data_2BND
#
_model_server_result.job_id            oHpW4Eui9T-ECqRCCO_ubQ 
_model_server_result.datetime_utc      '2025-03-04 14:58:56' 
_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          2bnd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":1242}' 
#
_entry.id    2BND 
#
_exptl.entry_id    2BND 
_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         120 
_cell.entry_id            2BND 
_cell.length_a            140.434 
_cell.length_b            140.434 
_cell.length_c            59.993 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2BND 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3' 
#
_pdbx_struct_assembly.method_details        PQS 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,G,H,I,J,K,L 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 140.434 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 70.217 121.619412 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 I 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 381 n n 
N1 C6 UDP sing 382 n n 
N1 C1' UDP sing 383 n n 
C2 N3 UDP sing 384 n n 
C2 O2 UDP doub 385 n n 
N3 C4 UDP sing 386 n n 
N3 HN3 UDP sing 387 n n 
C4 C5 UDP sing 388 n n 
C4 O4 UDP doub 389 n n 
C5 C6 UDP doub 390 n n 
C5 H5 UDP sing 391 n n 
C6 H6 UDP sing 392 n n 
C1' C2' UDP sing 393 n n 
C1' O4' UDP sing 394 n n 
C1' H1' UDP sing 395 n n 
C2' O2' UDP sing 396 n n 
C2' C3' UDP sing 397 n n 
C2' H2' UDP sing 398 n n 
O2' HO2' UDP sing 399 n n 
C3' C4' UDP sing 400 n n 
C3' O3' UDP sing 401 n n 
C3' H3' UDP sing 402 n n 
C4' O4' UDP sing 403 n n 
C4' C5' UDP sing 404 n n 
C4' H4' UDP sing 405 n n 
O3' HO3' UDP sing 406 n n 
C5' O5' UDP sing 407 n n 
C5' "H5'1" UDP sing 408 n n 
C5' "H5'2" UDP sing 409 n n 
O5' PA UDP sing 410 n n 
PA O1A UDP doub 411 n n 
PA O2A UDP sing 412 n n 
PA O3A UDP sing 413 n n 
O2A HOA2 UDP sing 414 n n 
O3A PB UDP sing 415 n n 
PB O1B UDP doub 416 n n 
PB O2B UDP sing 417 n n 
PB O3B UDP sing 418 n n 
O2B HOB2 UDP sing 419 n n 
O3B HOB3 UDP sing 420 n n 
#
_atom_sites.entry_id                     2BND 
_atom_sites.fract_transf_matrix[1][1]    0.007121 
_atom_sites.fract_transf_matrix[1][2]    0.004111 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008222 
_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]    0.016669 
_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 1242 1242 UDP UDP . 
D 3 GOL A 1 1243 1243 GOL GOL . 
E 3 GOL A 1 1244 1244 GOL GOL . 
F 3 GOL A 1 1245 1245 GOL GOL . 
G 3 GOL A 1 1246 1246 GOL GOL . 
H 4 POP A 1 1247 1247 POP POP . 
I 2 UDP B 1 1242 1242 UDP UDP . 
J 3 GOL B 1 1243 1243 GOL GOL . 
K 5 HOH A 1 2001 2001 HOH HOH . 
K 5 HOH A 2 2002 2002 HOH HOH . 
K 5 HOH A 3 2003 2003 HOH HOH . 
K 5 HOH A 4 2004 2004 HOH HOH . 
K 5 HOH A 5 2005 2005 HOH HOH . 
K 5 HOH A 6 2006 2006 HOH HOH . 
K 5 HOH A 7 2007 2007 HOH HOH . 
K 5 HOH A 8 2008 2008 HOH HOH . 
K 5 HOH A 9 2009 2009 HOH HOH . 
K 5 HOH A 10 2010 2010 HOH HOH . 
K 5 HOH A 11 2011 2011 HOH HOH . 
K 5 HOH A 12 2012 2012 HOH HOH . 
K 5 HOH A 13 2013 2013 HOH HOH . 
K 5 HOH A 14 2014 2014 HOH HOH . 
K 5 HOH A 15 2015 2015 HOH HOH . 
K 5 HOH A 16 2016 2016 HOH HOH . 
K 5 HOH A 17 2017 2017 HOH HOH . 
K 5 HOH A 18 2018 2018 HOH HOH . 
K 5 HOH A 19 2019 2019 HOH HOH . 
K 5 HOH A 20 2020 2020 HOH HOH . 
K 5 HOH A 21 2021 2021 HOH HOH . 
K 5 HOH A 22 2022 2022 HOH HOH . 
K 5 HOH A 23 2023 2023 HOH HOH . 
K 5 HOH A 24 2024 2024 HOH HOH . 
K 5 HOH A 25 2025 2025 HOH HOH . 
K 5 HOH A 26 2026 2026 HOH HOH . 
K 5 HOH A 27 2027 2027 HOH HOH . 
K 5 HOH A 28 2028 2028 HOH HOH . 
K 5 HOH A 29 2029 2029 HOH HOH . 
K 5 HOH A 30 2030 2030 HOH HOH . 
K 5 HOH A 31 2031 2031 HOH HOH . 
K 5 HOH A 32 2032 2032 HOH HOH . 
K 5 HOH A 33 2033 2033 HOH HOH . 
K 5 HOH A 34 2034 2034 HOH HOH . 
K 5 HOH A 35 2035 2035 HOH HOH . 
K 5 HOH A 36 2036 2036 HOH HOH . 
K 5 HOH A 37 2037 2037 HOH HOH . 
K 5 HOH A 38 2038 2038 HOH HOH . 
K 5 HOH A 39 2039 2039 HOH HOH . 
K 5 HOH A 40 2040 2040 HOH HOH . 
K 5 HOH A 41 2041 2041 HOH HOH . 
K 5 HOH A 42 2042 2042 HOH HOH . 
K 5 HOH A 43 2043 2043 HOH HOH . 
K 5 HOH A 44 2044 2044 HOH HOH . 
K 5 HOH A 45 2045 2045 HOH HOH . 
K 5 HOH A 46 2046 2046 HOH HOH . 
K 5 HOH A 47 2047 2047 HOH HOH . 
K 5 HOH A 48 2048 2048 HOH HOH . 
K 5 HOH A 49 2049 2049 HOH HOH . 
K 5 HOH A 50 2050 2050 HOH HOH . 
L 5 HOH B 1 2001 2001 HOH HOH . 
L 5 HOH B 2 2002 2002 HOH HOH . 
L 5 HOH B 3 2003 2003 HOH HOH . 
L 5 HOH B 4 2004 2004 HOH HOH . 
L 5 HOH B 5 2005 2005 HOH HOH . 
L 5 HOH B 6 2006 2006 HOH HOH . 
L 5 HOH B 7 2007 2007 HOH HOH . 
L 5 HOH B 8 2008 2008 HOH HOH . 
L 5 HOH B 9 2009 2009 HOH HOH . 
L 5 HOH B 10 2010 2010 HOH HOH . 
L 5 HOH B 11 2011 2011 HOH HOH . 
L 5 HOH B 12 2012 2012 HOH HOH . 
L 5 HOH B 13 2013 2013 HOH HOH . 
L 5 HOH B 14 2014 2014 HOH HOH . 
L 5 HOH B 15 2015 2015 HOH HOH . 
L 5 HOH B 16 2016 2016 HOH HOH . 
L 5 HOH B 17 2017 2017 HOH HOH . 
L 5 HOH B 18 2018 2018 HOH HOH . 
L 5 HOH B 19 2019 2019 HOH HOH . 
L 5 HOH B 20 2020 2020 HOH HOH . 
L 5 HOH B 21 2021 2021 HOH HOH . 
L 5 HOH B 22 2022 2022 HOH HOH . 
L 5 HOH B 23 2023 2023 HOH HOH . 
L 5 HOH B 24 2024 2024 HOH HOH . 
L 5 HOH B 25 2025 2025 HOH HOH . 
L 5 HOH B 26 2026 2026 HOH HOH . 
L 5 HOH B 27 2027 2027 HOH HOH . 
L 5 HOH B 28 2028 2028 HOH HOH . 
L 5 HOH B 29 2029 2029 HOH HOH . 
L 5 HOH B 30 2030 2030 HOH HOH . 
L 5 HOH B 31 2031 2031 HOH HOH . 
L 5 HOH B 32 2032 2032 HOH HOH . 
L 5 HOH B 33 2033 2033 HOH HOH . 
L 5 HOH B 34 2034 2034 HOH HOH . 
L 5 HOH B 35 2035 2035 HOH HOH . 
L 5 HOH B 36 2036 2036 HOH HOH . 
L 5 HOH B 37 2037 2037 HOH HOH . 
L 5 HOH B 38 2038 2038 HOH HOH . 
L 5 HOH B 39 2039 2039 HOH HOH . 
L 5 HOH B 40 2040 2040 HOH HOH . 
L 5 HOH B 41 2041 2041 HOH HOH . 
L 5 HOH B 42 2042 2042 HOH HOH . 
L 5 HOH B 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 . . . I 2 92.088 43.925 0.461 1 18.89 ? N1 UDP 1242 B 1 
HETATM 2 C C2 UDP . . . I 2 91.659 42.848 1.253 1 17.98 ? C2 UDP 1242 B 1 
HETATM 3 N N3 UDP . . . I 2 91.369 41.688 0.542 1 17.19 ? N3 UDP 1242 B 1 
HETATM 4 C C4 UDP . . . I 2 91.523 41.47 -0.833 1 15.35 ? C4 UDP 1242 B 1 
HETATM 5 C C5 UDP . . . I 2 91.989 42.606 -1.583 1 14.19 ? C5 UDP 1242 B 1 
HETATM 6 C C6 UDP . . . I 2 92.244 43.764 -0.935 1 17.56 ? C6 UDP 1242 B 1 
HETATM 7 O O2 UDP . . . I 2 91.671 42.876 2.474 1 18.6 ? O2 UDP 1242 B 1 
HETATM 8 O O4 UDP . . . I 2 91.361 40.334 -1.282 1 18.69 ? O4 UDP 1242 B 1 
HETATM 9 C C1' UDP . . . I 2 92.332 45.212 1.164 1 18.43 ? C1' UDP 1242 B 1 
HETATM 10 C C2' UDP . . . I 2 93.729 45.382 1.741 1 19.31 ? C2' UDP 1242 B 1 
HETATM 11 O O2' UDP . . . I 2 93.671 46.117 2.944 1 18.28 ? O2' UDP 1242 B 1 
HETATM 12 C C3' UDP . . . I 2 94.472 46.094 0.598 1 19.64 ? C3' UDP 1242 B 1 
HETATM 13 C C4' UDP . . . I 2 93.382 46.978 -0.014 1 20.53 ? C4' UDP 1242 B 1 
HETATM 14 O O4' UDP . . . I 2 92.111 46.339 0.33 1 21.83 ? O4' UDP 1242 B 1 
HETATM 15 O O3' UDP . . . I 2 95.594 46.874 1.041 1 14.86 ? O3' UDP 1242 B 1 
HETATM 16 C C5' UDP . . . I 2 93.433 47.105 -1.51 1 23.09 ? C5' UDP 1242 B 1 
HETATM 17 O O5' UDP . . . I 2 94.628 47.713 -1.908 1 24.52 ? O5' UDP 1242 B 1 
HETATM 18 P PA UDP . . . I 2 95.796 46.878 -2.568 1 25.73 ? PA UDP 1242 B 1 
HETATM 19 O O1A UDP . . . I 2 97.043 47.075 -1.767 1 26.76 ? O1A UDP 1242 B 1 
HETATM 20 O O2A UDP . . . I 2 95.336 45.508 -2.905 1 25.56 ? O2A UDP 1242 B 1 
HETATM 21 O O3A UDP . . . I 2 95.858 47.728 -3.929 1 27.87 ? O3A UDP 1242 B 1 
HETATM 22 P PB UDP . . . I 2 97.037 48.135 -4.896 1 31.68 ? PB UDP 1242 B 1 
HETATM 23 O O1B UDP . . . I 2 97.158 49.562 -5.163 1 32.63 ? O1B UDP 1242 B 1 
HETATM 24 O O2B UDP . . . I 2 96.89 47.247 -6.022 1 33.98 ? O2B UDP 1242 B 1 
HETATM 25 O O3B UDP . . . I 2 98.312 47.709 -4.029 1 29.15 ? O3B UDP 1242 B 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           61 
_model_server_stats.create_model_time_ms    57 
_model_server_stats.query_time_ms           389 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#