data_6JBW
#
_model_server_result.job_id            J5R5EvB-n0_kroJPRMCikA 
_model_server_result.datetime_utc      '2024-12-02 19:49:08' 
_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          6jbw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":900}' 
#
_entry.id    6JBW 
#
_exptl.entry_id    6JBW 
_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         90 
_cell.entry_id            6JBW 
_cell.length_a            92.751 
_cell.length_b            99.295 
_cell.length_c            121.708 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6JBW 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    'P 2 2ab (z,x,y)' 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 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 D 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 358 n n 
N1 C6 UDP sing 359 n n 
N1 C1' UDP sing 360 n n 
C2 N3 UDP sing 361 n n 
C2 O2 UDP doub 362 n n 
N3 C4 UDP sing 363 n n 
N3 HN3 UDP sing 364 n n 
C4 C5 UDP sing 365 n n 
C4 O4 UDP doub 366 n n 
C5 C6 UDP doub 367 n n 
C5 H5 UDP sing 368 n n 
C6 H6 UDP sing 369 n n 
C1' C2' UDP sing 370 n n 
C1' O4' UDP sing 371 n n 
C1' H1' UDP sing 372 n n 
C2' O2' UDP sing 373 n n 
C2' C3' UDP sing 374 n n 
C2' H2' UDP sing 375 n n 
O2' HO2' UDP sing 376 n n 
C3' C4' UDP sing 377 n n 
C3' O3' UDP sing 378 n n 
C3' H3' UDP sing 379 n n 
C4' O4' UDP sing 380 n n 
C4' C5' UDP sing 381 n n 
C4' H4' UDP sing 382 n n 
O3' HO3' UDP sing 383 n n 
C5' O5' UDP sing 384 n n 
C5' "H5'1" UDP sing 385 n n 
C5' "H5'2" UDP sing 386 n n 
O5' PA UDP sing 387 n n 
PA O1A UDP doub 388 n n 
PA O2A UDP sing 389 n n 
PA O3A UDP sing 390 n n 
O2A HOA2 UDP sing 391 n n 
O3A PB UDP sing 392 n n 
PB O1B UDP doub 393 n n 
PB O2B UDP sing 394 n n 
PB O3B UDP sing 395 n n 
O2B HOB2 UDP sing 396 n n 
O3B HOB3 UDP sing 397 n n 
#
_atom_sites.entry_id                     6JBW 
_atom_sites.fract_transf_matrix[1][1]    0.010782 
_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]    0.010071 
_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]    0.008216 
_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 1 901 901 UDP UDP . 
D 2 UDP B 1 900 900 UDP UDP . 
E 3 HOH A 1 1001 24 HOH HOH . 
E 3 HOH A 2 1002 10 HOH HOH . 
E 3 HOH A 3 1003 26 HOH HOH . 
E 3 HOH A 4 1004 33 HOH HOH . 
E 3 HOH A 5 1005 18 HOH HOH . 
E 3 HOH A 6 1006 6 HOH HOH . 
E 3 HOH A 7 1007 20 HOH HOH . 
E 3 HOH A 8 1008 32 HOH HOH . 
E 3 HOH A 9 1009 9 HOH HOH . 
E 3 HOH A 10 1010 49 HOH HOH . 
E 3 HOH A 11 1011 12 HOH HOH . 
E 3 HOH A 12 1012 35 HOH HOH . 
E 3 HOH A 13 1013 21 HOH HOH . 
E 3 HOH A 14 1014 25 HOH HOH . 
E 3 HOH A 15 1015 39 HOH HOH . 
E 3 HOH A 16 1016 40 HOH HOH . 
E 3 HOH A 17 1017 16 HOH HOH . 
E 3 HOH A 18 1018 22 HOH HOH . 
F 3 HOH B 1 1001 31 HOH HOH . 
F 3 HOH B 2 1002 28 HOH HOH . 
F 3 HOH B 3 1003 15 HOH HOH . 
F 3 HOH B 4 1004 50 HOH HOH . 
F 3 HOH B 5 1005 13 HOH HOH . 
F 3 HOH B 6 1006 17 HOH HOH . 
F 3 HOH B 7 1007 14 HOH HOH . 
F 3 HOH B 8 1008 29 HOH HOH . 
F 3 HOH B 9 1009 47 HOH HOH . 
F 3 HOH B 10 1010 48 HOH HOH . 
F 3 HOH B 11 1011 34 HOH HOH . 
F 3 HOH B 12 1012 5 HOH HOH . 
F 3 HOH B 13 1013 37 HOH HOH . 
F 3 HOH B 14 1014 41 HOH HOH . 
F 3 HOH B 15 1015 2 HOH HOH . 
F 3 HOH B 16 1016 43 HOH HOH . 
F 3 HOH B 17 1017 45 HOH HOH . 
F 3 HOH B 18 1018 4 HOH HOH . 
F 3 HOH B 19 1019 36 HOH HOH . 
F 3 HOH B 20 1020 38 HOH HOH . 
F 3 HOH B 21 1021 30 HOH HOH . 
F 3 HOH B 22 1022 42 HOH HOH . 
F 3 HOH B 23 1023 3 HOH HOH . 
F 3 HOH B 24 1024 44 HOH HOH . 
F 3 HOH B 25 1025 7 HOH HOH . 
F 3 HOH B 26 1026 27 HOH HOH . 
F 3 HOH B 27 1027 19 HOH HOH . 
F 3 HOH B 28 1028 23 HOH HOH . 
F 3 HOH B 29 1029 8 HOH HOH . 
F 3 HOH B 30 1030 46 HOH HOH . 
F 3 HOH B 31 1031 1 HOH HOH . 
F 3 HOH B 32 1032 11 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 . . . D 2 1.211 32.509 -13.319 1 45.29 ? N1 UDP 900 B 1 
HETATM 2 C C2 UDP . . . D 2 0.891 33.198 -14.48 1 53.07 ? C2 UDP 900 B 1 
HETATM 3 N N3 UDP . . . D 2 1.172 34.551 -14.54 1 53.25 ? N3 UDP 900 B 1 
HETATM 4 C C4 UDP . . . D 2 1.76 35.197 -13.468 1 54.2 ? C4 UDP 900 B 1 
HETATM 5 C C5 UDP . . . D 2 2.066 34.472 -12.329 1 42.47 ? C5 UDP 900 B 1 
HETATM 6 C C6 UDP . . . D 2 1.488 33.222 -12.196 1 48.82 ? C6 UDP 900 B 1 
HETATM 7 O O2 UDP . . . D 2 0.356 32.622 -15.45 1 54.83 ? O2 UDP 900 B 1 
HETATM 8 O O4 UDP . . . D 2 2.034 36.4 -13.533 1 52.28 ? O4 UDP 900 B 1 
HETATM 9 C C1' UDP . . . D 2 0.903 31.062 -13.233 1 47.42 ? C1' UDP 900 B 1 
HETATM 10 C C2' UDP . . . D 2 1.645 30.266 -12.166 1 43.21 ? C2' UDP 900 B 1 
HETATM 11 O O2' UDP . . . D 2 2.974 29.938 -12.501 1 57.42 ? O2' UDP 900 B 1 
HETATM 12 C C3' UDP . . . D 2 0.801 29.006 -12.133 1 51.58 ? C3' UDP 900 B 1 
HETATM 13 C C4' UDP . . . D 2 -0.579 29.457 -12.603 1 52.03 ? C4' UDP 900 B 1 
HETATM 14 O O4' UDP . . . D 2 -0.458 30.819 -12.969 1 53.08 ? O4' UDP 900 B 1 
HETATM 15 O O3' UDP . . . D 2 1.316 28.06 -13.046 1 43.78 ? O3' UDP 900 B 1 
HETATM 16 C C5' UDP . . . D 2 -1.648 29.292 -11.533 1 44.35 ? C5' UDP 900 B 1 
HETATM 17 O O5' UDP . . . D 2 -2.187 27.997 -11.613 1 47.59 ? O5' UDP 900 B 1 
HETATM 18 P PA UDP . . . D 2 -2.878 27.323 -10.32 1 59.04 ? PA UDP 900 B 1 
HETATM 19 O O1A UDP . . . D 2 -3.283 25.928 -10.618 1 59.69 ? O1A UDP 900 B 1 
HETATM 20 O O2A UDP . . . D 2 -1.942 27.464 -9.162 1 42.9 ? O2A UDP 900 B 1 
HETATM 21 O O3A UDP . . . D 2 -4.232 28.166 -10.101 1 56.74 ? O3A UDP 900 B 1 
HETATM 22 P PB UDP . . . D 2 -5.311 28.455 -11.255 1 50.53 ? PB UDP 900 B 1 
HETATM 23 O O1B UDP . . . D 2 -5.177 27.524 -12.423 1 53.79 ? O1B UDP 900 B 1 
HETATM 24 O O2B UDP . . . D 2 -5.123 29.844 -11.695 1 41.63 ? O2B UDP 900 B 1 
HETATM 25 O O3B UDP . . . D 2 -6.654 28.307 -10.647 1 53.4 ? O3B UDP 900 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           25 
#