data_4AY6
#
_model_server_result.job_id            r-QZmdWAAZMZPiXqYSzBvQ 
_model_server_result.datetime_utc      '2024-11-23 22:07:36' 
_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          4ay6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1200}' 
#
_entry.id    4AY6 
#
_exptl.entry_id    4AY6 
_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            4AY6 
_cell.length_a            275.439 
_cell.length_b            275.439 
_cell.length_c            142.632 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4AY6 
_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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_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 P N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
covale ? covale1 E N DNP 7 E DNP 1395 1_555 E C TYR 6 E TYR 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale2 E C DNP 7 E DNP 1395 1_555 E N SER 8 E SER 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale3 F N DNP 7 F DNP 1395 1_555 F C TYR 6 F TYR 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.369 ? 
covale ? covale4 F C DNP 7 F DNP 1395 1_555 F N SER 8 F SER 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? 
covale ? covale5 G C DNP 7 G DNP 1395 1_555 G N SER 8 G SER 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.294 ? 
covale ? covale6 G N DNP 7 G DNP 1395 1_555 G C TYR 6 G TYR 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? 
covale ? covale7 H C DNP 7 H DNP 1395 1_555 H N SER 8 H SER 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? 
covale ? covale8 H N DNP 7 H DNP 1395 1_555 H C TYR 6 H TYR 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
#
_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' 
#
_atom_sites.entry_id                     4AY6 
_atom_sites.fract_transf_matrix[1][1]    0.003631 
_atom_sites.fract_transf_matrix[1][2]    0.002096 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004192 
_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]    0.007011 
_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 1100 1100 SO4 SO4 . 
J 4 12V A 1 1200 1200 12V 12V . 
K 3 SO4 B 1 1100 1100 SO4 SO4 . 
L 4 12V B 1 1200 1200 12V 12V . 
M 3 SO4 C 1 1100 1100 SO4 SO4 . 
N 4 12V C 1 1200 1200 12V 12V . 
O 3 SO4 D 1 1100 1100 SO4 SO4 . 
P 4 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 . . . J 4 137.509 -22.92 29.818 1 31.12 ? N1 12V 1200 A 1 
HETATM 2 C C2 12V . . . J 4 138.249 -22.728 28.695 1 30.48 ? C2 12V 1200 A 1 
HETATM 3 O O2 12V . . . J 4 139.152 -23.48 28.341 1 29.93 ? O2 12V 1200 A 1 
HETATM 4 N N3 12V . . . J 4 138.017 -21.627 27.894 1 31.26 ? N3 12V 1200 A 1 
HETATM 5 C C4 12V . . . J 4 137.005 -20.719 28.23 1 31.24 ? C4 12V 1200 A 1 
HETATM 6 O O4 12V . . . J 4 136.817 -19.765 27.489 1 32.51 ? O4 12V 1200 A 1 
HETATM 7 C C5 12V . . . J 4 136.227 -20.888 29.365 1 29.83 ? C5 12V 1200 A 1 
HETATM 8 C C6 12V . . . J 4 136.474 -21.999 30.158 1 31.01 ? C6 12V 1200 A 1 
HETATM 9 P PA 12V . . . J 4 133.492 -26.435 34.126 1 34.69 ? PA 12V 1200 A 1 
HETATM 10 P PB 12V . . . J 4 134.117 -25.67 36.845 1 43.7 ? PB 12V 1200 A 1 
HETATM 11 C C1' 12V . . . J 4 134.065 -28.212 37.361 1 52.92 ? C1' 12V 1200 A 1 
HETATM 12 O O1' 12V . . . J 4 134.628 -26.902 37.68 1 46.15 ? O1' 12V 1200 A 1 
HETATM 13 O O1A 12V . . . J 4 132.971 -27.795 34.315 1 34.65 ? O1A 12V 1200 A 1 
HETATM 14 C C1B 12V . . . J 4 137.739 -24.139 30.667 1 31.07 ? C1B 12V 1200 A 1 
HETATM 15 O O1B 12V . . . J 4 134.856 -24.456 37.257 1 43.27 ? O1B 12V 1200 A 1 
HETATM 16 C C2' 12V . . . J 4 133.36 -28.889 38.547 1 56.9 ? C2' 12V 1200 A 1 
HETATM 17 N N2' 12V . . . J 4 132.281 -27.986 38.971 1 59.33 ? N2' 12V 1200 A 1 
HETATM 18 O O2' 12V . . . J 4 139.408 -23.671 32.293 1 34.35 ? O2' 12V 1200 A 1 
HETATM 19 O O2A 12V . . . J 4 132.515 -25.308 34.05 1 36.51 ? O2A 12V 1200 A 1 
HETATM 20 C C2B 12V . . . J 4 138.036 -23.971 32.133 1 30.89 ? C2B 12V 1200 A 1 
HETATM 21 O O2B 12V . . . J 4 132.621 -25.7 36.92 1 45.06 ? O2B 12V 1200 A 1 
HETATM 22 C C3' 12V . . . J 4 134.36 -29.189 39.679 1 58.69 ? C3' 12V 1200 A 1 
HETATM 23 O O3' 12V . . . J 4 133.659 -29.571 40.885 1 58.43 ? O3' 12V 1200 A 1 
HETATM 24 O O3A 12V . . . J 4 134.583 -26.115 35.355 1 39.11 ? O3A 12V 1200 A 1 
HETATM 25 C C3B 12V . . . J 4 137.783 -25.386 32.591 1 29.39 ? C3B 12V 1200 A 1 
HETATM 26 O O3B 12V . . . J 4 138.786 -26.289 32.034 1 28.33 ? O3B 12V 1200 A 1 
HETATM 27 C C4' 12V . . . J 4 135.393 -30.279 39.295 1 58.55 ? C4' 12V 1200 A 1 
HETATM 28 O O4' 12V . . . J 4 136.327 -30.404 40.381 1 59.01 ? O4' 12V 1200 A 1 
HETATM 29 C C4B 12V . . . J 4 136.49 -25.656 31.9 1 29.9 ? C4B 12V 1200 A 1 
HETATM 30 O O4B 12V . . . J 4 136.458 -24.755 30.761 1 30.82 ? O4B 12V 1200 A 1 
HETATM 31 C C5' 12V . . . J 4 136.203 -29.906 38.06 1 57.37 ? C5' 12V 1200 A 1 
HETATM 32 S S5' 12V . . . J 4 135.351 -29.234 36.673 1 55.45 ? S5' 12V 1200 A 1 
HETATM 33 C C5B 12V . . . J 4 135.32 -25.301 32.783 1 29.7 ? C5B 12V 1200 A 1 
HETATM 34 O O5B 12V . . . J 4 134.458 -26.421 32.882 1 30.52 ? O5B 12V 1200 A 1 
HETATM 35 C C6' 12V . . . J 4 136.621 -31.144 37.274 1 60.62 ? C6' 12V 1200 A 1 
HETATM 36 O O6' 12V . . . J 4 136.877 -32.248 38.138 1 64.92 ? O6' 12V 1200 A 1 
HETATM 37 C C7' 12V . . . J 4 131.025 -28.189 38.572 1 63.92 ? C7' 12V 1200 A 1 
HETATM 38 O O7' 12V . . . J 4 130.671 -29.149 37.891 1 70.59 ? O7' 12V 1200 A 1 
HETATM 39 C C8' 12V . . . J 4 130.011 -27.163 39.059 1 62.93 ? C8' 12V 1200 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           39 
#