data_6CI5
#
_model_server_result.job_id            w-bgYzk31Vph6IKVJUUpow 
_model_server_result.datetime_utc      '2024-11-29 02:30:54' 
_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          6ci5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    6CI5 
#
_exptl.entry_id    6CI5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              618.38 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R,3R,4S,5R,6S)-3-(acetylamino)-5-(formylamino)-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          103.47 
_cell.angle_gamma         90 
_cell.entry_id            6CI5 
_cell.length_a            96.42 
_cell.length_b            73.78 
_cell.length_c            41.8 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6CI5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C18 H28 N4 O16 P2' 
_chem_comp.formula_weight    618.38 
_chem_comp.id                F5G 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R,3R,4S,5R,6S)-3-(acetylamino)-5-(formylamino)-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)' 
_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
O29 C18 F5G sing 127 n n 
O30 C17 F5G sing 128 n n 
C16 C17 F5G sing 129 n n 
C16 O28 F5G sing 130 n n 
C16 C15 F5G sing 131 n n 
C18 C17 F5G sing 132 n n 
C18 C19 F5G sing 133 n n 
O28 C19 F5G sing 134 n n 
C19 N20 F5G sing 135 n n 
C15 O14 F5G sing 136 n n 
O27 C21 F5G doub 137 n n 
N20 C21 F5G sing 138 n n 
N20 C25 F5G sing 139 n n 
O14 P13 F5G sing 140 n n 
C21 N22 F5G sing 141 n n 
O12 P13 F5G sing 142 n n 
O12 P10 F5G sing 143 n n 
C25 C24 F5G doub 144 n n 
O11 P10 F5G doub 145 n n 
P13 O32 F5G doub 146 n n 
P13 O31 F5G sing 147 n n 
N22 C23 F5G sing 148 n n 
P10 O33 F5G sing 149 n n 
P10 O09 F5G sing 150 n n 
C24 C23 F5G sing 151 n n 
C23 O26 F5G doub 152 n n 
O09 C08 F5G sing 153 n n 
C08 C34 F5G sing 154 n n 
C08 O07 F5G sing 155 n n 
C34 N35 F5G sing 156 n n 
C34 C39 F5G sing 157 n n 
O07 C05 F5G sing 158 n n 
N35 C36 F5G sing 159 n n 
C37 C36 F5G sing 160 n n 
O40 C39 F5G sing 161 n n 
C36 O38 F5G doub 162 n n 
C39 C01 F5G sing 163 n n 
C05 C01 F5G sing 164 n n 
C05 C06 F5G sing 165 n n 
C01 N02 F5G sing 166 n n 
C03 N02 F5G sing 167 n n 
C03 O04 F5G doub 168 n n 
C15 H152 F5G sing 169 n n 
C15 H151 F5G sing 170 n n 
C17 H171 F5G sing 171 n n 
C24 H241 F5G sing 172 n n 
C01 H011 F5G sing 173 n n 
C03 H031 F5G sing 174 n n 
C05 H051 F5G sing 175 n n 
C06 H062 F5G sing 176 n n 
C06 H063 F5G sing 177 n n 
C06 H061 F5G sing 178 n n 
C08 H081 F5G sing 179 n n 
C16 H161 F5G sing 180 n n 
C18 H181 F5G sing 181 n n 
C19 H191 F5G sing 182 n n 
C25 H251 F5G sing 183 n n 
C34 H341 F5G sing 184 n n 
C37 H372 F5G sing 185 n n 
C37 H373 F5G sing 186 n n 
C37 H371 F5G sing 187 n n 
C39 H391 F5G sing 188 n n 
N02 H021 F5G sing 189 n n 
N22 H221 F5G sing 190 n n 
N35 H351 F5G sing 191 n n 
O29 H291 F5G sing 192 n n 
O30 H301 F5G sing 193 n n 
O31 H1 F5G sing 194 n n 
O33 H2 F5G sing 195 n n 
O40 H401 F5G sing 196 n n 
#
_atom_sites.entry_id                     6CI5 
_atom_sites.fract_transf_matrix[1][1]    0.010371 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002484 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013554 
_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]    0.0246 
_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
B 2 SO4 A 1 301 1 SO4 SO4 . 
C 3 F5G A 1 302 2 F5G LIG . 
D 4 1YJ A 1 303 1 1YJ THF . 
E 5 HOH A 1 401 27 HOH HOH . 
E 5 HOH A 2 402 16 HOH HOH . 
E 5 HOH A 3 403 9 HOH HOH . 
E 5 HOH A 4 404 31 HOH HOH . 
E 5 HOH A 5 405 12 HOH HOH . 
E 5 HOH A 6 406 25 HOH HOH . 
E 5 HOH A 7 407 26 HOH HOH . 
E 5 HOH A 8 408 2 HOH HOH . 
E 5 HOH A 9 409 30 HOH HOH . 
E 5 HOH A 10 410 18 HOH HOH . 
E 5 HOH A 11 411 14 HOH HOH . 
E 5 HOH A 12 412 4 HOH HOH . 
E 5 HOH A 13 413 6 HOH HOH . 
E 5 HOH A 14 414 5 HOH HOH . 
E 5 HOH A 15 415 1 HOH HOH . 
E 5 HOH A 16 416 11 HOH HOH . 
E 5 HOH A 17 417 7 HOH HOH . 
E 5 HOH A 18 418 24 HOH HOH . 
E 5 HOH A 19 419 15 HOH HOH . 
E 5 HOH A 20 420 23 HOH HOH . 
E 5 HOH A 21 421 28 HOH HOH . 
E 5 HOH A 22 422 19 HOH HOH . 
E 5 HOH A 23 423 22 HOH HOH . 
E 5 HOH A 24 424 3 HOH HOH . 
E 5 HOH A 25 425 8 HOH HOH . 
E 5 HOH A 26 426 17 HOH HOH . 
E 5 HOH A 27 427 10 HOH HOH . 
E 5 HOH A 28 428 20 HOH HOH . 
E 5 HOH A 29 429 13 HOH HOH . 
E 5 HOH A 30 430 21 HOH HOH . 
E 5 HOH A 31 431 29 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 C C15 F5G . . . C 3 32.234 27.536 -1.336 0.77 60.77 ? C15 F5G 302 A 1 
HETATM 2 C C17 F5G . . . C 3 34.495 27.679 -1.799 0.77 56.96 ? C17 F5G 302 A 1 
HETATM 3 C C21 F5G . . . C 3 36.36 31.221 0.084 0.77 56.6 ? C21 F5G 302 A 1 
HETATM 4 C C24 F5G . . . C 3 34.441 30.572 2.298 0.77 59.01 ? C24 F5G 302 A 1 
HETATM 5 C C01 F5G . . . C 3 30.704 22.754 6.847 0.77 49.91 ? C01 F5G 302 A 1 
HETATM 6 C C03 F5G . . . C 3 31.702 20.635 7.914 0.77 51.33 ? C03 F5G 302 A 1 
HETATM 7 C C05 F5G . . . C 3 32.059 22.992 6.182 0.77 54.25 ? C05 F5G 302 A 1 
HETATM 8 C C06 F5G . . . C 3 33.017 23.563 7.169 0.77 49.9 ? C06 F5G 302 A 1 
HETATM 9 C C08 F5G . . . C 3 30.953 23.412 4.046 0.77 54.83 ? C08 F5G 302 A 1 
HETATM 10 C C16 F5G . . . C 3 33.351 28.227 -2.089 0.77 58.83 ? C16 F5G 302 A 1 
HETATM 11 C C18 F5G . . . C 3 35.493 28.807 -1.946 0.77 57.37 ? C18 F5G 302 A 1 
HETATM 12 C C19 F5G . . . C 3 34.697 30.085 -1.546 0.77 58.74 ? C19 F5G 302 A 1 
HETATM 13 C C23 F5G . . . C 3 35.68 31.27 2.594 0.77 56.55 ? C23 F5G 302 A 1 
HETATM 14 C C25 F5G . . . C 3 34.132 30.188 0.931 0.77 59.44 ? C25 F5G 302 A 1 
HETATM 15 C C34 F5G . . . C 3 29.588 23.144 4.695 0.77 54.08 ? C34 F5G 302 A 1 
HETATM 16 C C36 F5G . . . C 3 27.589 24.614 5.332 0.77 69.89 ? C36 F5G 302 A 1 
HETATM 17 C C37 F5G . . . C 3 26.625 23.461 5.065 0.77 67 ? C37 F5G 302 A 1 
HETATM 18 C C39 F5G . . . C 3 29.714 22.233 5.864 0.77 56.23 ? C39 F5G 302 A 1 
HETATM 19 N N02 F5G . . . C 3 30.841 21.804 7.992 0.77 54.19 ? N02 F5G 302 A 1 
HETATM 20 N N20 F5G . . . C 3 35.047 30.492 -0.156 0.77 57.47 ? N20 F5G 302 A 1 
HETATM 21 N N22 F5G . . . C 3 36.619 31.593 1.536 0.77 52.7 ? N22 F5G 302 A 1 
HETATM 22 N N35 F5G . . . C 3 29.02 24.443 5.146 0.77 63.76 ? N35 F5G 302 A 1 
HETATM 23 O O04 F5G . . . C 3 31.786 19.903 8.842 0.77 54.23 ? O04 F5G 302 A 1 
HETATM 24 O O07 F5G . . . C 3 31.928 23.922 5.025 0.77 50.87 ? O07 F5G 302 A 1 
HETATM 25 O O09 F5G . . . C 3 30.826 24.335 3.046 0.77 52.95 ? O09 F5G 302 A 1 
HETATM 26 O O11 F5G . . . C 3 32.136 23.045 1.237 0.77 57.65 -1 O11 F5G 302 A 1 
HETATM 27 O O12 F5G . . . C 3 31.711 25.557 0.804 0.77 54.71 ? O12 F5G 302 A 1 
HETATM 28 O O14 F5G . . . C 3 32.195 28.059 -0.037 0.77 62.08 ? O14 F5G 302 A 1 
HETATM 29 O O26 F5G . . . C 3 35.924 31.581 3.712 0.77 50.04 ? O26 F5G 302 A 1 
HETATM 30 O O27 F5G . . . C 3 37.116 31.475 -0.79 0.77 57.86 ? O27 F5G 302 A 1 
HETATM 31 O O28 F5G . . . C 3 33.459 29.776 -1.617 0.77 57.43 ? O28 F5G 302 A 1 
HETATM 32 O O29 F5G . . . C 3 35.916 28.897 -3.236 0.77 57.5 ? O29 F5G 302 A 1 
HETATM 33 O O30 F5G . . . C 3 34.816 26.572 -2.771 0.77 65.8 ? O30 F5G 302 A 1 
HETATM 34 O O31 F5G . . . C 3 32.227 27.458 2.478 0.77 59.57 -1 O31 F5G 302 A 1 
HETATM 35 O O32 F5G . . . C 3 30.067 27.486 1.296 0.77 64.52 ? O32 F5G 302 A 1 
HETATM 36 O O33 F5G . . . C 3 33.335 24.696 2.608 0.77 56.5 ? O33 F5G 302 A 1 
HETATM 37 O O38 F5G . . . C 3 27.166 25.659 5.692 0.77 75.31 ? O38 F5G 302 A 1 
HETATM 38 O O40 F5G . . . C 3 30.157 20.925 5.395 0.77 51.7 ? O40 F5G 302 A 1 
HETATM 39 P P10 F5G . . . C 3 32.026 24.387 1.918 0.77 56.75 ? P10 F5G 302 A 1 
HETATM 40 P P13 F5G . . . C 3 31.535 27.154 1.171 0.77 58.71 ? P13 F5G 302 A 1 
HETATM 41 H H152 F5G . . . C 3 32.404 26.582 -1.299 0.77 72.41 ? H152 F5G 302 A 1 
HETATM 42 H H151 F5G . . . C 3 31.388 27.701 -1.78 0.77 72.41 ? H151 F5G 302 A 1 
HETATM 43 H H171 F5G . . . C 3 34.49 27.348 -0.887 0.77 67.84 ? H171 F5G 302 A 1 
HETATM 44 H H241 F5G . . . C 3 33.845 30.37 2.983 0.77 70.29 ? H241 F5G 302 A 1 
HETATM 45 H H011 F5G . . . C 3 30.378 23.603 7.186 0.77 59.37 ? H011 F5G 302 A 1 
HETATM 46 H H031 F5G . . . C 3 32.185 20.462 7.139 0.77 61.08 ? H031 F5G 302 A 1 
HETATM 47 H H051 F5G . . . C 3 32.402 22.143 5.862 0.77 64.58 ? H051 F5G 302 A 1 
HETATM 48 H H062 F5G . . . C 3 32.526 23.944 7.913 0.77 59.36 ? H062 F5G 302 A 1 
HETATM 49 H H063 F5G . . . C 3 33.547 24.254 6.743 0.77 59.36 ? H063 F5G 302 A 1 
HETATM 50 H H061 F5G . . . C 3 33.603 22.861 7.494 0.77 59.36 ? H061 F5G 302 A 1 
HETATM 51 H H081 F5G . . . C 3 31.29 22.582 3.673 0.77 65.28 ? H081 F5G 302 A 1 
HETATM 52 H H161 F5G . . . C 3 33.194 28.182 -3.045 0.77 70.08 ? H161 F5G 302 A 1 
HETATM 53 H H181 F5G . . . C 3 36.243 28.674 -1.345 0.77 68.32 ? H181 F5G 302 A 1 
HETATM 54 H H191 F5G . . . C 3 34.894 30.804 -2.167 0.77 69.97 ? H191 F5G 302 A 1 
HETATM 55 H H251 F5G . . . C 3 33.337 29.741 0.749 0.77 70.82 ? H251 F5G 302 A 1 
HETATM 56 H H341 F5G . . . C 3 28.997 22.741 4.039 0.77 64.38 ? H341 F5G 302 A 1 
HETATM 57 H H372 F5G . . . C 3 26.777 23.113 4.173 0.77 79.88 ? H372 F5G 302 A 1 
HETATM 58 H H373 F5G . . . C 3 25.712 23.78 5.137 0.77 79.88 ? H373 F5G 302 A 1 
HETATM 59 H H371 F5G . . . C 3 26.775 22.758 5.716 0.77 79.88 ? H371 F5G 302 A 1 
HETATM 60 H H391 F5G . . . C 3 28.85 22.148 6.296 0.77 66.95 ? H391 F5G 302 A 1 
HETATM 61 H H021 F5G . . . C 3 30.399 21.952 8.715 0.77 64.51 ? H021 F5G 302 A 1 
HETATM 62 H H221 F5G . . . C 3 37.346 32.006 1.736 0.77 62.72 ? H221 F5G 302 A 1 
HETATM 63 H H351 F5G . . . C 3 29.548 25.104 5.301 0.77 76 ? H351 F5G 302 A 1 
HETATM 64 H H291 F5G . . . C 3 36.474 29.535 -3.308 0.77 68.49 ? H291 F5G 302 A 1 
HETATM 65 H H301 F5G . . . C 3 35.373 26.036 -2.417 0.77 78.44 ? H301 F5G 302 A 1 
HETATM 66 H H401 F5G . . . C 3 29.637 20.324 5.698 0.77 61.52 ? H401 F5G 302 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           66 
#