data_2VXL
#
_model_server_result.job_id            CEn0onOJASI_tTuM0TAmfg 
_model_server_result.datetime_utc      '2024-10-13 09:16:27' 
_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          2vxl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    2VXL 
#
_exptl.entry_id    2VXL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            2VXL 
_cell.length_a            70.197 
_cell.length_b            70.197 
_cell.length_c            126.991 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2VXL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        PQS 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 A OD2 ASP 144 A ASP 225 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc2 A OD1 ASP 146 A ASP 227 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc3 A OD2 ASP 146 A ASP 227 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? 
metalc ? metalc4 B MN MN . A MN 400 1_555 C O2B UDP . A UDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc5 B MN MN . A MN 400 1_555 C O1A UDP . A UDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
#
_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                     2VXL 
_atom_sites.fract_transf_matrix[1][1]    0.014246 
_atom_sites.fract_transf_matrix[1][2]    0.008225 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016449 
_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]    0.007875 
_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
B 2 MN A 1 400 400 MN MN . 
C 3 UDP A 1 401 401 UDP UDP . 
D 4 HOH A 1 2001 2001 HOH HOH . 
D 4 HOH A 2 2002 2002 HOH HOH . 
D 4 HOH A 3 2003 2003 HOH HOH . 
D 4 HOH A 4 2004 2004 HOH HOH . 
D 4 HOH A 5 2005 2005 HOH HOH . 
D 4 HOH A 6 2006 2006 HOH HOH . 
D 4 HOH A 7 2007 2007 HOH HOH . 
D 4 HOH A 8 2008 2008 HOH HOH . 
D 4 HOH A 9 2009 2009 HOH HOH . 
D 4 HOH A 10 2010 2010 HOH HOH . 
D 4 HOH A 11 2011 2011 HOH HOH . 
D 4 HOH A 12 2012 2012 HOH HOH . 
D 4 HOH A 13 2013 2013 HOH HOH . 
D 4 HOH A 14 2014 2014 HOH HOH . 
D 4 HOH A 15 2015 2015 HOH HOH . 
D 4 HOH A 16 2016 2016 HOH HOH . 
D 4 HOH A 17 2017 2017 HOH HOH . 
D 4 HOH A 18 2018 2018 HOH HOH . 
D 4 HOH A 19 2019 2019 HOH HOH . 
D 4 HOH A 20 2020 2020 HOH HOH . 
D 4 HOH A 21 2021 2021 HOH HOH . 
D 4 HOH A 22 2022 2022 HOH HOH . 
D 4 HOH A 23 2023 2023 HOH HOH . 
D 4 HOH A 24 2024 2024 HOH HOH . 
D 4 HOH A 25 2025 2025 HOH HOH . 
D 4 HOH A 26 2026 2026 HOH HOH . 
D 4 HOH A 27 2027 2027 HOH HOH . 
D 4 HOH A 28 2028 2028 HOH HOH . 
D 4 HOH A 29 2029 2029 HOH HOH . 
D 4 HOH A 30 2030 2030 HOH HOH . 
D 4 HOH A 31 2031 2031 HOH HOH . 
D 4 HOH A 32 2032 2032 HOH HOH . 
D 4 HOH A 33 2033 2033 HOH HOH . 
D 4 HOH A 34 2034 2034 HOH HOH . 
D 4 HOH A 35 2035 2035 HOH HOH . 
D 4 HOH A 36 2036 2036 HOH HOH . 
D 4 HOH A 37 2037 2037 HOH HOH . 
D 4 HOH A 38 2038 2038 HOH HOH . 
D 4 HOH A 39 2039 2039 HOH HOH . 
D 4 HOH A 40 2040 2040 HOH HOH . 
D 4 HOH A 41 2041 2041 HOH HOH . 
D 4 HOH A 42 2042 2042 HOH HOH . 
D 4 HOH A 43 2043 2043 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 . . . C 3 -0.001 -38.526 25.379 1 24.1 ? N1 UDP 401 A 1 
HETATM 2 C C2 UDP . . . C 3 1.356 -38.74 25.215 1 24.28 ? C2 UDP 401 A 1 
HETATM 3 N N3 UDP . . . C 3 1.884 -40.005 25.374 1 24.06 ? N3 UDP 401 A 1 
HETATM 4 C C4 UDP . . . C 3 1.054 -41.059 25.695 1 24.23 ? C4 UDP 401 A 1 
HETATM 5 C C5 UDP . . . C 3 -0.311 -40.863 25.863 1 23.59 ? C5 UDP 401 A 1 
HETATM 6 C C6 UDP . . . C 3 -0.823 -39.582 25.704 1 23.96 ? C6 UDP 401 A 1 
HETATM 7 O O2 UDP . . . C 3 2.105 -37.813 24.928 1 25.05 ? O2 UDP 401 A 1 
HETATM 8 O O4 UDP . . . C 3 1.537 -42.179 25.833 1 25.07 ? O4 UDP 401 A 1 
HETATM 9 C C1' UDP . . . C 3 -0.576 -37.176 25.216 1 23.99 ? C1' UDP 401 A 1 
HETATM 10 C C2' UDP . . . C 3 -0.532 -36.733 23.756 1 23.45 ? C2' UDP 401 A 1 
HETATM 11 O O2' UDP . . . C 3 -0.347 -35.333 23.647 1 22.43 ? O2' UDP 401 A 1 
HETATM 12 C C3' UDP . . . C 3 -1.917 -37.111 23.283 1 23.45 ? C3' UDP 401 A 1 
HETATM 13 C C4' UDP . . . C 3 -2.757 -36.786 24.516 1 23.9 ? C4' UDP 401 A 1 
HETATM 14 O O4' UDP . . . C 3 -1.951 -37.218 25.598 1 23.99 ? O4' UDP 401 A 1 
HETATM 15 O O3' UDP . . . C 3 -2.328 -36.392 22.149 1 23.6 ? O3' UDP 401 A 1 
HETATM 16 C C5' UDP . . . C 3 -4.121 -37.457 24.548 1 23.39 ? C5' UDP 401 A 1 
HETATM 17 O O5' UDP . . . C 3 -3.926 -38.819 24.27 1 23.19 ? O5' UDP 401 A 1 
HETATM 18 P PA UDP . . . C 3 -4.505 -39.428 22.903 1 21.96 ? PA UDP 401 A 1 
HETATM 19 O O1A UDP . . . C 3 -4.173 -38.627 21.706 1 21.59 ? O1A UDP 401 A 1 
HETATM 20 O O2A UDP . . . C 3 -4.007 -40.815 22.839 1 22.57 ? O2A UDP 401 A 1 
HETATM 21 O O3A UDP . . . C 3 -6.084 -39.261 23.079 1 21.93 ? O3A UDP 401 A 1 
HETATM 22 P PB UDP . . . C 3 -7.07 -39.825 21.955 1 21.23 ? PB UDP 401 A 1 
HETATM 23 O O1B UDP . . . C 3 -6.67 -41.204 21.587 1 21.27 ? O1B UDP 401 A 1 
HETATM 24 O O2B UDP . . . C 3 -6.909 -38.937 20.79 1 22.99 ? O2B UDP 401 A 1 
HETATM 25 O O3B UDP . . . C 3 -8.473 -39.791 22.43 1 21.07 ? O3B UDP 401 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#