data_3UKP
#
_model_server_result.job_id            kF85KbuNaWOjNrTH8HV8CA 
_model_server_result.datetime_utc      '2024-11-14 23:58:57' 
_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":"J","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 . . . J 3 10.869 89.306 93.855 1 139.04 ? N1 GDU 602 A 1 
HETATM 2 C C2 GDU . . . J 3 12.122 88.99 93.485 1 121.73 ? C2 GDU 602 A 1 
HETATM 3 N N3 GDU . . . J 3 12.819 89.676 92.574 1 54.07 ? N3 GDU 602 A 1 
HETATM 4 C C4 GDU . . . J 3 12.269 90.749 91.985 1 107.4 ? C4 GDU 602 A 1 
HETATM 5 C C5 GDU . . . J 3 10.974 91.114 92.338 1 149.91 ? C5 GDU 602 A 1 
HETATM 6 C C6 GDU . . . J 3 10.277 90.37 93.285 1 135.66 ? C6 GDU 602 A 1 
HETATM 7 O O2 GDU . . . J 3 12.673 88.012 94.014 1 85.92 ? O2 GDU 602 A 1 
HETATM 8 O O4 GDU . . . J 3 12.963 91.477 91.05 1 93.85 ? O4 GDU 602 A 1 
HETATM 9 C C1D GDU . . . J 3 10.133 88.513 94.861 1 118.67 ? C1D GDU 602 A 1 
HETATM 10 C C2D GDU . . . J 3 10.035 89.159 96.181 1 114.28 ? C2D GDU 602 A 1 
HETATM 11 O O2D GDU . . . J 3 10.78 88.419 97.111 1 80.34 ? O2D GDU 602 A 1 
HETATM 12 C C3D GDU . . . J 3 8.639 89.173 96.528 1 98.61 ? C3D GDU 602 A 1 
HETATM 13 C C4D GDU . . . J 3 7.912 88.815 95.323 1 122.93 ? C4D GDU 602 A 1 
HETATM 14 O O4D GDU . . . J 3 8.839 88.202 94.44 1 102.25 ? O4D GDU 602 A 1 
HETATM 15 O O3D GDU . . . J 3 8.355 88.228 97.536 1 50.69 ? O3D GDU 602 A 1 
HETATM 16 C C5D GDU . . . J 3 7.344 90.048 94.699 1 134.8 ? C5D GDU 602 A 1 
HETATM 17 O O5D GDU . . . J 3 6.008 90.052 94.315 1 150.56 ? O5D GDU 602 A 1 
HETATM 18 P PA GDU . . . J 3 4.855 89.556 95.308 1 177.93 ? PA GDU 602 A 1 
HETATM 19 O O1A GDU . . . J 3 3.557 90.197 94.916 1 109.95 ? O1A GDU 602 A 1 
HETATM 20 O O2A GDU . . . J 3 4.731 88.038 95.229 1 77.63 ? O2A GDU 602 A 1 
HETATM 21 O O3A GDU . . . J 3 5.221 89.971 96.786 1 162.94 ? O3A GDU 602 A 1 
HETATM 22 P PB GDU . . . J 3 4.249 89.602 98.026 1 203.62 ? PB GDU 602 A 1 
HETATM 23 O O1B GDU . . . J 3 4.86 90.152 99.29 1 151.29 ? O1B GDU 602 A 1 
HETATM 24 O O2B GDU . . . J 3 4.185 88.067 98.161 1 30.16 ? O2B GDU 602 A 1 
HETATM 25 O O3B GDU . . . J 3 2.818 90.185 97.836 1 158.56 ? O3B GDU 602 A 1 
HETATM 26 C C1' GDU . . . J 3 2.534 91.502 98.199 1 108.26 ? C1' GDU 602 A 1 
HETATM 27 C C2' GDU . . . J 3 1.502 91.563 99.305 1 115.4 ? C2' GDU 602 A 1 
HETATM 28 C C3' GDU . . . J 3 0.095 91.753 98.884 1 107.39 ? C3' GDU 602 A 1 
HETATM 29 C C4' GDU . . . J 3 -0.046 92.708 97.854 1 109.12 ? C4' GDU 602 A 1 
HETATM 30 C C5' GDU . . . J 3 0.809 92.378 96.682 1 125.96 ? C5' GDU 602 A 1 
HETATM 31 C C6' GDU . . . J 3 0.617 93.322 95.557 1 96.16 ? C6' GDU 602 A 1 
HETATM 32 O O2' GDU . . . J 3 1.582 90.401 100.104 1 85.76 ? O2' GDU 602 A 1 
HETATM 33 O O3' GDU . . . J 3 -0.695 92.169 100.023 1 33.93 ? O3' GDU 602 A 1 
HETATM 34 O O4' GDU . . . J 3 0.302 94.016 98.395 1 60.27 ? O4' GDU 602 A 1 
HETATM 35 O O5' GDU . . . J 3 2.247 92.273 97.059 1 75.61 ? O5' GDU 602 A 1 
HETATM 36 O O6' GDU . . . J 3 -0.643 93.403 95.016 1 38.08 ? O6' GDU 602 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    66 
_model_server_stats.query_time_ms           474 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           36 
#