data_3WKA
#
_model_server_result.job_id            4qasQ9LLPDG3Tn1dJ-9gZA 
_model_server_result.datetime_utc      '2024-11-24 17:43:11' 
_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          3wka 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":603}' 
#
_entry.id    3WKA 
#
_exptl.entry_id    3WKA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              224.26 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            6-amino-1-methyl-5-(piperidin-1-yl)pyrimidine-2,4(1H,3H)-dione 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            3WKA 
_cell.length_a            92.345 
_cell.length_b            92.345 
_cell.length_c            242.936 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3WKA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 11_455 -x+y-1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 -92.345 0 121.468 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
metalc ? metalc1 A OD2 ASP 9 A ASP 9 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? 
metalc ? metalc2 A O ASP 11 A ASP 11 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? 
metalc ? metalc3 A OD1 ASP 185 A ASP 185 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc4 B MG MG . A MG 601 1_555 C O1 PO4 . A PO4 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
#
_chem_comp.formula           'C10 H16 N4 O2' 
_chem_comp.formula_weight    224.26 
_chem_comp.id                S0G 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              6-amino-1-methyl-5-(piperidin-1-yl)pyrimidine-2,4(1H,3H)-dione 
_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
C16 C15 S0G sing 281 n n 
C16 C14 S0G sing 282 n n 
C15 C12 S0G sing 283 n n 
C14 C13 S0G sing 284 n n 
C12 N7 S0G sing 285 n n 
C13 N7 S0G sing 286 n n 
O9 C6 S0G doub 287 n n 
N7 C3 S0G sing 288 n n 
C6 C3 S0G sing 289 n n 
C6 N5 S0G sing 290 n n 
C3 C1 S0G doub 291 n n 
N5 C4 S0G sing 292 n n 
C1 N10 S0G sing 293 n n 
C1 N2 S0G sing 294 n n 
C4 N2 S0G sing 295 n n 
C4 O8 S0G doub 296 n n 
N2 C11 S0G sing 297 n n 
C16 H1 S0G sing 298 n n 
C16 H2 S0G sing 299 n n 
C15 H3 S0G sing 300 n n 
C15 H4 S0G sing 301 n n 
C14 H5 S0G sing 302 n n 
C14 H6 S0G sing 303 n n 
C12 H7 S0G sing 304 n n 
C12 H8 S0G sing 305 n n 
C13 H9 S0G sing 306 n n 
C13 H10 S0G sing 307 n n 
C11 H11 S0G sing 308 n n 
C11 H12 S0G sing 309 n n 
C11 H13 S0G sing 310 n n 
N5 H14 S0G sing 311 n n 
N10 H15 S0G sing 312 n n 
N10 H16 S0G sing 313 n n 
#
_atom_sites.entry_id                     3WKA 
_atom_sites.fract_transf_matrix[1][1]    0.010829 
_atom_sites.fract_transf_matrix[1][2]    0.006252 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012504 
_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]    0.004116 
_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 MG A 1 601 782 MG MG . 
C 3 PO4 A 1 602 783 PO4 PO4 . 
D 4 S0G A 1 603 1 S0G S0G . 
E 5 HOH A 1 701 1 HOH HOH . 
E 5 HOH A 2 702 2 HOH HOH . 
E 5 HOH A 3 703 3 HOH HOH . 
E 5 HOH A 4 704 4 HOH HOH . 
E 5 HOH A 5 705 5 HOH HOH . 
E 5 HOH A 6 706 6 HOH HOH . 
E 5 HOH A 7 707 7 HOH HOH . 
E 5 HOH A 8 708 8 HOH HOH . 
E 5 HOH A 9 709 9 HOH HOH . 
E 5 HOH A 10 710 10 HOH HOH . 
E 5 HOH A 11 711 11 HOH HOH . 
E 5 HOH A 12 712 12 HOH HOH . 
E 5 HOH A 13 713 13 HOH HOH . 
E 5 HOH A 14 714 14 HOH HOH . 
E 5 HOH A 15 715 15 HOH HOH . 
E 5 HOH A 16 716 16 HOH HOH . 
E 5 HOH A 17 717 17 HOH HOH . 
E 5 HOH A 18 718 18 HOH HOH . 
E 5 HOH A 19 719 19 HOH HOH . 
E 5 HOH A 20 720 20 HOH HOH . 
E 5 HOH A 21 721 21 HOH HOH . 
E 5 HOH A 22 722 22 HOH HOH . 
E 5 HOH A 23 723 23 HOH HOH . 
E 5 HOH A 24 724 24 HOH HOH . 
E 5 HOH A 25 725 25 HOH HOH . 
E 5 HOH A 26 726 26 HOH HOH . 
E 5 HOH A 27 727 27 HOH HOH . 
E 5 HOH A 28 728 28 HOH HOH . 
E 5 HOH A 29 729 29 HOH HOH . 
E 5 HOH A 30 730 30 HOH HOH . 
E 5 HOH A 31 731 31 HOH HOH . 
E 5 HOH A 32 732 32 HOH HOH . 
E 5 HOH A 33 733 33 HOH HOH . 
E 5 HOH A 34 734 34 HOH HOH . 
E 5 HOH A 35 735 35 HOH HOH . 
E 5 HOH A 36 736 36 HOH HOH . 
E 5 HOH A 37 737 37 HOH HOH . 
E 5 HOH A 38 738 38 HOH HOH . 
E 5 HOH A 39 739 39 HOH HOH . 
E 5 HOH A 40 740 40 HOH HOH . 
E 5 HOH A 41 741 41 HOH HOH . 
E 5 HOH A 42 742 42 HOH HOH . 
E 5 HOH A 43 743 43 HOH HOH . 
E 5 HOH A 44 744 44 HOH HOH . 
E 5 HOH A 45 745 45 HOH HOH . 
E 5 HOH A 46 746 46 HOH HOH . 
E 5 HOH A 47 747 47 HOH HOH . 
E 5 HOH A 48 748 48 HOH HOH . 
E 5 HOH A 49 749 49 HOH HOH . 
E 5 HOH A 50 750 50 HOH HOH . 
E 5 HOH A 51 751 51 HOH HOH . 
E 5 HOH A 52 752 52 HOH HOH . 
E 5 HOH A 53 753 53 HOH HOH . 
E 5 HOH A 54 754 54 HOH HOH . 
E 5 HOH A 55 755 55 HOH HOH . 
E 5 HOH A 56 756 56 HOH HOH . 
E 5 HOH A 57 757 57 HOH HOH . 
E 5 HOH A 58 758 58 HOH HOH . 
E 5 HOH A 59 759 59 HOH HOH . 
E 5 HOH A 60 760 60 HOH HOH . 
E 5 HOH A 61 761 61 HOH HOH . 
E 5 HOH A 62 762 62 HOH HOH . 
E 5 HOH A 63 763 63 HOH HOH . 
E 5 HOH A 64 764 64 HOH HOH . 
E 5 HOH A 65 765 65 HOH HOH . 
E 5 HOH A 66 766 66 HOH HOH . 
E 5 HOH A 67 767 67 HOH HOH . 
E 5 HOH A 68 768 68 HOH HOH . 
E 5 HOH A 69 769 69 HOH HOH . 
E 5 HOH A 70 770 70 HOH HOH . 
E 5 HOH A 71 771 71 HOH HOH . 
E 5 HOH A 72 772 72 HOH HOH . 
E 5 HOH A 73 773 73 HOH HOH . 
E 5 HOH A 74 774 74 HOH HOH . 
E 5 HOH A 75 775 75 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 C3 S0G . . . D 4 -16.454 -9.494 70.678 1 26.13 ? C3 S0G 603 A 1 
HETATM 2 C C1 S0G . . . D 4 -16.255 -9.859 71.953 1 26.49 ? C1 S0G 603 A 1 
HETATM 3 C C6 S0G . . . D 4 -16.109 -8.094 70.277 1 26.38 ? C6 S0G 603 A 1 
HETATM 4 C C4 S0G . . . D 4 -15.39 -7.663 72.563 1 28.17 ? C4 S0G 603 A 1 
HETATM 5 C C16 S0G . . . D 4 -17.905 -12.156 67.597 1 27.21 ? C16 S0G 603 A 1 
HETATM 6 C C15 S0G . . . D 4 -16.545 -12.355 68.254 1 28.71 ? C15 S0G 603 A 1 
HETATM 7 C C14 S0G . . . D 4 -18.861 -11.394 68.485 1 25.18 ? C14 S0G 603 A 1 
HETATM 8 C C12 S0G . . . D 4 -15.966 -11.083 68.886 1 25.88 ? C12 S0G 603 A 1 
HETATM 9 C C13 S0G . . . D 4 -18.253 -10.123 69.068 1 26.29 ? C13 S0G 603 A 1 
HETATM 10 C C11 S0G . . . D 4 -15.522 -9.452 74.28 1 25.63 ? C11 S0G 603 A 1 
HETATM 11 N N5 S0G . . . D 4 -15.614 -7.281 71.264 1 27.12 ? N5 S0G 603 A 1 
HETATM 12 N N7 S0G . . . D 4 -16.96 -10.371 69.721 1 29.24 ? N7 S0G 603 A 1 
HETATM 13 N N2 S0G . . . D 4 -15.727 -8.985 72.902 1 29.74 ? N2 S0G 603 A 1 
HETATM 14 N N10 S0G . . . D 4 -16.584 -11.142 72.295 1 25.55 ? N10 S0G 603 A 1 
HETATM 15 O O9 S0G . . . D 4 -16.261 -7.649 69.147 1 26.36 ? O9 S0G 603 A 1 
HETATM 16 O O8 S0G . . . D 4 -14.92 -6.842 73.333 1 29.09 ? O8 S0G 603 A 1 
#
_model_server_stats.io_time_ms              72 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           16 
#