data_5XHP
#
_model_server_result.job_id            G5aBkKAcDagwUmiiofVSKw 
_model_server_result.datetime_utc      '2024-11-30 18:47:36' 
_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          5xhp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":403}' 
#
_entry.id    5XHP 
#
_exptl.entry_id    5XHP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          4 
_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            5XHP 
_cell.length_a            50.116 
_cell.length_b            50.116 
_cell.length_c            201.704 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XHP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
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,D,E 1 1 
B,F,G,H 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
? 4 E N N 
? 4 H 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 A OD2 ASP 241 F ASP 241 1_555 D MN MN . F MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? 
metalc ? metalc2 A OD1 ASN 338 F ASN 338 1_555 D MN MN . F MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc3 D MN MN . F MN 402 1_555 E O1B UDP . F UDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc4 D MN MN . F MN 402 1_555 E O1A UDP . F UDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc5 B OD2 ASP 241 E ASP 241 1_555 G MN MN . E MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? 
metalc ? metalc6 B OD1 ASN 338 E ASN 338 1_555 G MN MN . E MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc7 G MN MN . E MN 402 1_555 H O2B UDP . E UDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc8 G MN MN . E MN 402 1_555 H O2A UDP . E UDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? 
#
_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 356 n n 
N1 C6 UDP sing 357 n n 
N1 C1' UDP sing 358 n n 
C2 N3 UDP sing 359 n n 
C2 O2 UDP doub 360 n n 
N3 C4 UDP sing 361 n n 
N3 HN3 UDP sing 362 n n 
C4 C5 UDP sing 363 n n 
C4 O4 UDP doub 364 n n 
C5 C6 UDP doub 365 n n 
C5 H5 UDP sing 366 n n 
C6 H6 UDP sing 367 n n 
C1' C2' UDP sing 368 n n 
C1' O4' UDP sing 369 n n 
C1' H1' UDP sing 370 n n 
C2' O2' UDP sing 371 n n 
C2' C3' UDP sing 372 n n 
C2' H2' UDP sing 373 n n 
O2' HO2' UDP sing 374 n n 
C3' C4' UDP sing 375 n n 
C3' O3' UDP sing 376 n n 
C3' H3' UDP sing 377 n n 
C4' O4' UDP sing 378 n n 
C4' C5' UDP sing 379 n n 
C4' H4' UDP sing 380 n n 
O3' HO3' UDP sing 381 n n 
C5' O5' UDP sing 382 n n 
C5' "H5'1" UDP sing 383 n n 
C5' "H5'2" UDP sing 384 n n 
O5' PA UDP sing 385 n n 
PA O1A UDP doub 386 n n 
PA O2A UDP sing 387 n n 
PA O3A UDP sing 388 n n 
O2A HOA2 UDP sing 389 n n 
O3A PB UDP sing 390 n n 
PB O1B UDP doub 391 n n 
PB O2B UDP sing 392 n n 
PB O3B UDP sing 393 n n 
O2B HOB2 UDP sing 394 n n 
O3B HOB3 UDP sing 395 n n 
#
_atom_sites.entry_id                     5XHP 
_atom_sites.fract_transf_matrix[1][1]    0.019954 
_atom_sites.fract_transf_matrix[1][2]    0.01152 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023041 
_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]    0.004958 
_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 ARG F 1 401 1 ARG ARG . 
D 3 MN F 1 402 1 MN MN . 
E 4 UDP F 1 403 2 UDP UDP . 
F 2 ARG E 1 401 1 ARG ARG . 
G 3 MN E 1 402 1 MN MN . 
H 4 UDP E 1 403 2 UDP UDP . 
#
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 . . . H 4 31.29 -10.888 -38.733 1 54.08 ? N1 UDP 403 E 1 
HETATM 2 C C2 UDP . . . H 4 32.62 -10.92 -38.238 1 51.87 ? C2 UDP 403 E 1 
HETATM 3 N N3 UDP . . . H 4 33.625 -10.498 -39.014 1 52.4 ? N3 UDP 403 E 1 
HETATM 4 C C4 UDP . . . H 4 33.376 -10.061 -40.256 1 55.54 ? C4 UDP 403 E 1 
HETATM 5 C C5 UDP . . . H 4 32.089 -10.016 -40.771 1 57.99 ? C5 UDP 403 E 1 
HETATM 6 C C6 UDP . . . H 4 31.036 -10.439 -39.972 1 58.35 ? C6 UDP 403 E 1 
HETATM 7 O O2 UDP . . . H 4 32.868 -11.329 -37.081 1 49.58 ? O2 UDP 403 E 1 
HETATM 8 O O4 UDP . . . H 4 34.305 -9.68 -40.971 1 54.17 ? O4 UDP 403 E 1 
HETATM 9 C C1' UDP . . . H 4 30.189 -11.35 -37.898 1 53.71 ? C1' UDP 403 E 1 
HETATM 10 C C2' UDP . . . H 4 29.858 -10.342 -36.832 1 55.04 ? C2' UDP 403 E 1 
HETATM 11 O O2' UDP . . . H 4 29.686 -11.028 -35.592 1 54.85 ? O2' UDP 403 E 1 
HETATM 12 C C3' UDP . . . H 4 28.537 -9.771 -37.267 1 59.23 ? C3' UDP 403 E 1 
HETATM 13 C C4' UDP . . . H 4 27.891 -10.938 -37.988 1 60.36 ? C4' UDP 403 E 1 
HETATM 14 O O4' UDP . . . H 4 28.996 -11.57 -38.647 1 56.77 ? O4' UDP 403 E 1 
HETATM 15 O O3' UDP . . . H 4 27.774 -9.322 -36.144 1 60.54 ? O3' UDP 403 E 1 
HETATM 16 C C5' UDP . . . H 4 26.782 -10.515 -38.947 1 61.6 ? C5' UDP 403 E 1 
HETATM 17 O O5' UDP . . . H 4 27.341 -10.083 -40.19 1 63.23 ? O5' UDP 403 E 1 
HETATM 18 P PA UDP . . . H 4 26.491 -9.146 -41.205 1 63.54 ? PA UDP 403 E 1 
HETATM 19 O O1A UDP . . . H 4 27.386 -8.004 -41.653 1 65.36 ? O1A UDP 403 E 1 
HETATM 20 O O2A UDP . . . H 4 25.178 -8.762 -40.534 1 60.48 ? O2A UDP 403 E 1 
HETATM 21 O O3A UDP . . . H 4 26.317 -10.124 -42.488 1 51.93 ? O3A UDP 403 E 1 
HETATM 22 P PB UDP . . . H 4 25.07 -11.11 -42.732 1 54.41 ? PB UDP 403 E 1 
HETATM 23 O O1B UDP . . . H 4 25.027 -11.025 -44.235 1 50.79 ? O1B UDP 403 E 1 
HETATM 24 O O2B UDP . . . H 4 23.882 -10.538 -42.005 1 52.56 ? O2B UDP 403 E 1 
HETATM 25 O O3B UDP . . . H 4 25.415 -12.469 -42.173 1 60.33 ? O3B UDP 403 E 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           35 
_model_server_stats.create_model_time_ms    74 
_model_server_stats.query_time_ms           1149 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           25 
#