data_2BVM
#
_model_server_result.job_id            1JYqDjGti9L7FPI_vdfCOA 
_model_server_result.datetime_utc      '2024-11-24 14:24:11' 
_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          2bvm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1543}' 
#
_entry.id    2BVM 
#
_exptl.entry_id    2BVM 
_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         90 
_cell.entry_id            2BVM 
_cell.length_a            65.777 
_cell.length_b            97.298 
_cell.length_c            114.448 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2BVM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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,E,F 
_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 288 A ASP 288 1_555 B MN MN . A MN 1542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc2 A OE1 GLU 515 A GLU 515 1_555 B MN MN . A MN 1542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc3 B MN MN . A MN 1542 1_555 C O3B UDP . A UDP 1543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc4 B MN MN . A MN 1542 1_555 C O1A UDP . A UDP 1543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? 
metalc ? metalc5 B MN MN . A MN 1542 1_555 F O HOH . A HOH 2124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc6 B MN MN . A MN 1542 1_555 F O HOH . A HOH 2125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
#
_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 386 n n 
N1 C6 UDP sing 387 n n 
N1 C1' UDP sing 388 n n 
C2 N3 UDP sing 389 n n 
C2 O2 UDP doub 390 n n 
N3 C4 UDP sing 391 n n 
N3 HN3 UDP sing 392 n n 
C4 C5 UDP sing 393 n n 
C4 O4 UDP doub 394 n n 
C5 C6 UDP doub 395 n n 
C5 H5 UDP sing 396 n n 
C6 H6 UDP sing 397 n n 
C1' C2' UDP sing 398 n n 
C1' O4' UDP sing 399 n n 
C1' H1' UDP sing 400 n n 
C2' O2' UDP sing 401 n n 
C2' C3' UDP sing 402 n n 
C2' H2' UDP sing 403 n n 
O2' HO2' UDP sing 404 n n 
C3' C4' UDP sing 405 n n 
C3' O3' UDP sing 406 n n 
C3' H3' UDP sing 407 n n 
C4' O4' UDP sing 408 n n 
C4' C5' UDP sing 409 n n 
C4' H4' UDP sing 410 n n 
O3' HO3' UDP sing 411 n n 
C5' O5' UDP sing 412 n n 
C5' "H5'1" UDP sing 413 n n 
C5' "H5'2" UDP sing 414 n n 
O5' PA UDP sing 415 n n 
PA O1A UDP doub 416 n n 
PA O2A UDP sing 417 n n 
PA O3A UDP sing 418 n n 
O2A HOA2 UDP sing 419 n n 
O3A PB UDP sing 420 n n 
PB O1B UDP doub 421 n n 
PB O2B UDP sing 422 n n 
PB O3B UDP sing 423 n n 
O2B HOB2 UDP sing 424 n n 
O3B HOB3 UDP sing 425 n n 
#
_atom_sites.entry_id                     2BVM 
_atom_sites.fract_transf_matrix[1][1]    0.015203 
_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]    0.010278 
_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]    0.008738 
_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 1542 1542 MN MN . 
C 3 UDP A 1 1543 1543 UDP UDP . 
D 4 GLC A 1 1544 1544 GLC GLC . 
E 5 SO4 A 1 1545 1545 SO4 SO4 . 
F 6 HOH A 1 2001 2001 HOH HOH . 
F 6 HOH A 2 2002 2002 HOH HOH . 
F 6 HOH A 3 2003 2003 HOH HOH . 
F 6 HOH A 4 2004 2004 HOH HOH . 
F 6 HOH A 5 2005 2005 HOH HOH . 
F 6 HOH A 6 2006 2006 HOH HOH . 
F 6 HOH A 7 2007 2007 HOH HOH . 
F 6 HOH A 8 2008 2008 HOH HOH . 
F 6 HOH A 9 2009 2009 HOH HOH . 
F 6 HOH A 10 2010 2010 HOH HOH . 
F 6 HOH A 11 2011 2011 HOH HOH . 
F 6 HOH A 12 2012 2012 HOH HOH . 
F 6 HOH A 13 2013 2013 HOH HOH . 
F 6 HOH A 14 2014 2014 HOH HOH . 
F 6 HOH A 15 2015 2015 HOH HOH . 
F 6 HOH A 16 2016 2016 HOH HOH . 
F 6 HOH A 17 2017 2017 HOH HOH . 
F 6 HOH A 18 2018 2018 HOH HOH . 
F 6 HOH A 19 2019 2019 HOH HOH . 
F 6 HOH A 20 2020 2020 HOH HOH . 
F 6 HOH A 21 2021 2021 HOH HOH . 
F 6 HOH A 22 2022 2022 HOH HOH . 
F 6 HOH A 23 2023 2023 HOH HOH . 
F 6 HOH A 24 2024 2024 HOH HOH . 
F 6 HOH A 25 2025 2025 HOH HOH . 
F 6 HOH A 26 2026 2026 HOH HOH . 
F 6 HOH A 27 2027 2027 HOH HOH . 
F 6 HOH A 28 2028 2028 HOH HOH . 
F 6 HOH A 29 2029 2029 HOH HOH . 
F 6 HOH A 30 2030 2030 HOH HOH . 
F 6 HOH A 31 2031 2031 HOH HOH . 
F 6 HOH A 32 2032 2032 HOH HOH . 
F 6 HOH A 33 2033 2033 HOH HOH . 
F 6 HOH A 34 2034 2034 HOH HOH . 
F 6 HOH A 35 2035 2035 HOH HOH . 
F 6 HOH A 36 2036 2036 HOH HOH . 
F 6 HOH A 37 2037 2037 HOH HOH . 
F 6 HOH A 38 2038 2038 HOH HOH . 
F 6 HOH A 39 2039 2039 HOH HOH . 
F 6 HOH A 40 2040 2040 HOH HOH . 
F 6 HOH A 41 2041 2041 HOH HOH . 
F 6 HOH A 42 2042 2042 HOH HOH . 
F 6 HOH A 43 2043 2043 HOH HOH . 
F 6 HOH A 44 2044 2044 HOH HOH . 
F 6 HOH A 45 2045 2045 HOH HOH . 
F 6 HOH A 46 2046 2046 HOH HOH . 
F 6 HOH A 47 2047 2047 HOH HOH . 
F 6 HOH A 48 2048 2048 HOH HOH . 
F 6 HOH A 49 2049 2049 HOH HOH . 
F 6 HOH A 50 2050 2050 HOH HOH . 
F 6 HOH A 51 2051 2051 HOH HOH . 
F 6 HOH A 52 2052 2052 HOH HOH . 
F 6 HOH A 53 2053 2053 HOH HOH . 
F 6 HOH A 54 2054 2054 HOH HOH . 
F 6 HOH A 55 2055 2055 HOH HOH . 
F 6 HOH A 56 2056 2056 HOH HOH . 
F 6 HOH A 57 2057 2057 HOH HOH . 
F 6 HOH A 58 2058 2058 HOH HOH . 
F 6 HOH A 59 2059 2059 HOH HOH . 
F 6 HOH A 60 2060 2060 HOH HOH . 
F 6 HOH A 61 2061 2061 HOH HOH . 
F 6 HOH A 62 2062 2062 HOH HOH . 
F 6 HOH A 63 2063 2063 HOH HOH . 
F 6 HOH A 64 2064 2064 HOH HOH . 
F 6 HOH A 65 2065 2065 HOH HOH . 
F 6 HOH A 66 2066 2066 HOH HOH . 
F 6 HOH A 67 2067 2067 HOH HOH . 
F 6 HOH A 68 2068 2068 HOH HOH . 
F 6 HOH A 69 2069 2069 HOH HOH . 
F 6 HOH A 70 2070 2070 HOH HOH . 
F 6 HOH A 71 2071 2071 HOH HOH . 
F 6 HOH A 72 2072 2072 HOH HOH . 
F 6 HOH A 73 2073 2073 HOH HOH . 
F 6 HOH A 74 2074 2074 HOH HOH . 
F 6 HOH A 75 2075 2075 HOH HOH . 
F 6 HOH A 76 2076 2076 HOH HOH . 
F 6 HOH A 77 2077 2077 HOH HOH . 
F 6 HOH A 78 2078 2078 HOH HOH . 
F 6 HOH A 79 2079 2079 HOH HOH . 
F 6 HOH A 80 2080 2080 HOH HOH . 
F 6 HOH A 81 2081 2081 HOH HOH . 
F 6 HOH A 82 2082 2082 HOH HOH . 
F 6 HOH A 83 2083 2083 HOH HOH . 
F 6 HOH A 84 2084 2084 HOH HOH . 
F 6 HOH A 85 2085 2085 HOH HOH . 
F 6 HOH A 86 2086 2086 HOH HOH . 
F 6 HOH A 87 2087 2087 HOH HOH . 
F 6 HOH A 88 2088 2088 HOH HOH . 
F 6 HOH A 89 2089 2089 HOH HOH . 
F 6 HOH A 90 2090 2090 HOH HOH . 
F 6 HOH A 91 2091 2091 HOH HOH . 
F 6 HOH A 92 2092 2092 HOH HOH . 
F 6 HOH A 93 2093 2093 HOH HOH . 
F 6 HOH A 94 2094 2094 HOH HOH . 
F 6 HOH A 95 2095 2095 HOH HOH . 
F 6 HOH A 96 2096 2096 HOH HOH . 
F 6 HOH A 97 2097 2097 HOH HOH . 
F 6 HOH A 98 2098 2098 HOH HOH . 
F 6 HOH A 99 2099 2099 HOH HOH . 
F 6 HOH A 100 2100 2100 HOH HOH . 
F 6 HOH A 101 2101 2101 HOH HOH . 
F 6 HOH A 102 2102 2102 HOH HOH . 
F 6 HOH A 103 2103 2103 HOH HOH . 
F 6 HOH A 104 2104 2104 HOH HOH . 
F 6 HOH A 105 2105 2105 HOH HOH . 
F 6 HOH A 106 2106 2106 HOH HOH . 
F 6 HOH A 107 2107 2107 HOH HOH . 
F 6 HOH A 108 2108 2108 HOH HOH . 
F 6 HOH A 109 2109 2109 HOH HOH . 
F 6 HOH A 110 2110 2110 HOH HOH . 
F 6 HOH A 111 2111 2111 HOH HOH . 
F 6 HOH A 112 2112 2112 HOH HOH . 
F 6 HOH A 113 2113 2113 HOH HOH . 
F 6 HOH A 114 2114 2114 HOH HOH . 
F 6 HOH A 115 2115 2115 HOH HOH . 
F 6 HOH A 116 2116 2116 HOH HOH . 
F 6 HOH A 117 2117 2117 HOH HOH . 
F 6 HOH A 118 2118 2118 HOH HOH . 
F 6 HOH A 119 2119 2119 HOH HOH . 
F 6 HOH A 120 2120 2120 HOH HOH . 
F 6 HOH A 121 2121 2121 HOH HOH . 
F 6 HOH A 122 2122 2122 HOH HOH . 
F 6 HOH A 123 2123 2123 HOH HOH . 
F 6 HOH A 124 2124 2124 HOH HOH . 
F 6 HOH A 125 2125 2125 HOH HOH . 
F 6 HOH A 126 2126 2126 HOH HOH . 
F 6 HOH A 127 2127 2127 HOH HOH . 
F 6 HOH A 128 2128 2128 HOH HOH . 
F 6 HOH A 129 2129 2129 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 23.902 -3.564 56.278 1 44.9 ? N1 UDP 1543 A 1 
HETATM 2 C C2 UDP . . . C 3 24.595 -3.152 57.436 1 44.75 ? C2 UDP 1543 A 1 
HETATM 3 N N3 UDP . . . C 3 25.097 -4.115 58.309 1 43.88 ? N3 UDP 1543 A 1 
HETATM 4 C C4 UDP . . . C 3 24.913 -5.479 58.029 1 44.95 ? C4 UDP 1543 A 1 
HETATM 5 C C5 UDP . . . C 3 24.232 -5.894 56.89 1 43.98 ? C5 UDP 1543 A 1 
HETATM 6 C C6 UDP . . . C 3 23.723 -4.934 56.02 1 44.77 ? C6 UDP 1543 A 1 
HETATM 7 O O2 UDP . . . C 3 24.762 -1.955 57.689 1 45.4 ? O2 UDP 1543 A 1 
HETATM 8 O O4 UDP . . . C 3 25.368 -6.314 58.814 1 46.31 ? O4 UDP 1543 A 1 
HETATM 9 C C1' UDP . . . C 3 23.351 -2.535 55.355 1 44.08 ? C1' UDP 1543 A 1 
HETATM 10 C C2' UDP . . . C 3 24.455 -2.001 54.441 1 43.29 ? C2' UDP 1543 A 1 
HETATM 11 O O2' UDP . . . C 3 24.243 -0.587 54.298 1 43.34 ? O2' UDP 1543 A 1 
HETATM 12 C C3' UDP . . . C 3 24.132 -2.705 53.142 1 42.79 ? C3' UDP 1543 A 1 
HETATM 13 C C4' UDP . . . C 3 22.608 -2.589 53.155 1 41.31 ? C4' UDP 1543 A 1 
HETATM 14 O O4' UDP . . . C 3 22.295 -3.051 54.488 1 42.33 ? O4' UDP 1543 A 1 
HETATM 15 O O3' UDP . . . C 3 24.656 -1.982 52.048 1 42.77 ? O3' UDP 1543 A 1 
HETATM 16 C C5' UDP . . . C 3 22.001 -3.513 52.116 1 37.77 ? C5' UDP 1543 A 1 
HETATM 17 O O5' UDP . . . C 3 22.638 -4.77 52.166 1 35.17 ? O5' UDP 1543 A 1 
HETATM 18 P PA UDP . . . C 3 22.587 -5.767 50.905 1 34.72 ? PA UDP 1543 A 1 
HETATM 19 O O1A UDP . . . C 3 23.224 -5.165 49.723 1 34.74 ? O1A UDP 1543 A 1 
HETATM 20 O O2A UDP . . . C 3 23.043 -7.09 51.359 1 35.7 ? O2A UDP 1543 A 1 
HETATM 21 O O3A UDP . . . C 3 20.989 -5.828 50.665 1 34.76 ? O3A UDP 1543 A 1 
HETATM 22 P PB UDP . . . C 3 20.437 -6.313 49.196 1 33.9 ? PB UDP 1543 A 1 
HETATM 23 O O1B UDP . . . C 3 18.846 -6.179 49.295 1 32.76 ? O1B UDP 1543 A 1 
HETATM 24 O O2B UDP . . . C 3 20.741 -7.878 48.998 1 32.29 ? O2B UDP 1543 A 1 
HETATM 25 O O3B UDP . . . C 3 20.983 -5.516 48.063 1 34.38 ? O3B UDP 1543 A 1 
#
_model_server_stats.io_time_ms              75 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           339 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#