data_3VBK
#
_model_server_result.job_id            GnaO4hDBQbflFmH0Ttf98Q 
_model_server_result.datetime_utc      '2024-10-11 23:22:50' 
_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          3vbk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":1500}' 
#
_entry.id    3VBK 
#
_exptl.entry_id    3VBK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              547.345 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            dTDP-4-amino-4,6-dideoxyglucose 
_entity.pdbx_number_of_molecules    3 
_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            3VBK 
_cell.length_a            71.254 
_cell.length_b            71.254 
_cell.length_c            138.382 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VBK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 E N N 
? 3 I N N 
? 3 L N N 
#
_chem_comp.formula           'C16 H27 N3 O14 P2' 
_chem_comp.formula_weight    547.345 
_chem_comp.id                0FX 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              dTDP-4-amino-4,6-dideoxyglucose 
_chem_comp.type              non-polymer 
_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
O3G C3G 0FX sing 1 n n 
N4A C4G 0FX sing 2 n n 
C3G C4G 0FX sing 3 n n 
C3G C2G 0FX sing 4 n n 
C4G C5G 0FX sing 5 n n 
O2G C2G 0FX sing 6 n n 
O41 C41 0FX doub 7 n n 
C2G C1G 0FX sing 8 n n 
C5G C6G 0FX sing 9 n n 
C5G O5G 0FX sing 10 n n 
C41 N31 0FX sing 11 n n 
C41 C51 0FX sing 12 n n 
O1G C1G 0FX sing 13 n n 
O1G P2 0FX sing 14 n n 
N31 C21 0FX sing 15 n n 
C1G O5G 0FX sing 16 n n 
O3P P2 0FX doub 17 n n 
C5A C51 0FX sing 18 n n 
C51 C61 0FX doub 19 n n 
C21 O21 0FX doub 20 n n 
C21 N11 0FX sing 21 n n 
O2P P 0FX doub 22 n n 
P2 O4P 0FX sing 23 n n 
P2 OPP 0FX sing 24 n n 
O3 C3 0FX sing 25 n n 
C61 N11 0FX sing 26 n n 
N11 C1 0FX sing 27 n n 
C3 C2 0FX sing 28 n n 
C3 C4 0FX sing 29 n n 
C2 C1 0FX sing 30 n n 
O5 P 0FX sing 31 n n 
O5 C5 0FX sing 32 n n 
P OPP 0FX sing 33 n n 
P O1P 0FX sing 34 n n 
C1 O4 0FX sing 35 n n 
C4 C5 0FX sing 36 n n 
C4 O4 0FX sing 37 n n 
O4P H1 0FX sing 38 n n 
C1G H2 0FX sing 39 n n 
C2G H3 0FX sing 40 n n 
O2G H4 0FX sing 41 n n 
C3G H5 0FX sing 42 n n 
O3G H6 0FX sing 43 n n 
C4G H7 0FX sing 44 n n 
N4A H8 0FX sing 45 n n 
N4A H9 0FX sing 46 n n 
C5G H11 0FX sing 47 n n 
C6G H12 0FX sing 48 n n 
C6G H13 0FX sing 49 n n 
C6G H14 0FX sing 50 n n 
O1P H15 0FX sing 51 n n 
C5 H16 0FX sing 52 n n 
C5 H17 0FX sing 53 n n 
C4 H18 0FX sing 54 n n 
C3 H19 0FX sing 55 n n 
O3 H20 0FX sing 56 n n 
C2 H21 0FX sing 57 n n 
C2 H22 0FX sing 58 n n 
C1 H23 0FX sing 59 n n 
C61 H24 0FX sing 60 n n 
C5A H25 0FX sing 61 n n 
C5A H26 0FX sing 62 n n 
C5A H27 0FX sing 63 n n 
N31 H28 0FX sing 64 n n 
#
_atom_sites.entry_id                     3VBK 
_atom_sites.fract_transf_matrix[1][1]    0.014034 
_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]    0.014034 
_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]    0.007226 
_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
D 2 COA A 1 189 1 COA COA . 
E 3 0FX A 1 1500 1500 0FX NEW . 
F 4 CL A 1 190 1 CL CL . 
G 5 BCT A 1 453 453 BCT BCT . 
H 2 COA C 1 189 1 COA COA . 
I 3 0FX C 1 1500 1500 0FX NEW . 
J 5 BCT C 1 453 453 BCT BCT . 
K 2 COA E 1 189 1 COA COA . 
L 3 0FX E 1 1500 1500 0FX NEW . 
M 5 BCT E 1 453 453 BCT BCT . 
N 6 HOH A 1 191 2 HOH HOH . 
N 6 HOH A 2 192 3 HOH HOH . 
N 6 HOH A 3 193 4 HOH HOH . 
N 6 HOH A 4 194 5 HOH HOH . 
N 6 HOH A 5 195 6 HOH HOH . 
N 6 HOH A 6 196 8 HOH HOH . 
N 6 HOH A 7 197 9 HOH HOH . 
N 6 HOH A 8 198 10 HOH HOH . 
N 6 HOH A 9 199 11 HOH HOH . 
N 6 HOH A 10 200 12 HOH HOH . 
N 6 HOH A 11 201 13 HOH HOH . 
N 6 HOH A 12 202 15 HOH HOH . 
N 6 HOH A 13 203 16 HOH HOH . 
N 6 HOH A 14 204 17 HOH HOH . 
N 6 HOH A 15 205 18 HOH HOH . 
N 6 HOH A 16 206 19 HOH HOH . 
N 6 HOH A 17 207 20 HOH HOH . 
N 6 HOH A 18 208 21 HOH HOH . 
N 6 HOH A 19 209 22 HOH HOH . 
N 6 HOH A 20 210 23 HOH HOH . 
N 6 HOH A 21 211 24 HOH HOH . 
N 6 HOH A 22 212 25 HOH HOH . 
N 6 HOH A 23 213 33 HOH HOH . 
N 6 HOH A 24 214 36 HOH HOH . 
N 6 HOH A 25 215 37 HOH HOH . 
N 6 HOH A 26 216 39 HOH HOH . 
N 6 HOH A 27 217 41 HOH HOH . 
N 6 HOH A 28 218 44 HOH HOH . 
N 6 HOH A 29 219 56 HOH HOH . 
N 6 HOH A 30 220 57 HOH HOH . 
N 6 HOH A 31 221 58 HOH HOH . 
N 6 HOH A 32 222 59 HOH HOH . 
N 6 HOH A 33 223 60 HOH HOH . 
N 6 HOH A 34 224 61 HOH HOH . 
N 6 HOH A 35 225 62 HOH HOH . 
N 6 HOH A 36 226 66 HOH HOH . 
N 6 HOH A 37 227 67 HOH HOH . 
N 6 HOH A 38 228 68 HOH HOH . 
N 6 HOH A 39 229 69 HOH HOH . 
N 6 HOH A 40 230 70 HOH HOH . 
N 6 HOH A 41 231 75 HOH HOH . 
N 6 HOH A 42 232 76 HOH HOH . 
N 6 HOH A 43 233 77 HOH HOH . 
N 6 HOH A 44 234 78 HOH HOH . 
N 6 HOH A 45 235 79 HOH HOH . 
N 6 HOH A 46 236 80 HOH HOH . 
N 6 HOH A 47 237 81 HOH HOH . 
N 6 HOH A 48 238 82 HOH HOH . 
N 6 HOH A 49 239 83 HOH HOH . 
N 6 HOH A 50 240 84 HOH HOH . 
N 6 HOH A 51 241 85 HOH HOH . 
N 6 HOH A 52 242 86 HOH HOH . 
N 6 HOH A 53 243 89 HOH HOH . 
N 6 HOH A 54 244 90 HOH HOH . 
N 6 HOH A 55 245 91 HOH HOH . 
N 6 HOH A 56 246 92 HOH HOH . 
N 6 HOH A 57 247 93 HOH HOH . 
N 6 HOH A 58 248 95 HOH HOH . 
N 6 HOH A 59 249 98 HOH HOH . 
N 6 HOH A 60 250 99 HOH HOH . 
N 6 HOH A 61 251 100 HOH HOH . 
N 6 HOH A 62 252 104 HOH HOH . 
N 6 HOH A 63 253 105 HOH HOH . 
N 6 HOH A 64 254 108 HOH HOH . 
O 6 HOH C 1 190 26 HOH HOH . 
O 6 HOH C 2 191 27 HOH HOH . 
O 6 HOH C 3 192 28 HOH HOH . 
O 6 HOH C 4 193 29 HOH HOH . 
O 6 HOH C 5 194 30 HOH HOH . 
O 6 HOH C 6 195 31 HOH HOH . 
O 6 HOH C 7 196 32 HOH HOH . 
O 6 HOH C 8 197 34 HOH HOH . 
O 6 HOH C 9 198 35 HOH HOH . 
O 6 HOH C 10 199 45 HOH HOH . 
O 6 HOH C 11 200 46 HOH HOH . 
O 6 HOH C 12 201 47 HOH HOH . 
O 6 HOH C 13 202 71 HOH HOH . 
O 6 HOH C 14 203 87 HOH HOH . 
O 6 HOH C 15 204 88 HOH HOH . 
O 6 HOH C 16 205 106 HOH HOH . 
O 6 HOH C 17 206 107 HOH HOH . 
O 6 HOH C 18 207 109 HOH HOH . 
O 6 HOH C 19 208 110 HOH HOH . 
O 6 HOH C 20 209 111 HOH HOH . 
O 6 HOH C 21 210 112 HOH HOH . 
O 6 HOH C 22 211 113 HOH HOH . 
O 6 HOH C 23 212 115 HOH HOH . 
O 6 HOH C 24 213 116 HOH HOH . 
O 6 HOH C 25 214 117 HOH HOH . 
O 6 HOH C 26 215 118 HOH HOH . 
O 6 HOH C 27 216 119 HOH HOH . 
O 6 HOH C 28 217 120 HOH HOH . 
O 6 HOH C 29 218 124 HOH HOH . 
O 6 HOH C 30 219 125 HOH HOH . 
O 6 HOH C 31 220 128 HOH HOH . 
O 6 HOH C 32 221 129 HOH HOH . 
O 6 HOH C 33 222 130 HOH HOH . 
O 6 HOH C 34 223 131 HOH HOH . 
O 6 HOH C 35 224 132 HOH HOH . 
O 6 HOH C 36 225 133 HOH HOH . 
O 6 HOH C 37 226 134 HOH HOH . 
O 6 HOH C 38 227 135 HOH HOH . 
O 6 HOH C 39 228 136 HOH HOH . 
O 6 HOH C 40 229 137 HOH HOH . 
O 6 HOH C 41 230 139 HOH HOH . 
O 6 HOH C 42 231 140 HOH HOH . 
O 6 HOH C 43 232 141 HOH HOH . 
O 6 HOH C 44 233 145 HOH HOH . 
O 6 HOH C 45 234 146 HOH HOH . 
O 6 HOH C 46 235 156 HOH HOH . 
O 6 HOH C 47 236 160 HOH HOH . 
P 6 HOH E 1 190 14 HOH HOH . 
P 6 HOH E 2 191 38 HOH HOH . 
P 6 HOH E 3 192 40 HOH HOH . 
P 6 HOH E 4 193 42 HOH HOH . 
P 6 HOH E 5 194 43 HOH HOH . 
P 6 HOH E 6 195 48 HOH HOH . 
P 6 HOH E 7 196 49 HOH HOH . 
P 6 HOH E 8 197 50 HOH HOH . 
P 6 HOH E 9 198 51 HOH HOH . 
P 6 HOH E 10 199 52 HOH HOH . 
P 6 HOH E 11 200 53 HOH HOH . 
P 6 HOH E 12 201 54 HOH HOH . 
P 6 HOH E 13 202 55 HOH HOH . 
P 6 HOH E 14 203 64 HOH HOH . 
P 6 HOH E 15 204 65 HOH HOH . 
P 6 HOH E 16 205 72 HOH HOH . 
P 6 HOH E 17 206 73 HOH HOH . 
P 6 HOH E 18 207 94 HOH HOH . 
P 6 HOH E 19 208 96 HOH HOH . 
P 6 HOH E 20 209 101 HOH HOH . 
P 6 HOH E 21 210 102 HOH HOH . 
P 6 HOH E 22 211 103 HOH HOH . 
P 6 HOH E 23 212 122 HOH HOH . 
P 6 HOH E 24 213 138 HOH HOH . 
P 6 HOH E 25 214 142 HOH HOH . 
P 6 HOH E 26 215 143 HOH HOH . 
P 6 HOH E 27 216 144 HOH HOH . 
P 6 HOH E 28 217 147 HOH HOH . 
P 6 HOH E 29 218 148 HOH HOH . 
P 6 HOH E 30 219 149 HOH HOH . 
P 6 HOH E 31 220 150 HOH HOH . 
P 6 HOH E 32 221 151 HOH HOH . 
P 6 HOH E 33 222 154 HOH HOH . 
P 6 HOH E 34 223 155 HOH HOH . 
P 6 HOH E 35 224 157 HOH HOH . 
P 6 HOH E 36 225 158 HOH HOH . 
P 6 HOH E 37 226 159 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 O O4P 0FX . . . I 3 -3.613 -40.151 4.791 1 41.44 ? O4P 0FX 1500 C 1 
HETATM 2 P P2 0FX . . . I 3 -4.192 -40.281 3.403 1 47.85 ? P2 0FX 1500 C 1 
HETATM 3 O O3P 0FX . . . I 3 -5.355 -41.211 3.146 1 47.19 ? O3P 0FX 1500 C 1 
HETATM 4 O O1G 0FX . . . I 3 -2.928 -40.592 2.43 1 45.73 ? O1G 0FX 1500 C 1 
HETATM 5 C C1G 0FX . . . I 3 -1.98 -39.568 2.081 1 47.09 ? C1G 0FX 1500 C 1 
HETATM 6 C C2G 0FX . . . I 3 -1.266 -39.623 0.728 1 48.66 ? C2G 0FX 1500 C 1 
HETATM 7 O O2G 0FX . . . I 3 -2.137 -39.751 -0.405 1 47.01 ? O2G 0FX 1500 C 1 
HETATM 8 C C3G 0FX . . . I 3 -0.251 -40.773 0.849 1 48.81 ? C3G 0FX 1500 C 1 
HETATM 9 O O3G 0FX . . . I 3 0.51 -41.048 -0.338 1 48.82 ? O3G 0FX 1500 C 1 
HETATM 10 C C4G 0FX . . . I 3 0.73 -40.581 2.011 1 48.19 ? C4G 0FX 1500 C 1 
HETATM 11 N N4A 0FX . . . I 3 1.477 -41.826 2.105 1 48.12 ? N4A 0FX 1500 C 1 
HETATM 12 C C5G 0FX . . . I 3 -0.037 -40.22 3.291 1 47.05 ? C5G 0FX 1500 C 1 
HETATM 13 C C6G 0FX . . . I 3 0.853 -39.923 4.5 1 47.25 ? C6G 0FX 1500 C 1 
HETATM 14 O O5G 0FX . . . I 3 -1.01 -39.183 3.058 1 44.1 ? O5G 0FX 1500 C 1 
HETATM 15 O OPP 0FX . . . I 3 -4.733 -38.793 3.028 1 45.33 ? OPP 0FX 1500 C 1 
HETATM 16 P P 0FX . . . I 3 -5.438 -38.337 1.649 1 40.93 ? P 0FX 1500 C 1 
HETATM 17 O O1P 0FX . . . I 3 -4.909 -39.108 0.463 1 38.61 ? O1P 0FX 1500 C 1 
HETATM 18 O O2P 0FX . . . I 3 -5.336 -36.838 1.747 1 36.67 ? O2P 0FX 1500 C 1 
HETATM 19 O O5 0FX . . . I 3 -6.927 -38.927 1.868 1 40.51 ? O5 0FX 1500 C 1 
HETATM 20 C C5 0FX . . . I 3 -7.943 -38.347 2.687 1 37.61 ? C5 0FX 1500 C 1 
HETATM 21 C C4 0FX . . . I 3 -9.309 -38.829 2.192 1 38.12 ? C4 0FX 1500 C 1 
HETATM 22 O O4 0FX . . . I 3 -9.67 -38.13 1.005 1 37.36 ? O4 0FX 1500 C 1 
HETATM 23 C C3 0FX . . . I 3 -9.425 -40.292 1.773 1 38.94 ? C3 0FX 1500 C 1 
HETATM 24 O O3 0FX . . . I 3 -9.78 -41.14 2.863 1 43.52 ? O3 0FX 1500 C 1 
HETATM 25 C C2 0FX . . . I 3 -10.488 -40.332 0.682 1 38.65 ? C2 0FX 1500 C 1 
HETATM 26 C C1 0FX . . . I 3 -10.323 -38.957 0.029 1 37.75 ? C1 0FX 1500 C 1 
HETATM 27 N N11 0FX . . . I 3 -9.569 -39.024 -1.238 1 38.09 ? N11 0FX 1500 C 1 
HETATM 28 C C61 0FX . . . I 3 -8.272 -38.661 -1.288 1 37.43 ? C61 0FX 1500 C 1 
HETATM 29 C C51 0FX . . . I 3 -7.524 -38.729 -2.473 1 36.85 ? C51 0FX 1500 C 1 
HETATM 30 C C5A 0FX . . . I 3 -6.076 -38.301 -2.47 1 34.7 ? C5A 0FX 1500 C 1 
HETATM 31 C C21 0FX . . . I 3 -10.116 -39.469 -2.382 1 36.61 ? C21 0FX 1500 C 1 
HETATM 32 O O21 0FX . . . I 3 -11.303 -39.829 -2.418 1 40.96 ? O21 0FX 1500 C 1 
HETATM 33 N N31 0FX . . . I 3 -9.44 -39.542 -3.552 1 37.85 ? N31 0FX 1500 C 1 
HETATM 34 C C41 0FX . . . I 3 -8.132 -39.181 -3.639 1 37.09 ? C41 0FX 1500 C 1 
HETATM 35 O O41 0FX . . . I 3 -7.516 -39.265 -4.731 1 33.96 ? O41 0FX 1500 C 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           35 
#