data_4CVK
#
_model_server_result.job_id            APArkE7cEBmgqEbPcr9YFQ 
_model_server_result.datetime_utc      '2024-11-26 02:14:33' 
_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          4cvk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1452}' 
#
_entry.id    4CVK 
#
_exptl.entry_id    4CVK 
_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            4CVK 
_cell.length_a            57.81 
_cell.length_b            87.29 
_cell.length_c            92.61 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4CVK 
_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               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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
covale ? covale1 C PB UDP . A UDP 1452 1_555 D O1 MUB . A MUB 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.618 ? 
covale ? covale2 D C10 MUB . A MUB 1453 1_555 B N ALA 1 B ALA 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale3 B C ALA 1 B ALA 1454 1_555 B N FGA 2 B FGA 1455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.365 ? 
covale ? covale4 B CD FGA 2 B FGA 1455 1_555 B N API 3 B API 1456 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? 
#
_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 441 n n 
N1 C6 UDP sing 442 n n 
N1 C1' UDP sing 443 n n 
C2 N3 UDP sing 444 n n 
C2 O2 UDP doub 445 n n 
N3 C4 UDP sing 446 n n 
N3 HN3 UDP sing 447 n n 
C4 C5 UDP sing 448 n n 
C4 O4 UDP doub 449 n n 
C5 C6 UDP doub 450 n n 
C5 H5 UDP sing 451 n n 
C6 H6 UDP sing 452 n n 
C1' C2' UDP sing 453 n n 
C1' O4' UDP sing 454 n n 
C1' H1' UDP sing 455 n n 
C2' O2' UDP sing 456 n n 
C2' C3' UDP sing 457 n n 
C2' H2' UDP sing 458 n n 
O2' HO2' UDP sing 459 n n 
C3' C4' UDP sing 460 n n 
C3' O3' UDP sing 461 n n 
C3' H3' UDP sing 462 n n 
C4' O4' UDP sing 463 n n 
C4' C5' UDP sing 464 n n 
C4' H4' UDP sing 465 n n 
O3' HO3' UDP sing 466 n n 
C5' O5' UDP sing 467 n n 
C5' "H5'1" UDP sing 468 n n 
C5' "H5'2" UDP sing 469 n n 
O5' PA UDP sing 470 n n 
PA O1A UDP doub 471 n n 
PA O2A UDP sing 472 n n 
PA O3A UDP sing 473 n n 
O2A HOA2 UDP sing 474 n n 
O3A PB UDP sing 475 n n 
PB O1B UDP doub 476 n n 
PB O2B UDP sing 477 n n 
PB O3B UDP sing 478 n n 
O2B HOB2 UDP sing 479 n n 
O3B HOB3 UDP sing 480 n n 
#
_atom_sites.entry_id                     4CVK 
_atom_sites.fract_transf_matrix[1][1]    0.017298 
_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]    0.011456 
_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]    0.010798 
_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 3 UDP A 1 1452 1452 UDP UDP . 
D 4 MUB A 1 1453 1453 MUB MUB . 
E 5 HOH A 1 2001 2001 HOH HOH . 
E 5 HOH A 2 2002 2002 HOH HOH . 
E 5 HOH A 3 2003 2003 HOH HOH . 
E 5 HOH A 4 2004 2004 HOH HOH . 
E 5 HOH A 5 2005 2005 HOH HOH . 
E 5 HOH A 6 2006 2006 HOH HOH . 
E 5 HOH A 7 2007 2007 HOH HOH . 
E 5 HOH A 8 2008 2008 HOH HOH . 
E 5 HOH A 9 2009 2009 HOH HOH . 
E 5 HOH A 10 2010 2010 HOH HOH . 
E 5 HOH A 11 2011 2011 HOH HOH . 
E 5 HOH A 12 2012 2012 HOH HOH . 
E 5 HOH A 13 2013 2013 HOH HOH . 
E 5 HOH A 14 2014 2014 HOH HOH . 
E 5 HOH A 15 2015 2015 HOH HOH . 
E 5 HOH A 16 2016 2016 HOH HOH . 
E 5 HOH A 17 2017 2017 HOH HOH . 
E 5 HOH A 18 2018 2018 HOH HOH . 
E 5 HOH A 19 2019 2019 HOH HOH . 
E 5 HOH A 20 2020 2020 HOH HOH . 
E 5 HOH A 21 2021 2021 HOH HOH . 
E 5 HOH A 22 2022 2022 HOH HOH . 
E 5 HOH A 23 2023 2023 HOH HOH . 
E 5 HOH A 24 2024 2024 HOH HOH . 
E 5 HOH A 25 2025 2025 HOH HOH . 
E 5 HOH A 26 2026 2026 HOH HOH . 
E 5 HOH A 27 2027 2027 HOH HOH . 
E 5 HOH A 28 2028 2028 HOH HOH . 
E 5 HOH A 29 2029 2029 HOH HOH . 
E 5 HOH A 30 2030 2030 HOH HOH . 
E 5 HOH A 31 2031 2031 HOH HOH . 
E 5 HOH A 32 2032 2032 HOH HOH . 
E 5 HOH A 33 2033 2033 HOH HOH . 
E 5 HOH A 34 2034 2034 HOH HOH . 
E 5 HOH A 35 2035 2035 HOH HOH . 
E 5 HOH A 36 2036 2036 HOH HOH . 
E 5 HOH A 37 2037 2037 HOH HOH . 
E 5 HOH A 38 2038 2038 HOH HOH . 
E 5 HOH A 39 2039 2039 HOH HOH . 
E 5 HOH A 40 2040 2040 HOH HOH . 
E 5 HOH A 41 2041 2041 HOH HOH . 
E 5 HOH A 42 2042 2042 HOH HOH . 
E 5 HOH A 43 2043 2043 HOH HOH . 
E 5 HOH A 44 2044 2044 HOH HOH . 
E 5 HOH A 45 2045 2045 HOH HOH . 
E 5 HOH A 46 2046 2046 HOH HOH . 
E 5 HOH A 47 2047 2047 HOH HOH . 
E 5 HOH A 48 2048 2048 HOH HOH . 
E 5 HOH A 49 2049 2049 HOH HOH . 
E 5 HOH A 50 2050 2050 HOH HOH . 
E 5 HOH A 51 2051 2051 HOH HOH . 
E 5 HOH A 52 2052 2052 HOH HOH . 
E 5 HOH A 53 2053 2053 HOH HOH . 
E 5 HOH A 54 2054 2054 HOH HOH . 
E 5 HOH A 55 2055 2055 HOH HOH . 
E 5 HOH A 56 2056 2056 HOH HOH . 
E 5 HOH A 57 2057 2057 HOH HOH . 
E 5 HOH A 58 2058 2058 HOH HOH . 
E 5 HOH A 59 2059 2059 HOH HOH . 
E 5 HOH A 60 2060 2060 HOH HOH . 
E 5 HOH A 61 2061 2061 HOH HOH . 
E 5 HOH A 62 2062 2062 HOH HOH . 
E 5 HOH A 63 2063 2063 HOH HOH . 
E 5 HOH A 64 2064 2064 HOH HOH . 
E 5 HOH A 65 2065 2065 HOH HOH . 
E 5 HOH A 66 2066 2066 HOH HOH . 
E 5 HOH A 67 2067 2067 HOH HOH . 
E 5 HOH A 68 2068 2068 HOH HOH . 
E 5 HOH A 69 2069 2069 HOH HOH . 
E 5 HOH A 70 2070 2070 HOH HOH . 
E 5 HOH A 71 2071 2071 HOH HOH . 
E 5 HOH A 72 2072 2072 HOH HOH . 
E 5 HOH A 73 2073 2073 HOH HOH . 
E 5 HOH A 74 2074 2074 HOH HOH . 
E 5 HOH A 75 2075 2075 HOH HOH . 
E 5 HOH A 76 2076 2076 HOH HOH . 
E 5 HOH A 77 2077 2077 HOH HOH . 
E 5 HOH A 78 2078 2078 HOH HOH . 
E 5 HOH A 79 2079 2079 HOH HOH . 
E 5 HOH A 80 2080 2080 HOH HOH . 
E 5 HOH A 81 2081 2081 HOH HOH . 
E 5 HOH A 82 2082 2082 HOH HOH . 
E 5 HOH A 83 2083 2083 HOH HOH . 
E 5 HOH A 84 2084 2084 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 10.747 -26.7 -36.105 1 19.06 ? N1 UDP 1452 A 1 
HETATM 2 C C2 UDP . . . C 3 9.749 -27.344 -36.73 1 18.82 ? C2 UDP 1452 A 1 
HETATM 3 N N3 UDP . . . C 3 10.043 -28.322 -37.677 1 19.89 ? N3 UDP 1452 A 1 
HETATM 4 C C4 UDP . . . C 3 11.361 -28.624 -38 1 20.46 ? C4 UDP 1452 A 1 
HETATM 5 C C5 UDP . . . C 3 12.419 -27.967 -37.363 1 19.73 ? C5 UDP 1452 A 1 
HETATM 6 C C6 UDP . . . C 3 12.11 -27.016 -36.4 1 19.93 ? C6 UDP 1452 A 1 
HETATM 7 O O2 UDP . . . C 3 8.566 -27.125 -36.473 1 18.67 ? O2 UDP 1452 A 1 
HETATM 8 O O4 UDP . . . C 3 11.564 -29.481 -38.856 1 19.91 ? O4 UDP 1452 A 1 
HETATM 9 C C1' UDP . . . C 3 10.445 -25.696 -35.072 1 20.05 ? C1' UDP 1452 A 1 
HETATM 10 C C2' UDP . . . C 3 10.965 -26.184 -33.741 1 19.62 ? C2' UDP 1452 A 1 
HETATM 11 O O2' UDP . . . C 3 10.071 -27.171 -33.239 1 20.33 ? O2' UDP 1452 A 1 
HETATM 12 C C3' UDP . . . C 3 11.002 -24.908 -32.944 1 19.45 ? C3' UDP 1452 A 1 
HETATM 13 C C4' UDP . . . C 3 11.252 -23.856 -34.034 1 19.5 ? C4' UDP 1452 A 1 
HETATM 14 O O4' UDP . . . C 3 11.168 -24.472 -35.307 1 20.5 ? O4' UDP 1452 A 1 
HETATM 15 O O3' UDP . . . C 3 9.755 -24.574 -32.361 1 20.13 ? O3' UDP 1452 A 1 
HETATM 16 C C5' UDP . . . C 3 12.603 -23.23 -33.856 1 20.58 ? C5' UDP 1452 A 1 
HETATM 17 O O5' UDP . . . C 3 13.607 -24.198 -33.957 1 20.51 ? O5' UDP 1452 A 1 
HETATM 18 P PA UDP . . . C 3 15.016 -23.941 -33.212 1 24.19 ? PA UDP 1452 A 1 
HETATM 19 O O1A UDP . . . C 3 15.797 -22.851 -34.094 1 21.65 ? O1A UDP 1452 A 1 
HETATM 20 O O2A UDP . . . C 3 14.872 -23.46 -31.8 1 23.52 ? O2A UDP 1452 A 1 
HETATM 21 O O3A UDP . . . C 3 15.873 -25.251 -33.377 1 21.88 ? O3A UDP 1452 A 1 
HETATM 22 P PB UDP . . . C 3 15.475 -26.737 -32.916 1 22.75 ? PB UDP 1452 A 1 
HETATM 23 O O1B UDP . . . C 3 14.343 -27.444 -33.771 1 22.11 ? O1B UDP 1452 A 1 
HETATM 24 O O3B UDP . . . C 3 16.65 -27.548 -32.975 1 21.7 ? O3B UDP 1452 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           267 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           24 
#