data_4XI9
#
_model_server_result.job_id            pR0w0i2yYJFuCLjBUWhQjw 
_model_server_result.datetime_utc      '2024-11-27 17:59:37' 
_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          4xi9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1200}' 
#
_entry.id    4XI9 
#
_exptl.entry_id    4XI9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              623.419 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' 
_entity.pdbx_number_of_molecules    4 
_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            4XI9 
_cell.length_a            273.91 
_cell.length_b            273.91 
_cell.length_c            142.93 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XI9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 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
? dimeric 2 software_defined_assembly 1 
? dimeric 2 software_defined_assembly 2 
? dimeric 2 software_defined_assembly 3 
? dimeric 2 software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,I 1 1 
B,F,J 2 1 
C,G,K 3 1 
D,H,L 4 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 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
#
_chem_comp.formula           'C17 H27 N3 O16 P2 S' 
_chem_comp.formula_weight    623.419 
_chem_comp.id                12V 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE' 
#
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
C1B N1 12V sing 1 n n 
C2 N1 12V sing 2 n n 
N1 C6 12V sing 3 n n 
O2 C2 12V doub 4 n n 
C2 N3 12V sing 5 n n 
N3 C4 12V sing 6 n n 
C4 O4 12V doub 7 n n 
C4 C5 12V sing 8 n n 
C6 C5 12V doub 9 n n 
C5 H5 12V sing 10 n n 
C6 H6 12V sing 11 n n 
O5B PA 12V sing 12 n n 
O1A PA 12V doub 13 n n 
PA O3A 12V sing 14 n n 
PA O2A 12V sing 15 n n 
O3A PB 12V sing 16 n n 
O1' PB 12V sing 17 n n 
PB O1B 12V doub 18 n n 
PB O2B 12V sing 19 n n 
S5' C1' 12V sing 20 n n 
C1' C2' 12V sing 21 n n 
C1' O1' 12V sing 22 n n 
C1' H1' 12V sing 23 n n 
C1B O4B 12V sing 24 n n 
C1B C2B 12V sing 25 n n 
C1B H1B 12V sing 26 n n 
C3' C2' 12V sing 27 n n 
C2' N2' 12V sing 28 n n 
C2' H2' 12V sing 29 n n 
N2' C7' 12V sing 30 n n 
N2' HN2' 12V sing 31 n n 
O2' C2B 12V sing 32 n n 
O2' HO2' 12V sing 33 n n 
O2A HO2A 12V sing 34 n n 
C3B C2B 12V sing 35 n n 
C2B H2B 12V sing 36 n n 
O2B HO2B 12V sing 37 n n 
C4' C3' 12V sing 38 n n 
C3' O3' 12V sing 39 n n 
C3' H3' 12V sing 40 n n 
O3' HO3' 12V sing 41 n n 
O3B C3B 12V sing 42 n n 
C3B C4B 12V sing 43 n n 
C3B H3B 12V sing 44 n n 
O3B HO3B 12V sing 45 n n 
C5' C4' 12V sing 46 n n 
O4' C4' 12V sing 47 n n 
C4' H4' 12V sing 48 n n 
O4' HO4' 12V sing 49 n n 
C4B O4B 12V sing 50 n n 
C4B C5B 12V sing 51 n n 
C4B H4B 12V sing 52 n n 
C6' C5' 12V sing 53 n n 
C5' S5' 12V sing 54 n n 
C5' H5' 12V sing 55 n n 
O5B C5B 12V sing 56 n n 
C5B H5B 12V sing 57 n n 
C5B H5BA 12V sing 58 n n 
O6' C6' 12V sing 59 n n 
C6' H6' 12V sing 60 n n 
C6' "H6'A" 12V sing 61 n n 
O6' HO6' 12V sing 62 n n 
O7' C7' 12V doub 63 n n 
C7' C8' 12V sing 64 n n 
C8' H8' 12V sing 65 n n 
C8' "H8'A" 12V sing 66 n n 
C8' "H8'B" 12V sing 67 n n 
N3 HN3 12V sing 68 n n 
#
_atom_sites.entry_id                     4XI9 
_atom_sites.fract_transf_matrix[1][1]    0.003651 
_atom_sites.fract_transf_matrix[1][2]    0.002108 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004216 
_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]    0.006996 
_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 3 12V A 1 1200 1200 12V 12V . 
J 3 12V B 1 1200 1200 12V 12V . 
K 3 12V C 1 1200 1200 12V 12V . 
L 3 12V D 1 1200 1200 12V 12V . 
#
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 12V . . . K 3 113.173 48.377 61.944 1 21.46 ? N1 12V 1200 C 1 
HETATM 2 C C2 12V . . . K 3 114.123 47.669 61.284 1 21.88 ? C2 12V 1200 C 1 
HETATM 3 O O2 12V . . . K 3 114.098 47.528 60.064 1 22.65 ? O2 12V 1200 C 1 
HETATM 4 N N3 12V . . . K 3 115.171 47.048 61.956 1 21.61 ? N3 12V 1200 C 1 
HETATM 5 C C4 12V . . . K 3 115.27 47.166 63.324 1 20.99 ? C4 12V 1200 C 1 
HETATM 6 O O4 12V . . . K 3 116.22 46.598 63.851 1 21.04 ? O4 12V 1200 C 1 
HETATM 7 C C5 12V . . . K 3 114.31 47.906 64.032 1 20.71 ? C5 12V 1200 C 1 
HETATM 8 C C6 12V . . . K 3 113.256 48.53 63.351 1 20.68 ? C6 12V 1200 C 1 
HETATM 9 P PA 12V . . . K 3 109.593 54.331 62.645 1 20.8 ? PA 12V 1200 C 1 
HETATM 10 P PB 12V . . . K 3 107.125 53.6 63.828 1 20.76 ? PB 12V 1200 C 1 
HETATM 11 C C1' 12V . . . K 3 106.079 55.251 61.815 0.5 19.98 ? C1' 12V 1200 C 1 
HETATM 12 O O1' 12V . . . K 3 106.034 54.011 62.648 1 20.47 ? O1' 12V 1200 C 1 
HETATM 13 O O1A 12V . . . K 3 109.048 55.216 61.586 1 20.19 ? O1A 12V 1200 C 1 
HETATM 14 C C1B 12V . . . K 3 112.131 49.042 61.111 1 22.3 ? C1B 12V 1200 C 1 
HETATM 15 O O1B 12V . . . K 3 106.732 52.276 64.396 1 20.59 ? O1B 12V 1200 C 1 
HETATM 16 C C2' 12V . . . K 3 104.901 56.207 62.079 0.5 19.62 ? C2' 12V 1200 C 1 
HETATM 17 N N2' 12V . . . K 3 105.046 56.578 63.484 0.5 19.3 ? N2' 12V 1200 C 1 
HETATM 18 O O2' 12V . . . K 3 110.192 47.747 60.962 1 23.85 ? O2' 12V 1200 C 1 
HETATM 19 O O2A 12V . . . K 3 110.242 54.909 63.86 1 19.48 ? O2A 12V 1200 C 1 
HETATM 20 C C2B 12V . . . K 3 110.699 48.935 61.492 1 22.98 ? C2B 12V 1200 C 1 
HETATM 21 O O2B 12V . . . K 3 107.27 54.79 64.712 1 19.63 ? O2B 12V 1200 C 1 
HETATM 22 C C3' 12V . . . K 3 103.539 55.549 61.722 0.5 18.8 ? C3' 12V 1200 C 1 
HETATM 23 O O3' 12V . . . K 3 102.395 56.295 62.2 0.5 19.2 ? O3' 12V 1200 C 1 
HETATM 24 O O3A 12V . . . K 3 108.436 53.269 62.964 1 19.78 ? O3A 12V 1200 C 1 
HETATM 25 C C3B 12V . . . K 3 110.158 50.103 60.677 1 23.47 ? C3B 12V 1200 C 1 
HETATM 26 O O3B 12V . . . K 3 110.275 49.835 59.269 1 24.72 ? O3B 12V 1200 C 1 
HETATM 27 C C4' 12V . . . K 3 103.403 55.437 60.228 0.5 17.25 ? C4' 12V 1200 C 1 
HETATM 28 O O4' 12V . . . K 3 102.147 54.86 59.998 0.5 15.26 ? O4' 12V 1200 C 1 
HETATM 29 C C4B 12V . . . K 3 111.155 51.197 61.003 1 23.52 ? C4B 12V 1200 C 1 
HETATM 30 O O4B 12V . . . K 3 112.4 50.49 61.214 1 23.5 ? O4B 12V 1200 C 1 
HETATM 31 C C5' 12V . . . K 3 104.459 54.51 59.658 0.5 17.46 ? C5' 12V 1200 C 1 
HETATM 32 S S5' 12V . . . K 3 106.128 54.966 60.064 0.5 18.96 ? S5' 12V 1200 C 1 
HETATM 33 C C5B 12V . . . K 3 110.752 51.947 62.287 1 23.94 ? C5B 12V 1200 C 1 
HETATM 34 O O5B 12V . . . K 3 110.681 53.347 61.99 1 22.58 ? O5B 12V 1200 C 1 
HETATM 35 C C6' 12V . . . K 3 104.407 54.565 58.129 0.5 16.82 ? C6' 12V 1200 C 1 
HETATM 36 O O6' 12V . . . K 3 104.737 55.883 57.676 0.5 15.75 ? O6' 12V 1200 C 1 
HETATM 37 C C7' 12V . . . K 3 105.559 57.76 63.788 0.5 19.43 ? C7' 12V 1200 C 1 
HETATM 38 O O7' 12V . . . K 3 105.828 58.589 62.926 0.5 19.93 ? O7' 12V 1200 C 1 
HETATM 39 C C8' 12V . . . K 3 105.742 58.047 65.285 0.5 19.18 ? C8' 12V 1200 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           39 
#