data_7BIX
#
_model_server_result.job_id            Lawmi_NL4NA3fV90NNDZeA 
_model_server_result.datetime_utc      '2024-10-12 01:25:53' 
_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          7bix 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Y","auth_seq_id":302}' 
#
_entry.id    7BIX 
#
_exptl.entry_id    7BIX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          3 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          121.39 
_cell.angle_gamma         90 
_cell.entry_id            7BIX 
_cell.length_a            197.47 
_cell.length_b            152.82 
_cell.length_c            125.11 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7BIX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 hexameric 6 author_and_software_defined_assembly 1 
PISA hexameric 6 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,B,C,D,E,F,M,N,O,P,Q,R,S,AA,BA,CA,DA,EA,FA 1 1 
G,H,I,J,K,L,T,U,V,W,X,Y,Z,GA,HA,IA,JA,KA,LA 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
? 3 N N N 
? 3 P N N 
? 3 R N N 
? 3 S N N 
? 3 U N N 
? 3 W N N 
? 3 Y N N 
? 3 Z 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 330 n n 
N1 C6 UDP sing 331 n n 
N1 C1' UDP sing 332 n n 
C2 N3 UDP sing 333 n n 
C2 O2 UDP doub 334 n n 
N3 C4 UDP sing 335 n n 
N3 HN3 UDP sing 336 n n 
C4 C5 UDP sing 337 n n 
C4 O4 UDP doub 338 n n 
C5 C6 UDP doub 339 n n 
C5 H5 UDP sing 340 n n 
C6 H6 UDP sing 341 n n 
C1' C2' UDP sing 342 n n 
C1' O4' UDP sing 343 n n 
C1' H1' UDP sing 344 n n 
C2' O2' UDP sing 345 n n 
C2' C3' UDP sing 346 n n 
C2' H2' UDP sing 347 n n 
O2' HO2' UDP sing 348 n n 
C3' C4' UDP sing 349 n n 
C3' O3' UDP sing 350 n n 
C3' H3' UDP sing 351 n n 
C4' O4' UDP sing 352 n n 
C4' C5' UDP sing 353 n n 
C4' H4' UDP sing 354 n n 
O3' HO3' UDP sing 355 n n 
C5' O5' UDP sing 356 n n 
C5' "H5'1" UDP sing 357 n n 
C5' "H5'2" UDP sing 358 n n 
O5' PA UDP sing 359 n n 
PA O1A UDP doub 360 n n 
PA O2A UDP sing 361 n n 
PA O3A UDP sing 362 n n 
O2A HOA2 UDP sing 363 n n 
O3A PB UDP sing 364 n n 
PB O1B UDP doub 365 n n 
PB O2B UDP sing 366 n n 
PB O3B UDP sing 367 n n 
O2B HOB2 UDP sing 368 n n 
O3B HOB3 UDP sing 369 n n 
#
_atom_sites.entry_id                     7BIX 
_atom_sites.fract_transf_matrix[1][1]    0.005064 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00309 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006544 
_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]    0.009363 
_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
M 2 UTP A 1 301 1 UTP UTP . 
N 3 UDP B 1 300 300 UDP UDP . 
O 2 UTP C 1 301 2 UTP UTP . 
P 3 UDP C 1 302 300 UDP UDP . 
Q 2 UTP D 1 301 5 UTP UTP . 
R 3 UDP D 1 302 263 UDP UDP . 
S 3 UDP E 1 301 263 UDP UDP . 
T 2 UTP G 1 301 4 UTP UTP . 
U 3 UDP H 1 301 263 UDP UDP . 
V 2 UTP I 1 301 3 UTP UTP . 
W 3 UDP I 1 302 263 UDP UDP . 
X 2 UTP J 1 301 6 UTP UTP . 
Y 3 UDP J 1 302 263 UDP UDP . 
Z 3 UDP K 1 301 263 UDP UDP . 
AA 4 HOH A 1 401 26 HOH HOH . 
AA 4 HOH A 2 402 22 HOH HOH . 
AA 4 HOH A 3 403 21 HOH HOH . 
BA 4 HOH B 1 401 25 HOH HOH . 
BA 4 HOH B 2 402 23 HOH HOH . 
CA 4 HOH C 1 401 31 HOH HOH . 
CA 4 HOH C 2 402 32 HOH HOH . 
CA 4 HOH C 3 403 7 HOH HOH . 
CA 4 HOH C 4 404 34 HOH HOH . 
DA 4 HOH D 1 401 15 HOH HOH . 
DA 4 HOH D 2 402 24 HOH HOH . 
DA 4 HOH D 3 403 38 HOH HOH . 
DA 4 HOH D 4 404 20 HOH HOH . 
DA 4 HOH D 5 405 37 HOH HOH . 
EA 4 HOH E 1 401 6 HOH HOH . 
EA 4 HOH E 2 402 33 HOH HOH . 
EA 4 HOH E 3 403 5 HOH HOH . 
EA 4 HOH E 4 404 36 HOH HOH . 
EA 4 HOH E 5 405 27 HOH HOH . 
FA 4 HOH F 1 301 17 HOH HOH . 
FA 4 HOH F 2 302 19 HOH HOH . 
FA 4 HOH F 3 303 18 HOH HOH . 
FA 4 HOH F 4 304 16 HOH HOH . 
FA 4 HOH F 5 305 28 HOH HOH . 
FA 4 HOH F 6 306 35 HOH HOH . 
GA 4 HOH G 1 401 44 HOH HOH . 
GA 4 HOH G 2 402 2 HOH HOH . 
GA 4 HOH G 3 403 1 HOH HOH . 
GA 4 HOH G 4 404 30 HOH HOH . 
GA 4 HOH G 5 405 3 HOH HOH . 
GA 4 HOH G 6 406 4 HOH HOH . 
HA 4 HOH H 1 401 29 HOH HOH . 
IA 4 HOH I 1 401 46 HOH HOH . 
IA 4 HOH I 2 402 8 HOH HOH . 
IA 4 HOH I 3 403 45 HOH HOH . 
IA 4 HOH I 4 404 39 HOH HOH . 
IA 4 HOH I 5 405 40 HOH HOH . 
JA 4 HOH J 1 401 4 HOH HOH . 
JA 4 HOH J 2 402 13 HOH HOH . 
JA 4 HOH J 3 403 9 HOH HOH . 
JA 4 HOH J 4 404 42 HOH HOH . 
JA 4 HOH J 5 405 43 HOH HOH . 
JA 4 HOH J 6 406 14 HOH HOH . 
JA 4 HOH J 7 407 41 HOH HOH . 
JA 4 HOH J 8 408 2 HOH HOH . 
KA 4 HOH K 1 401 47 HOH HOH . 
KA 4 HOH K 2 402 1 HOH HOH . 
KA 4 HOH K 3 403 3 HOH HOH . 
KA 4 HOH K 4 404 12 HOH HOH . 
LA 4 HOH L 1 301 8 HOH HOH . 
LA 4 HOH L 2 302 5 HOH HOH . 
LA 4 HOH L 3 303 7 HOH HOH . 
LA 4 HOH L 4 304 6 HOH HOH . 
LA 4 HOH L 5 305 10 HOH HOH . 
LA 4 HOH L 6 306 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 . . . Y 3 -13.663 6.883 28.939 1 57.74 ? N1 UDP 302 J 1 
HETATM 2 C C2 UDP . . . Y 3 -12.663 7.479 28.195 1 57.46 ? C2 UDP 302 J 1 
HETATM 3 N N3 UDP . . . Y 3 -11.978 8.481 28.839 1 47.59 ? N3 UDP 302 J 1 
HETATM 4 C C4 UDP . . . Y 3 -12.192 8.938 30.124 1 48.09 ? C4 UDP 302 J 1 
HETATM 5 C C5 UDP . . . Y 3 -13.244 8.271 30.829 1 52.87 ? C5 UDP 302 J 1 
HETATM 6 C C6 UDP . . . Y 3 -13.934 7.285 30.227 1 56.99 ? C6 UDP 302 J 1 
HETATM 7 O O2 UDP . . . Y 3 -12.397 7.143 27.05 1 66.61 ? O2 UDP 302 J 1 
HETATM 8 O O4 UDP . . . Y 3 -11.492 9.859 30.573 1 49.17 ? O4 UDP 302 J 1 
HETATM 9 C C1' UDP . . . Y 3 -14.433 5.802 28.301 1 52.7 ? C1' UDP 302 J 1 
HETATM 10 C C2' UDP . . . Y 3 -13.608 4.539 28.023 1 45.31 ? C2' UDP 302 J 1 
HETATM 11 O O2' UDP . . . Y 3 -14.001 3.971 26.779 1 38.75 ? O2' UDP 302 J 1 
HETATM 12 C C3' UDP . . . Y 3 -14.002 3.64 29.194 1 50.48 ? C3' UDP 302 J 1 
HETATM 13 C C4' UDP . . . Y 3 -15.462 4.009 29.394 1 49.09 ? C4' UDP 302 J 1 
HETATM 14 O O4' UDP . . . Y 3 -15.499 5.432 29.164 1 51.38 ? O4' UDP 302 J 1 
HETATM 15 O O3' UDP . . . Y 3 -13.859 2.26 28.879 1 62.26 ? O3' UDP 302 J 1 
HETATM 16 C C5' UDP . . . Y 3 -16.025 3.7 30.757 1 50.95 ? C5' UDP 302 J 1 
HETATM 17 O O5' UDP . . . Y 3 -15.053 4.08 31.752 1 56.14 ? O5' UDP 302 J 1 
HETATM 18 P PA UDP . . . Y 3 -14.314 2.995 32.631 1 63.61 ? PA UDP 302 J 1 
HETATM 19 O O1A UDP . . . Y 3 -13.403 2.255 31.726 1 72.81 -1 O1A UDP 302 J 1 
HETATM 20 O O2A UDP . . . Y 3 -13.689 3.625 33.875 1 60.1 ? O2A UDP 302 J 1 
HETATM 21 O O3A UDP . . . Y 3 -15.486 2.033 33.147 0.9 66.24 ? O3A UDP 302 J 1 
HETATM 22 P PB UDP . . . Y 3 -15.725 1.47 34.61 0.9 61.03 ? PB UDP 302 J 1 
HETATM 23 O O1B UDP . . . Y 3 -14.728 0.302 34.703 0.9 56.55 -1 O1B UDP 302 J 1 
HETATM 24 O O2B UDP . . . Y 3 -15.259 2.619 35.507 0.9 69.72 ? O2B UDP 302 J 1 
HETATM 25 O O3B UDP . . . Y 3 -17.148 1.073 34.831 0.9 57.88 ? O3B UDP 302 J 1 
#
_model_server_stats.io_time_ms              41 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#