data_3UKP
#
_model_server_result.job_id            vbi5AEO6wStU9qoDix6RFQ 
_model_server_result.datetime_utc      '2024-11-15 00:10:45' 
_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          3ukp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":602}' 
#
_entry.id    3UKP 
#
_exptl.entry_id    3UKP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              566.302 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            "GALACTOSE-URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.01 
_cell.angle_gamma         90 
_cell.entry_id            3UKP 
_cell.length_a            129.6 
_cell.length_b            175.71 
_cell.length_c            135.347 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3UKP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 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,G,I,J,M,N,Q,R,U 1 1 
B,D,F,H,K,L,O,P,S,T,V 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 J N N 
? 3 L N N 
? 3 N N N 
? 3 P N N 
? 3 R N N 
? 3 T N N 
#
_chem_comp.formula           'C15 H24 N2 O17 P2' 
_chem_comp.formula_weight    566.302 
_chem_comp.id                GDU 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "GALACTOSE-URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     UDP-D-GALACTOPYRANOSE 
#
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 GDU sing 174 n n 
N1 C6 GDU sing 175 n n 
N1 C1D GDU sing 176 n n 
C2 N3 GDU sing 177 n n 
C2 O2 GDU doub 178 n n 
N3 C4 GDU sing 179 n n 
N3 HN3 GDU sing 180 n n 
C4 C5 GDU sing 181 n n 
C4 O4 GDU doub 182 n n 
C5 C6 GDU doub 183 n n 
C5 H5 GDU sing 184 n n 
C6 H6 GDU sing 185 n n 
C1D C2D GDU sing 186 n n 
C1D O4D GDU sing 187 n n 
C1D H1D GDU sing 188 n n 
C2D O2D GDU sing 189 n n 
C2D C3D GDU sing 190 n n 
C2D H2D GDU sing 191 n n 
O2D HO2' GDU sing 192 n n 
C3D C4D GDU sing 193 n n 
C3D O3D GDU sing 194 n n 
C3D H3D GDU sing 195 n n 
C4D O4D GDU sing 196 n n 
C4D C5D GDU sing 197 n n 
C4D H4D GDU sing 198 n n 
O3D HO3' GDU sing 199 n n 
C5D O5D GDU sing 200 n n 
C5D "H5'1" GDU sing 201 n n 
C5D "H5'2" GDU sing 202 n n 
O5D PA GDU sing 203 n n 
PA O1A GDU doub 204 n n 
PA O2A GDU sing 205 n n 
PA O3A GDU sing 206 n n 
O2A HOA2 GDU sing 207 n n 
O3A PB GDU sing 208 n n 
PB O1B GDU doub 209 n n 
PB O2B GDU sing 210 n n 
PB O3B GDU sing 211 n n 
O2B HOB2 GDU sing 212 n n 
O3B C1' GDU sing 213 n n 
C1' C2' GDU sing 214 n n 
C1' O5' GDU sing 215 n n 
C1' H1' GDU sing 216 n n 
C2' C3' GDU sing 217 n n 
C2' O2' GDU sing 218 n n 
C2' H2' GDU sing 219 n n 
C3' C4' GDU sing 220 n n 
C3' O3' GDU sing 221 n n 
C3' H3' GDU sing 222 n n 
C4' C5' GDU sing 223 n n 
C4' O4' GDU sing 224 n n 
C4' H4' GDU sing 225 n n 
C5' C6' GDU sing 226 n n 
C5' O5' GDU sing 227 n n 
C5' H5' GDU sing 228 n n 
C6' O6' GDU sing 229 n n 
C6' "H6'1" GDU sing 230 n n 
C6' "H6'2" GDU sing 231 n n 
O2' HO2A GDU sing 232 n n 
O3' HO3A GDU sing 233 n n 
O4' HO4' GDU sing 234 n n 
O6' HO6' GDU sing 235 n n 
#
_atom_sites.entry_id                     3UKP 
_atom_sites.fract_transf_matrix[1][1]    0.007716 
_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]    0.005691 
_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]    0.007388 
_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
I 2 FAD A 1 601 601 FAD FAD . 
J 3 GDU A 1 602 802 GDU GDU . 
K 2 FAD B 1 601 607 FAD FAD . 
L 3 GDU B 1 602 802 GDU GDU . 
M 2 FAD C 1 601 601 FAD FAD . 
N 3 GDU C 1 602 802 GDU GDU . 
O 2 FAD D 1 601 602 FAD FAD . 
P 3 GDU D 1 602 802 GDU GDU . 
Q 2 FAD E 1 601 606 FAD FAD . 
R 3 GDU E 1 602 802 GDU GDU . 
S 2 FAD F 1 601 605 FAD FAD . 
T 3 GDU F 1 602 802 GDU GDU . 
U 2 FAD G 1 601 604 FAD FAD . 
V 2 FAD H 1 601 603 FAD FAD . 
#
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 GDU . . . R 3 16.7 53.211 70.608 0.92 84.24 ? N1 GDU 602 E 1 
HETATM 2 C C2 GDU . . . R 3 17.675 53.853 71.263 0.92 98.64 ? C2 GDU 602 E 1 
HETATM 3 N N3 GDU . . . R 3 18.497 53.246 72.117 0.92 76.28 ? N3 GDU 602 E 1 
HETATM 4 C C4 GDU . . . R 3 18.361 51.932 72.352 0.92 77.43 ? C4 GDU 602 E 1 
HETATM 5 C C5 GDU . . . R 3 17.356 51.224 71.689 0.92 87.05 ? C5 GDU 602 E 1 
HETATM 6 C C6 GDU . . . R 3 16.518 51.895 70.808 0.92 38.56 ? C6 GDU 602 E 1 
HETATM 7 O O2 GDU . . . R 3 17.831 55.071 71.06 0.92 54.11 ? O2 GDU 602 E 1 
HETATM 8 O O4 GDU . . . R 3 19.207 51.3 73.232 0.92 100.35 ? O4 GDU 602 E 1 
HETATM 9 C C1D GDU . . . R 3 15.825 53.931 69.677 0.92 92.02 ? C1D GDU 602 E 1 
HETATM 10 C C2D GDU . . . R 3 15.86 53.375 68.32 0.92 99.81 ? C2D GDU 602 E 1 
HETATM 11 O O2D GDU . . . R 3 16.857 54.022 67.573 0.92 32.23 ? O2D GDU 602 E 1 
HETATM 12 C C3D GDU . . . R 3 14.549 53.654 67.82 0.92 104.11 ? C3D GDU 602 E 1 
HETATM 13 C C4D GDU . . . R 3 13.696 53.516 68.991 0.92 63.56 ? C4D GDU 602 E 1 
HETATM 14 O O4D GDU . . . R 3 14.493 53.915 70.095 0.92 79.28 ? O4D GDU 602 E 1 
HETATM 15 O O3D GDU . . . R 3 14.499 54.985 67.354 0.92 43.84 ? O3D GDU 602 E 1 
HETATM 16 C C5D GDU . . . R 3 13.261 52.097 69.186 0.92 83.9 ? C5D GDU 602 E 1 
HETATM 17 O O5D GDU . . . R 3 13.229 51.261 68.076 0.92 110.74 ? O5D GDU 602 E 1 
HETATM 18 P PA GDU . . . R 3 11.853 50.92 67.329 0.92 139.11 ? PA GDU 602 E 1 
HETATM 19 O O1A GDU . . . R 3 10.762 51.773 67.897 0.92 101.78 ? O1A GDU 602 E 1 
HETATM 20 O O2A GDU . . . R 3 12.019 51.222 65.843 0.92 65.99 ? O2A GDU 602 E 1 
HETATM 21 O O3A GDU . . . R 3 11.489 49.391 67.519 0.92 120.9 ? O3A GDU 602 E 1 
HETATM 22 P PB GDU . . . R 3 10.105 48.762 66.952 0.92 142.92 ? PB GDU 602 E 1 
HETATM 23 O O1B GDU . . . R 3 10.122 47.268 67.163 0.92 56.69 ? O1B GDU 602 E 1 
HETATM 24 O O2B GDU . . . R 3 9.995 49.035 65.438 0.92 116.66 ? O2B GDU 602 E 1 
HETATM 25 O O3B GDU . . . R 3 8.879 49.389 67.672 0.92 141.78 ? O3B GDU 602 E 1 
HETATM 26 C C1' GDU . . . R 3 7.754 48.64 68.011 0.92 110.48 ? C1' GDU 602 E 1 
HETATM 27 C C2' GDU . . . R 3 7.033 49.311 69.135 0.92 103.36 ? C2' GDU 602 E 1 
HETATM 28 C C3' GDU . . . R 3 7.96 49.587 70.255 0.92 122.3 ? C3' GDU 602 E 1 
HETATM 29 C C4' GDU . . . R 3 8.873 48.522 70.542 0.92 98.87 ? C4' GDU 602 E 1 
HETATM 30 C C5' GDU . . . R 3 8.776 47.245 69.738 0.92 122.24 ? C5' GDU 602 E 1 
HETATM 31 C C6' GDU . . . R 3 8.182 46.105 70.48 0.92 101.44 ? C6' GDU 602 E 1 
HETATM 32 O O2' GDU . . . R 3 6.419 50.494 68.667 0.92 45.65 ? O2' GDU 602 E 1 
HETATM 33 O O3' GDU . . . R 3 7.216 49.938 71.45 0.92 53.59 ? O3' GDU 602 E 1 
HETATM 34 O O4' GDU . . . R 3 8.84 48.24 71.972 0.92 22.28 ? O4' GDU 602 E 1 
HETATM 35 O O5' GDU . . . R 3 8.102 47.349 68.403 0.92 104.19 ? O5' GDU 602 E 1 
HETATM 36 O O6' GDU . . . R 3 8.201 44.879 69.849 0.92 45.74 ? O6' GDU 602 E 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    167 
_model_server_stats.query_time_ms           456 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           36 
#