data_2V54
#
_model_server_result.job_id            1aQhrle1PRtuuK-Vgyb0Fw 
_model_server_result.datetime_utc      '2024-12-04 02:40:08' 
_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          2v54 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1205}' 
#
_entry.id    2V54 
#
_exptl.entry_id    2V54 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-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            2V54 
_cell.length_a            56.77 
_cell.length_b            55.59 
_cell.length_c            161.17 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2V54 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_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 
#
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 F N 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 B OD1 ASP 13 B ASP 13 1_555 D MG MG . B MG 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc2 B OE2 GLU 145 B GLU 145 1_555 D MG MG . B MG 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? 
metalc ? metalc3 D MG MG . B MG 1205 1_555 E O4 POP . B POP 1206 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.26 ? 
metalc ? metalc4 D MG MG . B MG 1205 1_555 F O2B TYD . B TYD 1207 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc5 D MG MG . B MG 1205 1_555 H O HOH . B HOH 2046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.841 ? 
#
_chem_comp.formula           'C10 H16 N2 O11 P2' 
_chem_comp.formula_weight    402.188 
_chem_comp.id                TYD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-5'-DIPHOSPHATE" 
_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
PA O1A TYD doub 344 n n 
PA O2A TYD sing 345 n n 
PA O3A TYD sing 346 n n 
PA O5' TYD sing 347 n n 
O2A HOA2 TYD sing 348 n n 
O3A PB TYD sing 349 n n 
PB O1B TYD doub 350 n n 
PB O2B TYD sing 351 n n 
PB O3B TYD sing 352 n n 
O2B HOB2 TYD sing 353 n n 
O3B HOB3 TYD sing 354 n n 
O5' C5' TYD sing 355 n n 
C5' C4' TYD sing 356 n n 
C5' "H5'1" TYD sing 357 n n 
C5' "H5'2" TYD sing 358 n n 
C4' O4' TYD sing 359 n n 
C4' C3' TYD sing 360 n n 
C4' H4' TYD sing 361 n n 
O4' C1' TYD sing 362 n n 
C3' O3' TYD sing 363 n n 
C3' C2' TYD sing 364 n n 
C3' H3' TYD sing 365 n n 
O3' HO3' TYD sing 366 n n 
C2' C1' TYD sing 367 n n 
C2' "H2'1" TYD sing 368 n n 
C2' "H2'2" TYD sing 369 n n 
C1' N1 TYD sing 370 n n 
C1' H1' TYD sing 371 n n 
N1 C2 TYD sing 372 n y 
N1 C6 TYD sing 373 n y 
C2 O2 TYD doub 374 n n 
C2 N3 TYD sing 375 n y 
N3 C4 TYD sing 376 n y 
N3 HN3 TYD sing 377 n n 
C4 O4 TYD doub 378 n n 
C4 C5 TYD sing 379 n y 
C5 C5M TYD sing 380 n n 
C5 C6 TYD doub 381 n y 
C5M H51 TYD sing 382 n n 
C5M H52 TYD sing 383 n n 
C5M H53 TYD sing 384 n n 
C6 H6 TYD sing 385 n n 
#
_atom_sites.entry_id                     2V54 
_atom_sites.fract_transf_matrix[1][1]    0.017615 
_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]    0.017989 
_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]    0.006205 
_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 TYD A 1 1205 1205 TYD TYD . 
D 3 MG B 1 1205 1205 MG MG . 
E 4 POP B 1 1206 1206 POP POP . 
F 2 TYD B 1 1207 1207 TYD TYD . 
G 5 HOH A 1 2001 2001 HOH HOH . 
G 5 HOH A 2 2002 2002 HOH HOH . 
G 5 HOH A 3 2003 2003 HOH HOH . 
G 5 HOH A 4 2004 2004 HOH HOH . 
G 5 HOH A 5 2005 2005 HOH HOH . 
G 5 HOH A 6 2006 2006 HOH HOH . 
G 5 HOH A 7 2007 2007 HOH HOH . 
G 5 HOH A 8 2008 2008 HOH HOH . 
G 5 HOH A 9 2009 2009 HOH HOH . 
G 5 HOH A 10 2010 2010 HOH HOH . 
G 5 HOH A 11 2011 2011 HOH HOH . 
G 5 HOH A 12 2012 2012 HOH HOH . 
G 5 HOH A 13 2013 2013 HOH HOH . 
G 5 HOH A 14 2014 2014 HOH HOH . 
G 5 HOH A 15 2015 2015 HOH HOH . 
G 5 HOH A 16 2016 2016 HOH HOH . 
G 5 HOH A 17 2017 2017 HOH HOH . 
G 5 HOH A 18 2018 2018 HOH HOH . 
G 5 HOH A 19 2019 2019 HOH HOH . 
G 5 HOH A 20 2020 2020 HOH HOH . 
G 5 HOH A 21 2021 2021 HOH HOH . 
G 5 HOH A 22 2022 2022 HOH HOH . 
G 5 HOH A 23 2023 2023 HOH HOH . 
G 5 HOH A 24 2024 2024 HOH HOH . 
G 5 HOH A 25 2025 2025 HOH HOH . 
G 5 HOH A 26 2026 2026 HOH HOH . 
G 5 HOH A 27 2027 2027 HOH HOH . 
G 5 HOH A 28 2028 2028 HOH HOH . 
G 5 HOH A 29 2029 2029 HOH HOH . 
G 5 HOH A 30 2030 2030 HOH HOH . 
G 5 HOH A 31 2031 2031 HOH HOH . 
G 5 HOH A 32 2032 2032 HOH HOH . 
G 5 HOH A 33 2033 2033 HOH HOH . 
G 5 HOH A 34 2034 2034 HOH HOH . 
G 5 HOH A 35 2035 2035 HOH HOH . 
G 5 HOH A 36 2036 2036 HOH HOH . 
G 5 HOH A 37 2037 2037 HOH HOH . 
G 5 HOH A 38 2038 2038 HOH HOH . 
G 5 HOH A 39 2039 2039 HOH HOH . 
G 5 HOH A 40 2040 2040 HOH HOH . 
G 5 HOH A 41 2041 2041 HOH HOH . 
G 5 HOH A 42 2042 2042 HOH HOH . 
G 5 HOH A 43 2043 2043 HOH HOH . 
G 5 HOH A 44 2044 2044 HOH HOH . 
G 5 HOH A 45 2045 2045 HOH HOH . 
G 5 HOH A 46 2046 2046 HOH HOH . 
H 5 HOH B 1 2001 2001 HOH HOH . 
H 5 HOH B 2 2002 2002 HOH HOH . 
H 5 HOH B 3 2003 2003 HOH HOH . 
H 5 HOH B 4 2004 2004 HOH HOH . 
H 5 HOH B 5 2005 2005 HOH HOH . 
H 5 HOH B 6 2006 2006 HOH HOH . 
H 5 HOH B 7 2007 2007 HOH HOH . 
H 5 HOH B 8 2008 2008 HOH HOH . 
H 5 HOH B 9 2009 2009 HOH HOH . 
H 5 HOH B 10 2010 2010 HOH HOH . 
H 5 HOH B 11 2011 2011 HOH HOH . 
H 5 HOH B 12 2012 2012 HOH HOH . 
H 5 HOH B 13 2013 2013 HOH HOH . 
H 5 HOH B 14 2014 2014 HOH HOH . 
H 5 HOH B 15 2015 2015 HOH HOH . 
H 5 HOH B 16 2016 2016 HOH HOH . 
H 5 HOH B 17 2017 2017 HOH HOH . 
H 5 HOH B 18 2018 2018 HOH HOH . 
H 5 HOH B 19 2019 2019 HOH HOH . 
H 5 HOH B 20 2020 2020 HOH HOH . 
H 5 HOH B 21 2021 2021 HOH HOH . 
H 5 HOH B 22 2022 2022 HOH HOH . 
H 5 HOH B 23 2023 2023 HOH HOH . 
H 5 HOH B 24 2024 2024 HOH HOH . 
H 5 HOH B 25 2025 2025 HOH HOH . 
H 5 HOH B 26 2026 2026 HOH HOH . 
H 5 HOH B 27 2027 2027 HOH HOH . 
H 5 HOH B 28 2028 2028 HOH HOH . 
H 5 HOH B 29 2029 2029 HOH HOH . 
H 5 HOH B 30 2030 2030 HOH HOH . 
H 5 HOH B 31 2031 2031 HOH HOH . 
H 5 HOH B 32 2032 2032 HOH HOH . 
H 5 HOH B 33 2033 2033 HOH HOH . 
H 5 HOH B 34 2034 2034 HOH HOH . 
H 5 HOH B 35 2035 2035 HOH HOH . 
H 5 HOH B 36 2036 2036 HOH HOH . 
H 5 HOH B 37 2037 2037 HOH HOH . 
H 5 HOH B 38 2038 2038 HOH HOH . 
H 5 HOH B 39 2039 2039 HOH HOH . 
H 5 HOH B 40 2040 2040 HOH HOH . 
H 5 HOH B 41 2041 2041 HOH HOH . 
H 5 HOH B 42 2042 2042 HOH HOH . 
H 5 HOH B 43 2043 2043 HOH HOH . 
H 5 HOH B 44 2044 2044 HOH HOH . 
H 5 HOH B 45 2045 2045 HOH HOH . 
H 5 HOH B 46 2046 2046 HOH HOH . 
H 5 HOH B 47 2047 2047 HOH HOH . 
H 5 HOH B 48 2048 2048 HOH HOH . 
H 5 HOH B 49 2049 2049 HOH HOH . 
H 5 HOH B 50 2050 2050 HOH HOH . 
H 5 HOH B 51 2051 2051 HOH HOH . 
H 5 HOH B 52 2052 2052 HOH HOH . 
H 5 HOH B 53 2053 2053 HOH HOH . 
H 5 HOH B 54 2054 2054 HOH HOH . 
H 5 HOH B 55 2055 2055 HOH HOH . 
H 5 HOH B 56 2056 2056 HOH HOH . 
H 5 HOH B 57 2057 2057 HOH HOH . 
H 5 HOH B 58 2058 2058 HOH HOH . 
H 5 HOH B 59 2059 2059 HOH HOH . 
H 5 HOH B 60 2060 2060 HOH HOH . 
H 5 HOH B 61 2061 2061 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 P PA TYD . . . C 2 11.386 20.28 2.118 1 40.13 ? PA TYD 1205 A 1 
HETATM 2 O O1A TYD . . . C 2 12.333 19.782 1.096 1 41.39 ? O1A TYD 1205 A 1 
HETATM 3 O O2A TYD . . . C 2 10.409 19.329 2.692 1 39.84 ? O2A TYD 1205 A 1 
HETATM 4 O O3A TYD . . . C 2 12.266 20.918 3.305 1 45.39 ? O3A TYD 1205 A 1 
HETATM 5 P PB TYD . . . C 2 11.66 21.197 4.769 1 48.85 ? PB TYD 1205 A 1 
HETATM 6 O O1B TYD . . . C 2 12.31 20.371 5.812 1 51.85 ? O1B TYD 1205 A 1 
HETATM 7 O O2B TYD . . . C 2 11.843 22.777 5.019 1 49.91 ? O2B TYD 1205 A 1 
HETATM 8 O O3B TYD . . . C 2 10.072 20.955 4.682 1 50.42 ? O3B TYD 1205 A 1 
HETATM 9 O O5' TYD . . . C 2 10.608 21.571 1.552 1 38.22 ? O5' TYD 1205 A 1 
HETATM 10 C C5' TYD . . . C 2 11.34 22.774 1.305 1 34.53 ? C5' TYD 1205 A 1 
HETATM 11 C C4' TYD . . . C 2 10.412 23.968 1.073 1 31.74 ? C4' TYD 1205 A 1 
HETATM 12 O O4' TYD . . . C 2 9.641 23.732 -0.119 1 30.27 ? O4' TYD 1205 A 1 
HETATM 13 C C3' TYD . . . C 2 9.41 24.11 2.224 1 30.69 ? C3' TYD 1205 A 1 
HETATM 14 O O3' TYD . . . C 2 9.185 25.496 2.498 1 31.53 ? O3' TYD 1205 A 1 
HETATM 15 C C2' TYD . . . C 2 8.158 23.473 1.624 1 30.14 ? C2' TYD 1205 A 1 
HETATM 16 C C1' TYD . . . C 2 8.271 24.023 0.202 1 28.57 ? C1' TYD 1205 A 1 
HETATM 17 N N1 TYD . . . C 2 7.397 23.319 -0.765 1 26.48 ? N1 TYD 1205 A 1 
HETATM 18 C C2 TYD . . . C 2 6.47 24.016 -1.549 1 21.87 ? C2 TYD 1205 A 1 
HETATM 19 O O2 TYD . . . C 2 6.35 25.234 -1.438 1 21.82 ? O2 TYD 1205 A 1 
HETATM 20 N N3 TYD . . . C 2 5.705 23.326 -2.5 1 21.4 ? N3 TYD 1205 A 1 
HETATM 21 C C4 TYD . . . C 2 5.875 21.95 -2.671 1 22.04 ? C4 TYD 1205 A 1 
HETATM 22 O O4 TYD . . . C 2 5.234 21.353 -3.539 1 19.37 ? O4 TYD 1205 A 1 
HETATM 23 C C5 TYD . . . C 2 6.796 21.258 -1.89 1 23.55 ? C5 TYD 1205 A 1 
HETATM 24 C C5M TYD . . . C 2 6.979 19.748 -2.065 1 22.59 ? C5M TYD 1205 A 1 
HETATM 25 C C6 TYD . . . C 2 7.55 21.936 -0.944 1 25.33 ? C6 TYD 1205 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           375 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           25 
#