030 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 UDP . . . D 2 -17.505 12.243 54.512 1 43.26 ? N1 UDP 900 B 1 
HETATM 2 C C2 UDP . . . D 2 -17.421 12.632 55.819 1 42.72 ? C2 UDP 900 B 1 
HETATM 3 N N3 UDP . . . D 2 -16.512 12.05 56.669 1 42.32 ? N3 UDP 900 B 1 
HETATM 4 C C4 UDP . . . D 2 -15.689 11.059 56.196 1 42.34 ? C4 UDP 900 B 1 
HETATM 5 C C5 UDP . . . D 2 -15.774 10.654 54.885 1 42.61 ? C5 UDP 900 B 1 
HETATM 6 C C6 UDP . . . D 2 -16.688 11.244 54.04 1 41.88 ? C6 UDP 900 B 1 
HETATM 7 O O2 UDP . . . D 2 -18.158 13.509 56.227 1 42.54 ? O2 UDP 900 B 1 
HETATM 8 O O4 UDP . . . D 2 -14.882 10.543 56.948 1 41.94 ? O4 UDP 900 B 1 
HETATM 9 C C1' UDP . . . D 2 -18.498 12.849 53.632 1 45.54 ? C1' UDP 900 B 1 
HETATM 10 C C2' UDP . . . D 2 -18.033 13.639 52.446 1 46.85 ? C2' UDP 900 B 1 
HETATM 11 O O2' UDP . . . D 2 -18.106 15.017 52.755 1 48.22 ? O2' UDP 900 B 1 
HETATM 12 C C3' UDP . . . D 2 -19.155 13.369 51.49 1 47.21 ? C3' UDP 900 B 1 
HETATM 13 C C4' UDP . . . D 2 -19.656 11.999 51.875 1 46.43 ? C4' UDP 900 B 1 
HETATM 14 O O4' UDP . . . D 2 -18.94 11.657 53.031 1 46.36 ? O4' UDP 900 B 1 
HETATM 15 O O3' UDP . . . D 2 -20.17 14.284 51.81 1 47.58 ? O3' UDP 900 B 1 
HETATM 16 C C5' UDP . . . D 2 -19.206 11.01 50.824 1 47.62 ? C5' UDP 900 B 1 
HETATM 17 O O5' UDP . . . D 2 -20.279 10.62 50.027 1 48.58 ? O5' UDP 900 B 1 
HETATM 18 P PA UDP . . . D 2 -20.069 9.708 48.807 1 47.87 ? PA UDP 900 B 1 
HETATM 19 O O1A UDP . . . D 2 -21.068 8.561 49.014 1 45.15 ? O1A UDP 900 B 1 
HETATM 20 O O2A UDP . . . D 2 -18.717 9.218 48.643 1 49.51 ? O2A UDP 900 B 1 
HETATM 21 O O3A UDP . . . D 2 -20.671 10.488 47.597 1 50.18 ? O3A UDP 900 B 1 
HETATM 22 P PB UDP . . . D 2 -19.87 11.217 46.487 1 49.66 ? PB UDP 900 B 1 
HETATM 23 O O1B UDP . . . D 2 -19.819 10.23 45.31 1 51.92 ? O1B UDP 900 B 1 
HETATM 24 O O2B UDP . . . D 2 -18.445 11.359 46.952 1 44.81 ? O2B UDP 900 B 1 
HETATM 25 O O3B UDP . . . D 2 -20.488 12.484 46.176 1 48.93 ? O3B UDP 900 B 1 
#
_model_server_stats.io_time_ms              58 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#