data_4AY6
#
_model_server_result.job_id            bAq2N_4FnSnwwiRGElwY8g 
_model_server_result.datetime_utc      '2024-10-19 00:46:50' 
_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          4ay6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","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 . . . L 4 99.202 27.471 25.432 1 36.25 ? N1 12V 1200 B 1 
HETATM 2 C C2 12V . . . L 4 98.597 28.625 25.71 1 35.59 ? C2 12V 1200 B 1 
HETATM 3 O O2 12V . . . L 4 99.194 29.515 26.325 1 39.07 ? O2 12V 1200 B 1 
HETATM 4 N N3 12V . . . L 4 97.284 28.827 25.333 1 33.25 ? N3 12V 1200 B 1 
HETATM 5 C C4 12V . . . L 4 96.591 27.882 24.646 1 31.92 ? C4 12V 1200 B 1 
HETATM 6 O O4 12V . . . L 4 95.438 28.106 24.302 1 31.62 ? O4 12V 1200 B 1 
HETATM 7 C C5 12V . . . L 4 97.212 26.695 24.341 1 33.94 ? C5 12V 1200 B 1 
HETATM 8 C C6 12V . . . L 4 98.525 26.481 24.721 1 35.21 ? C6 12V 1200 B 1 
HETATM 9 P PA 12V . . . L 4 104.312 23.661 22.755 1 47.75 ? PA 12V 1200 B 1 
HETATM 10 P PB 12V . . . L 4 104.608 21.35 24.26 1 46.11 ? PB 12V 1200 B 1 
HETATM 11 C C1' 12V . . . L 4 107.156 21.814 24.111 1 52.15 ? C1' 12V 1200 B 1 
HETATM 12 O O1' 12V . . . L 4 106.068 21.258 24.891 1 47.83 ? O1' 12V 1200 B 1 
HETATM 13 O O1A 12V . . . L 4 105.682 23.854 22.219 1 43.77 ? O1A 12V 1200 B 1 
HETATM 14 C C1B 12V . . . L 4 100.639 27.309 25.816 1 38.6 ? C1B 12V 1200 B 1 
HETATM 15 O O1B 12V . . . L 4 103.609 20.824 25.225 1 47.4 ? O1B 12V 1200 B 1 
HETATM 16 C C2' 12V . . . L 4 108.302 20.821 23.834 1 54.03 ? C2' 12V 1200 B 1 
HETATM 17 N N2' 12V . . . L 4 107.707 19.713 23.079 1 63.99 ? N2' 12V 1200 B 1 
HETATM 18 O O2' 12V . . . L 4 100.83 26.331 27.963 1 35.81 ? O2' 12V 1200 B 1 
HETATM 19 O O2A 12V . . . L 4 103.273 22.921 21.98 1 48.83 ? O2A 12V 1200 B 1 
HETATM 20 C C2B 12V . . . L 4 101.058 26.101 26.59 1 38.41 ? C2B 12V 1200 B 1 
HETATM 21 O O2B 12V . . . L 4 104.664 20.82 22.879 1 45.88 ? O2B 12V 1200 B 1 
HETATM 22 C C3' 12V . . . L 4 108.978 20.343 25.113 1 50.63 ? C3' 12V 1200 B 1 
HETATM 23 O O3' 12V . . . L 4 109.894 19.3 24.849 1 46.51 ? O3' 12V 1200 B 1 
HETATM 24 O O3A 12V . . . L 4 104.449 22.911 24.172 1 47.77 ? O3A 12V 1200 B 1 
HETATM 25 C C3B 12V . . . L 4 102.545 26.186 26.286 1 39.43 ? C3B 12V 1200 B 1 
HETATM 26 O O3B 12V . . . L 4 103.115 27.397 26.851 1 43.66 ? O3B 12V 1200 B 1 
HETATM 27 C C4' 12V . . . L 4 109.775 21.429 25.751 1 52.4 ? C4' 12V 1200 B 1 
HETATM 28 O O4' 12V . . . L 4 110.351 20.843 26.925 1 53.46 ? O4' 12V 1200 B 1 
HETATM 29 C C4B 12V . . . L 4 102.567 26.414 24.809 1 38.78 ? C4B 12V 1200 B 1 
HETATM 30 O O4B 12V . . . L 4 101.347 27.101 24.547 1 40.19 ? O4B 12V 1200 B 1 
HETATM 31 C C5' 12V . . . L 4 108.89 22.628 26.143 1 55.65 ? C5' 12V 1200 B 1 
HETATM 32 S S5' 12V . . . L 4 107.781 23.255 24.907 1 54.31 ? S5' 12V 1200 B 1 
HETATM 33 C C5B 12V . . . L 4 102.538 25.109 24.041 1 39.06 ? C5B 12V 1200 B 1 
HETATM 34 O O5B 12V . . . L 4 103.68 25.095 23.192 1 43.64 ? O5B 12V 1200 B 1 
HETATM 35 C C6' 12V . . . L 4 109.672 23.942 26.184 1 57.29 ? C6' 12V 1200 B 1 
HETATM 36 O O6' 12V . . . L 4 111.032 23.746 26.567 1 66.91 ? O6' 12V 1200 B 1 
HETATM 37 C C7' 12V . . . L 4 107.773 19.681 21.74 1 68.83 ? C7' 12V 1200 B 1 
HETATM 38 O O7' 12V . . . L 4 108.37 20.523 21.071 1 70.96 ? O7' 12V 1200 B 1 
HETATM 39 C C8' 12V . . . L 4 107.085 18.486 21.077 1 67.7 ? C8' 12V 1200 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           341 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#