data_4XIF
#
_model_server_result.job_id            RjxRghENAFQN0O0m3cZtFg 
_model_server_result.datetime_utc      '2024-11-15 01:55:09' 
_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          4xif 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1102}' 
#
_entry.id    4XIF 
#
_exptl.entry_id    4XIF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              623.419 
_entity.id                          4 
_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            4XIF 
_cell.length_a            275.138 
_cell.length_b            275.138 
_cell.length_c            143.136 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XIF 
_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,J 1 1 
B,F,K,L 2 1 
C,G,M,N 3 1 
D,H,O,P 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
? 4 J N N 
? 4 L N N 
? 4 N N N 
? 4 O 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                     4XIF 
_atom_sites.fract_transf_matrix[1][1]    0.003635 
_atom_sites.fract_transf_matrix[1][2]    0.002098 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004197 
_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]    0.006986 
_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 SO4 A 1 1101 1 SO4 SO4 . 
J 4 12V A 1 1102 1200 12V 12V . 
K 3 SO4 B 1 1101 1 SO4 SO4 . 
L 4 12V B 1 1102 1200 12V 12V . 
M 3 SO4 C 1 1101 1 SO4 SO4 . 
N 4 12V C 1 1102 1200 12V 12V . 
O 4 12V D 1 1200 1200 12V 12V . 
P 3 SO4 H 1 2101 1 SO4 SO4 . 
#
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 . . . J 4 -0.493 215.117 29.872 1 43.56 ? N1 12V 1102 A 1 
HETATM 2 C C2 12V . . . J 4 0.209 215.178 28.736 1 44.06 ? C2 12V 1102 A 1 
HETATM 3 O O2 12V . . . J 4 0.935 214.252 28.416 1 46.32 ? O2 12V 1102 A 1 
HETATM 4 N N3 12V . . . J 4 0.14 216.262 27.899 1 44.22 ? N3 12V 1102 A 1 
HETATM 5 C C4 12V . . . J 4 -0.685 217.312 28.244 1 44.6 ? C4 12V 1102 A 1 
HETATM 6 O O4 12V . . . J 4 -0.726 218.279 27.485 1 46.19 ? O4 12V 1102 A 1 
HETATM 7 C C5 12V . . . J 4 -1.431 217.274 29.42 1 44.2 ? C5 12V 1102 A 1 
HETATM 8 C C6 12V . . . J 4 -1.35 216.17 30.254 1 44.19 ? C6 12V 1102 A 1 
HETATM 9 P PA 12V . . . J 4 -4.303 211.587 34.033 1 41.15 ? PA 12V 1102 A 1 
HETATM 10 P PB 12V . . . J 4 -3.633 212.336 36.74 1 40.24 ? PB 12V 1102 A 1 
HETATM 11 C C1' 12V . . . J 4 -3.619 209.708 37.129 1 42.84 ? C1' 12V 1102 A 1 
HETATM 12 O O1' 12V . . . J 4 -3.03 211.027 37.398 1 41.67 ? O1' 12V 1102 A 1 
HETATM 13 O O1A 12V . . . J 4 -4.679 210.198 34.244 1 41.65 ? O1A 12V 1102 A 1 
HETATM 14 C C1B 12V . . . J 4 -0.366 213.878 30.668 1 41.25 ? C1B 12V 1102 A 1 
HETATM 15 O O1B 12V . . . J 4 -2.796 213.465 37.193 1 39.71 ? O1B 12V 1102 A 1 
HETATM 16 C C2' 12V . . . J 4 -4.227 209.068 38.371 1 43.28 ? C2' 12V 1102 A 1 
HETATM 17 N N2' 12V . . . J 4 -5.279 209.959 38.823 1 45.41 ? N2' 12V 1102 A 1 
HETATM 18 O O2' 12V . . . J 4 1.436 214.609 32.033 1 41.22 ? O2' 12V 1102 A 1 
HETATM 19 O O2A 12V . . . J 4 -5.393 212.571 33.866 1 43.21 ? O2A 12V 1102 A 1 
HETATM 20 C C2B 12V . . . J 4 0.119 214.105 32.053 1 41.39 ? C2B 12V 1102 A 1 
HETATM 21 O O2B 12V . . . J 4 -5.101 212.317 36.984 1 38.83 ? O2B 12V 1102 A 1 
HETATM 22 C C3' 12V . . . J 4 -3.19 208.784 39.482 1 43.84 ? C3' 12V 1102 A 1 
HETATM 23 O O3' 12V . . . J 4 -3.836 208.252 40.632 1 42.12 ? O3' 12V 1102 A 1 
HETATM 24 O O3A 12V . . . J 4 -3.233 212.043 35.208 1 40.21 ? O3A 12V 1102 A 1 
HETATM 25 C C3B 12V . . . J 4 0.163 212.674 32.384 1 41.37 ? C3B 12V 1102 A 1 
HETATM 26 O O3B 12V . . . J 4 1.243 212.065 31.617 1 42.08 ? O3B 12V 1102 A 1 
HETATM 27 C C4' 12V . . . J 4 -2.179 207.734 39.008 1 45.53 ? C4' 12V 1102 A 1 
HETATM 28 O O4' 12V . . . J 4 -1.305 207.367 40.077 1 46.87 ? O4' 12V 1102 A 1 
HETATM 29 C C4B 12V . . . J 4 -1.224 212.223 31.882 1 40.5 ? C4B 12V 1102 A 1 
HETATM 30 O O4B 12V . . . J 4 -1.622 213.17 30.894 1 38.99 ? O4B 12V 1102 A 1 
HETATM 31 C C5' 12V . . . J 4 -1.355 208.241 37.825 1 45.46 ? C5' 12V 1102 A 1 
HETATM 32 S S5' 12V . . . J 4 -2.497 208.477 36.482 1 44.3 ? S5' 12V 1102 A 1 
HETATM 33 C C5B 12V . . . J 4 -2.167 212.357 33.05 1 39.33 ? C5B 12V 1102 A 1 
HETATM 34 O O5B 12V . . . J 4 -3.386 211.716 32.761 1 39.84 ? O5B 12V 1102 A 1 
HETATM 35 C C6' 12V . . . J 4 -0.282 207.202 37.414 1 46.58 ? C6' 12V 1102 A 1 
HETATM 36 O O6' 12V . . . J 4 -0.838 205.912 37.102 1 47.09 ? O6' 12V 1102 A 1 
HETATM 37 C C7' 12V . . . J 4 -6.537 209.669 38.535 1 47.9 ? C7' 12V 1102 A 1 
HETATM 38 O O7' 12V . . . J 4 -6.873 208.659 37.904 1 49 ? O7' 12V 1102 A 1 
HETATM 39 C C8' 12V . . . J 4 -7.555 210.677 39.09 1 48.95 ? C8' 12V 1102 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           39 
#