data_2BNE
#
_model_server_result.job_id            KR5GOeNYHcmWmcxTDT-tMg 
_model_server_result.datetime_utc      '2025-03-04 15:20:25' 
_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          2bne 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":1242}' 
#
_entry.id    2BNE 
#
_exptl.entry_id    2BNE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              324.181 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-MONOPHOSPHATE" 
_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            2BNE 
_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                 2BNE 
_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,M 
_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 H N N 
#
_chem_comp.formula           'C9 H13 N2 O9 P' 
_chem_comp.formula_weight    324.181 
_chem_comp.id                U5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_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 U5P sing 371 n n 
N1 C6 U5P sing 372 n n 
N1 C1' U5P sing 373 n n 
C2 N3 U5P sing 374 n n 
C2 O2 U5P doub 375 n n 
N3 C4 U5P sing 376 n n 
N3 HN3 U5P sing 377 n n 
C4 C5 U5P sing 378 n n 
C4 O4 U5P doub 379 n n 
C5 C6 U5P doub 380 n n 
C5 H5 U5P sing 381 n n 
C6 H6 U5P sing 382 n n 
C1' C2' U5P sing 383 n n 
C1' O4' U5P sing 384 n n 
C1' H1' U5P sing 385 n n 
C2' O2' U5P sing 386 n n 
C2' C3' U5P sing 387 n n 
C2' H2' U5P sing 388 n n 
O2' HO2' U5P sing 389 n n 
C3' C4' U5P sing 390 n n 
C3' O3' U5P sing 391 n n 
C3' H3' U5P sing 392 n n 
C4' O4' U5P sing 393 n n 
C4' C5' U5P sing 394 n n 
C4' H4' U5P sing 395 n n 
O3' HO3' U5P sing 396 n n 
C5' O5' U5P sing 397 n n 
C5' "H5'1" U5P sing 398 n n 
C5' "H5'2" U5P sing 399 n n 
O5' P U5P sing 400 n n 
P O1P U5P doub 401 n n 
P O2P U5P sing 402 n n 
P O3P U5P sing 403 n n 
O2P HOP2 U5P sing 404 n n 
O3P HOP3 U5P sing 405 n n 
#
_atom_sites.entry_id                     2BNE 
_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 U5P A 1 1242 1242 U5P U5P . 
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 2 U5P B 1 1242 1242 U5P U5P . 
I 3 GOL B 1 1243 1243 GOL GOL . 
J 3 GOL B 1 1244 1244 GOL GOL . 
K 3 GOL B 1 1245 1245 GOL GOL . 
L 4 HOH A 1 2001 2001 HOH HOH . 
L 4 HOH A 2 2002 2002 HOH HOH . 
L 4 HOH A 3 2003 2003 HOH HOH . 
L 4 HOH A 4 2004 2004 HOH HOH . 
L 4 HOH A 5 2005 2005 HOH HOH . 
L 4 HOH A 6 2006 2006 HOH HOH . 
L 4 HOH A 7 2007 2007 HOH HOH . 
L 4 HOH A 8 2008 2008 HOH HOH . 
L 4 HOH A 9 2009 2009 HOH HOH . 
L 4 HOH A 10 2010 2010 HOH HOH . 
L 4 HOH A 11 2011 2011 HOH HOH . 
L 4 HOH A 12 2012 2012 HOH HOH . 
L 4 HOH A 13 2013 2013 HOH HOH . 
L 4 HOH A 14 2014 2014 HOH HOH . 
L 4 HOH A 15 2015 2015 HOH HOH . 
L 4 HOH A 16 2016 2016 HOH HOH . 
L 4 HOH A 17 2017 2017 HOH HOH . 
L 4 HOH A 18 2018 2018 HOH HOH . 
L 4 HOH A 19 2019 2019 HOH HOH . 
L 4 HOH A 20 2020 2020 HOH HOH . 
L 4 HOH A 21 2021 2021 HOH HOH . 
L 4 HOH A 22 2022 2022 HOH HOH . 
L 4 HOH A 23 2023 2023 HOH HOH . 
L 4 HOH A 24 2024 2024 HOH HOH . 
L 4 HOH A 25 2025 2025 HOH HOH . 
L 4 HOH A 26 2026 2026 HOH HOH . 
L 4 HOH A 27 2027 2027 HOH HOH . 
L 4 HOH A 28 2028 2028 HOH HOH . 
L 4 HOH A 29 2029 2029 HOH HOH . 
L 4 HOH A 30 2030 2030 HOH HOH . 
L 4 HOH A 31 2031 2031 HOH HOH . 
L 4 HOH A 32 2032 2032 HOH HOH . 
L 4 HOH A 33 2033 2033 HOH HOH . 
L 4 HOH A 34 2034 2034 HOH HOH . 
L 4 HOH A 35 2035 2035 HOH HOH . 
L 4 HOH A 36 2036 2036 HOH HOH . 
L 4 HOH A 37 2037 2037 HOH HOH . 
L 4 HOH A 38 2038 2038 HOH HOH . 
L 4 HOH A 39 2039 2039 HOH HOH . 
L 4 HOH A 40 2040 2040 HOH HOH . 
L 4 HOH A 41 2041 2041 HOH HOH . 
L 4 HOH A 42 2042 2042 HOH HOH . 
L 4 HOH A 43 2043 2043 HOH HOH . 
M 4 HOH B 1 2001 2001 HOH HOH . 
M 4 HOH B 2 2002 2002 HOH HOH . 
M 4 HOH B 3 2003 2003 HOH HOH . 
M 4 HOH B 4 2004 2004 HOH HOH . 
M 4 HOH B 5 2005 2005 HOH HOH . 
M 4 HOH B 6 2006 2006 HOH HOH . 
M 4 HOH B 7 2007 2007 HOH HOH . 
M 4 HOH B 8 2008 2008 HOH HOH . 
M 4 HOH B 9 2009 2009 HOH HOH . 
M 4 HOH B 10 2010 2010 HOH HOH . 
M 4 HOH B 11 2011 2011 HOH HOH . 
M 4 HOH B 12 2012 2012 HOH HOH . 
M 4 HOH B 13 2013 2013 HOH HOH . 
M 4 HOH B 14 2014 2014 HOH HOH . 
M 4 HOH B 15 2015 2015 HOH HOH . 
M 4 HOH B 16 2016 2016 HOH HOH . 
M 4 HOH B 17 2017 2017 HOH HOH . 
M 4 HOH B 18 2018 2018 HOH HOH . 
M 4 HOH B 19 2019 2019 HOH HOH . 
M 4 HOH B 20 2020 2020 HOH HOH . 
M 4 HOH B 21 2021 2021 HOH HOH . 
M 4 HOH B 22 2022 2022 HOH HOH . 
M 4 HOH B 23 2023 2023 HOH HOH . 
M 4 HOH B 24 2024 2024 HOH HOH . 
M 4 HOH B 25 2025 2025 HOH HOH . 
M 4 HOH B 26 2026 2026 HOH HOH . 
M 4 HOH B 27 2027 2027 HOH HOH . 
M 4 HOH B 28 2028 2028 HOH HOH . 
M 4 HOH B 29 2029 2029 HOH HOH . 
M 4 HOH B 30 2030 2030 HOH HOH . 
M 4 HOH B 31 2031 2031 HOH HOH . 
M 4 HOH B 32 2032 2032 HOH HOH . 
M 4 HOH B 33 2033 2033 HOH HOH . 
M 4 HOH B 34 2034 2034 HOH HOH . 
M 4 HOH B 35 2035 2035 HOH HOH . 
M 4 HOH B 36 2036 2036 HOH HOH . 
M 4 HOH B 37 2037 2037 HOH HOH . 
M 4 HOH B 38 2038 2038 HOH HOH . 
M 4 HOH B 39 2039 2039 HOH HOH . 
M 4 HOH B 40 2040 2040 HOH HOH . 
M 4 HOH B 41 2041 2041 HOH HOH . 
M 4 HOH B 42 2042 2042 HOH HOH . 
M 4 HOH B 43 2043 2043 HOH HOH . 
M 4 HOH B 44 2044 2044 HOH HOH . 
M 4 HOH B 45 2045 2045 HOH HOH . 
M 4 HOH B 46 2046 2046 HOH HOH . 
M 4 HOH B 47 2047 2047 HOH HOH . 
M 4 HOH B 48 2048 2048 HOH HOH . 
M 4 HOH B 49 2049 2049 HOH HOH . 
M 4 HOH B 50 2050 2050 HOH HOH . 
M 4 HOH B 51 2051 2051 HOH HOH . 
M 4 HOH B 52 2052 2052 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 U5P . . . H 2 62.198 61.218 -0.413 1 20.17 ? N1 U5P 1242 B 1 
HETATM 2 C C2 U5P . . . H 2 61.534 60.272 -1.208 1 19.39 ? C2 U5P 1242 B 1 
HETATM 3 N N3 U5P . . . H 2 60.659 59.452 -0.521 1 18.33 ? N3 U5P 1242 B 1 
HETATM 4 C C4 U5P . . . H 2 60.429 59.414 0.852 1 17.7 ? C4 U5P 1242 B 1 
HETATM 5 C C5 U5P . . . H 2 61.172 60.375 1.622 1 18.74 ? C5 U5P 1242 B 1 
HETATM 6 C C6 U5P . . . H 2 62 61.229 0.981 1 19.86 ? C6 U5P 1242 B 1 
HETATM 7 O O2 U5P . . . H 2 61.718 60.156 -2.408 1 21.94 ? O2 U5P 1242 B 1 
HETATM 8 O O4 U5P . . . H 2 59.621 58.605 1.301 1 21.51 ? O4 U5P 1242 B 1 
HETATM 9 C C1' U5P . . . H 2 63.189 62.09 -1.103 1 20.9 ? C1' U5P 1242 B 1 
HETATM 10 C C2' U5P . . . H 2 62.686 63.444 -1.59 1 23.86 ? C2' U5P 1242 B 1 
HETATM 11 O O2' U5P . . . H 2 63.297 63.8 -2.821 1 23.76 ? O2' U5P 1242 B 1 
HETATM 12 C C3' U5P . . . H 2 63.047 64.366 -0.427 1 23.53 ? C3' U5P 1242 B 1 
HETATM 13 C C4' U5P . . . H 2 64.299 63.733 0.168 1 24.05 ? C4' U5P 1242 B 1 
HETATM 14 O O3' U5P . . . H 2 63.296 65.7 -0.835 1 26.82 ? O3' U5P 1242 B 1 
HETATM 15 O O4' U5P . . . H 2 64.31 62.356 -0.3 1 22.58 ? O4' U5P 1242 B 1 
HETATM 16 C C5' U5P . . . H 2 64.318 63.679 1.676 1 26.19 ? C5' U5P 1242 B 1 
HETATM 17 O O5' U5P . . . H 2 64.406 64.97 2.2 1 31.67 ? O5' U5P 1242 B 1 
HETATM 18 P P U5P . . . H 2 63.156 65.682 2.829 1 26.97 ? P U5P 1242 B 1 
HETATM 19 O O1P U5P . . . H 2 62.794 66.847 1.982 1 30.91 ? O1P U5P 1242 B 1 
HETATM 20 O O2P U5P . . . H 2 62.135 64.694 3.226 1 30.38 ? O2P U5P 1242 B 1 
HETATM 21 O O3P U5P . . . H 2 63.893 66.192 4.174 1 29.99 ? O3P U5P 1242 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           21 
#