data_7BL7
#
_model_server_result.job_id            0qnLb4zjv8_RxNScD2LD-w 
_model_server_result.datetime_utc      '2024-10-12 01:22:56' 
_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          7bl7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":302}' 
#
_entry.id    7BL7 
#
_exptl.entry_id    7BL7 
_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    8 
_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            7BL7 
_cell.length_a            151.23 
_cell.length_b            165.75 
_cell.length_c            125.02 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7BL7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    'P 2 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
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,T,CA,DA,EA,FA,GA,HA 1 1 
G,H,I,J,K,L,U,V,W,X,Y,Z,AA,BA,IA,JA,KA,LA,MA 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 M N N 
? 2 P N N 
? 2 R N N 
? 2 T N N 
? 2 V N N 
? 2 X N N 
? 2 Y N N 
? 2 BA 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                     7BL7 
_atom_sites.fract_transf_matrix[1][1]    0.006612 
_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]    0.006033 
_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]    0.007999 
_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 UDP B 1 301 5 UDP UDP . 
N 3 UTP A 1 301 4 UTP UTP . 
O 3 UTP F 1 301 1 UTP UTP . 
P 2 UDP E 1 301 6 UDP UDP . 
Q 3 UTP D 1 301 2 UTP UTP . 
R 2 UDP D 1 302 2 UDP UDP . 
S 3 UTP C 1 301 3 UTP UTP . 
T 2 UDP C 1 302 1 UDP UDP . 
U 3 UTP I 1 301 2 UTP UTP . 
V 2 UDP I 1 302 4 UDP UDP . 
W 3 UTP J 1 301 3 UTP UTP . 
X 2 UDP J 1 302 3 UDP UDP . 
Y 2 UDP K 1 301 8 UDP UDP . 
Z 3 UTP L 1 301 4 UTP UTP . 
AA 3 UTP G 1 301 1 UTP UTP . 
BA 2 UDP H 1 301 7 UDP UDP . 
CA 4 HOH B 1 401 19 HOH HOH . 
CA 4 HOH B 2 402 1 HOH HOH . 
CA 4 HOH B 3 403 32 HOH HOH . 
CA 4 HOH B 4 404 18 HOH HOH . 
CA 4 HOH B 5 405 24 HOH HOH . 
CA 4 HOH B 6 406 9 HOH HOH . 
CA 4 HOH B 7 407 10 HOH HOH . 
DA 4 HOH A 1 401 22 HOH HOH . 
EA 4 HOH F 1 401 31 HOH HOH . 
FA 4 HOH E 1 401 8 HOH HOH . 
FA 4 HOH E 2 402 21 HOH HOH . 
FA 4 HOH E 3 403 20 HOH HOH . 
FA 4 HOH E 4 404 2 HOH HOH . 
FA 4 HOH E 5 405 36 HOH HOH . 
FA 4 HOH E 6 406 34 HOH HOH . 
GA 4 HOH D 1 401 7 HOH HOH . 
GA 4 HOH D 2 402 41 HOH HOH . 
GA 4 HOH D 3 403 35 HOH HOH . 
GA 4 HOH D 4 404 40 HOH HOH . 
GA 4 HOH D 5 405 30 HOH HOH . 
GA 4 HOH D 6 406 42 HOH HOH . 
HA 4 HOH C 1 401 43 HOH HOH . 
HA 4 HOH C 2 402 6 HOH HOH . 
HA 4 HOH C 3 403 39 HOH HOH . 
HA 4 HOH C 4 404 38 HOH HOH . 
IA 4 HOH I 1 401 33 HOH HOH . 
IA 4 HOH I 2 402 4 HOH HOH . 
IA 4 HOH I 3 403 11 HOH HOH . 
JA 4 HOH J 1 401 16 HOH HOH . 
JA 4 HOH J 2 402 15 HOH HOH . 
JA 4 HOH J 3 403 17 HOH HOH . 
KA 4 HOH L 1 401 37 HOH HOH . 
LA 4 HOH G 1 401 29 HOH HOH . 
LA 4 HOH G 2 402 28 HOH HOH . 
LA 4 HOH G 3 403 27 HOH HOH . 
LA 4 HOH G 4 404 5 HOH HOH . 
MA 4 HOH H 1 401 3 HOH HOH . 
MA 4 HOH H 2 402 23 HOH HOH . 
MA 4 HOH H 3 403 14 HOH HOH . 
MA 4 HOH H 4 404 13 HOH HOH . 
MA 4 HOH H 5 405 12 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 . . . V 2 22.316 -17.925 -14.045 1 38.48 ? N1 UDP 302 I 1 
HETATM 2 C C2 UDP . . . V 2 23.486 -18.168 -14.707 1 46.49 ? C2 UDP 302 I 1 
HETATM 3 N N3 UDP . . . V 2 24.485 -18.708 -13.946 1 37.55 ? N3 UDP 302 I 1 
HETATM 4 C C4 UDP . . . V 2 24.416 -19.049 -12.635 1 32.47 ? C4 UDP 302 I 1 
HETATM 5 C C5 UDP . . . V 2 23.163 -18.796 -12.022 1 41.89 ? C5 UDP 302 I 1 
HETATM 6 C C6 UDP . . . V 2 22.175 -18.238 -12.734 1 40.4 ? C6 UDP 302 I 1 
HETATM 7 O O2 UDP . . . V 2 23.622 -17.944 -15.887 1 66.12 ? O2 UDP 302 I 1 
HETATM 8 O O4 UDP . . . V 2 25.401 -19.532 -12.08 1 23.19 ? O4 UDP 302 I 1 
HETATM 9 C C1' UDP . . . V 2 21.272 -17.234 -14.814 1 35.55 ? C1' UDP 302 I 1 
HETATM 10 C C2' UDP . . . V 2 20.519 -18.129 -15.787 1 42.06 ? C2' UDP 302 I 1 
HETATM 11 O O2' UDP . . . V 2 19.803 -17.416 -16.776 1 43.97 ? O2' UDP 302 I 1 
HETATM 12 C C3' UDP . . . V 2 19.465 -18.686 -14.866 1 33.39 ? C3' UDP 302 I 1 
HETATM 13 C C4' UDP . . . V 2 19.08 -17.466 -14.082 1 23.19 ? C4' UDP 302 I 1 
HETATM 14 O O4' UDP . . . V 2 20.308 -16.742 -13.911 1 23.19 ? O4' UDP 302 I 1 
HETATM 15 O O3' UDP . . . V 2 18.287 -19.152 -15.489 1 40.1 ? O3' UDP 302 I 1 
HETATM 16 C C5' UDP . . . V 2 18.492 -17.817 -12.753 1 26.24 ? C5' UDP 302 I 1 
HETATM 17 O O5' UDP . . . V 2 17.582 -18.856 -13.06 1 36.28 ? O5' UDP 302 I 1 
HETATM 18 P PA UDP . . . V 2 17.66 -20.188 -12.607 1 33.14 ? PA UDP 302 I 1 
HETATM 19 O O1A UDP . . . V 2 17.522 -21.109 -13.668 1 32.36 ? O1A UDP 302 I 1 
HETATM 20 O O2A UDP . . . V 2 18.737 -20.429 -11.69 1 34.12 ? O2A UDP 302 I 1 
HETATM 21 O O3A UDP . . . V 2 16.349 -20.05 -11.741 1 42.16 ? O3A UDP 302 I 1 
HETATM 22 P PB UDP . . . V 2 15.119 -20.927 -11.296 1 33.08 ? PB UDP 302 I 1 
HETATM 23 O O1B UDP . . . V 2 14.609 -21.663 -12.288 1 52.95 ? O1B UDP 302 I 1 
HETATM 24 O O2B UDP . . . V 2 15.622 -21.759 -10.271 1 45.04 ? O2B UDP 302 I 1 
HETATM 25 O O3B UDP . . . V 2 14.191 -19.993 -10.758 1 27.86 ? O3B UDP 302 I 1 
HETATM 26 H HN3 UDP . . . V 2 25.366 -18.865 -14.425 1 45.05 ? HN3 UDP 302 I 1 
HETATM 27 H H5 UDP . . . V 2 23.043 -19.067 -10.974 1 50.27 ? H5 UDP 302 I 1 
HETATM 28 H H6 UDP . . . V 2 21.233 -17.996 -12.261 1 48.48 ? H6 UDP 302 I 1 
HETATM 29 H H1' UDP . . . V 2 21.682 -16.357 -15.312 1 42.66 ? H1' UDP 302 I 1 
HETATM 30 H H2' UDP . . . V 2 21.117 -18.912 -16.251 1 50.47 ? H2' UDP 302 I 1 
HETATM 31 H HO2' UDP . . . V 2 20.152 -17.706 -17.659 1 52.77 ? HO2' UDP 302 I 1 
HETATM 32 H H3' UDP . . . V 2 19.862 -19.47 -14.223 1 40.07 ? H3' UDP 302 I 1 
HETATM 33 H H4' UDP . . . V 2 18.435 -16.793 -14.645 1 27.83 ? H4' UDP 302 I 1 
HETATM 34 H HO3' UDP . . . V 2 18.522 -19.991 -15.967 1 48.12 ? HO3' UDP 302 I 1 
HETATM 35 H "H5'1" UDP . . . V 2 19.258 -18.135 -12.048 1 31.49 ? "H5'1" UDP 302 I 1 
HETATM 36 H "H5'2" UDP . . . V 2 17.929 -17.009 -12.288 1 31.49 ? "H5'2" UDP 302 I 1 
HETATM 37 H HOA2 UDP . . . V 2 19.592 -20.895 -11.887 1 40.94 ? HOA2 UDP 302 I 1 
HETATM 38 H HOB2 UDP . . . V 2 16.582 -21.977 -10.145 1 54.05 ? HOB2 UDP 302 I 1 
HETATM 39 H HOB3 UDP . . . V 2 14.401 -19.06 -10.491 1 33.43 ? HOB3 UDP 302 I 1 
#
_model_server_stats.io_time_ms              59 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           39 
#