data_1CY6
#
_model_server_result.job_id            CwaXg6Yne5CyTu_9GE48GQ 
_model_server_result.datetime_utc      '2025-02-05 04:50:16' 
_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          1cy6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":600}' 
#
_entry.id    1CY6 
#
_exptl.entry_id    1CY6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              322.208 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-3'-PHOSPHATE" 
_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         90 
_cell.entry_id            1CY6 
_cell.length_a            64.63 
_cell.length_b            80.72 
_cell.length_c            143.53 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1CY6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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,F 
_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                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C10 H15 N2 O8 P' 
_chem_comp.formula_weight    322.208 
_chem_comp.id                T3P 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "THYMIDINE-3'-PHOSPHATE" 
_chem_comp.type              'dna linking' 
_chem_comp.pdbx_synonyms     "ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE" 
#
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
P OP1 T3P doub 294 n n 
P OP2 T3P sing 295 n n 
P OP3 T3P sing 296 n n 
P O3' T3P sing 297 n n 
OP2 HOP2 T3P sing 298 n n 
OP3 HOP3 T3P sing 299 n n 
O5' C5' T3P sing 300 n n 
O5' H5' T3P sing 301 n n 
C5' C4' T3P sing 302 n n 
C5' "H5'1" T3P sing 303 n n 
C5' "H5''" T3P sing 304 n n 
C4' O4' T3P sing 305 n n 
C4' C3' T3P sing 306 n n 
C4' H4' T3P sing 307 n n 
O4' C1' T3P sing 308 n n 
C3' O3' T3P sing 309 n n 
C3' C2' T3P sing 310 n n 
C3' H3' T3P sing 311 n n 
C2' C1' T3P sing 312 n n 
C2' H2' T3P sing 313 n n 
C2' "H2''" T3P sing 314 n n 
C1' N1 T3P sing 315 n n 
C1' H1' T3P sing 316 n n 
N1 C2 T3P sing 317 n n 
N1 C6 T3P sing 318 n n 
C2 O2 T3P doub 319 n n 
C2 N3 T3P sing 320 n n 
N3 C4 T3P sing 321 n n 
N3 H3 T3P sing 322 n n 
C4 O4 T3P doub 323 n n 
C4 C5 T3P sing 324 n n 
C5 C5M T3P sing 325 n n 
C5 C6 T3P doub 326 n n 
C5M H51 T3P sing 327 n n 
C5M H52 T3P sing 328 n n 
C5M H53 T3P sing 329 n n 
C6 H6 T3P sing 330 n n 
#
_atom_sites.entry_id                     1CY6 
_atom_sites.fract_transf_matrix[1][1]    0.015473 
_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]    0.012389 
_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]    0.006967 
_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 PO4 A 1 1001 1 PO4 PO4 . 
C 2 PO4 A 1 1002 2 PO4 PO4 . 
D 2 PO4 A 1 1003 3 PO4 PO4 . 
E 3 T3P A 1 600 600 T3P T3P . 
F 4 HOH A 1 1004 1 HOH HOH . 
F 4 HOH A 2 1005 2 HOH HOH . 
F 4 HOH A 3 1006 3 HOH HOH . 
F 4 HOH A 4 1007 4 HOH HOH . 
F 4 HOH A 5 1008 5 HOH HOH . 
F 4 HOH A 6 1009 6 HOH HOH . 
F 4 HOH A 7 1010 7 HOH HOH . 
F 4 HOH A 8 1011 8 HOH HOH . 
F 4 HOH A 9 1012 9 HOH HOH . 
F 4 HOH A 10 1013 10 HOH HOH . 
F 4 HOH A 11 1014 11 HOH HOH . 
F 4 HOH A 12 1015 12 HOH HOH . 
F 4 HOH A 13 1016 13 HOH HOH . 
F 4 HOH A 14 1017 14 HOH HOH . 
F 4 HOH A 15 1018 15 HOH HOH . 
F 4 HOH A 16 1019 16 HOH HOH . 
F 4 HOH A 17 1020 17 HOH HOH . 
F 4 HOH A 18 1021 18 HOH HOH . 
F 4 HOH A 19 1022 19 HOH HOH . 
F 4 HOH A 20 1023 20 HOH HOH . 
F 4 HOH A 21 1024 21 HOH HOH . 
F 4 HOH A 22 1025 22 HOH HOH . 
F 4 HOH A 23 1026 23 HOH HOH . 
F 4 HOH A 24 1027 24 HOH HOH . 
F 4 HOH A 25 1028 25 HOH HOH . 
F 4 HOH A 26 1029 26 HOH HOH . 
F 4 HOH A 27 1030 27 HOH HOH . 
F 4 HOH A 28 1031 28 HOH HOH . 
F 4 HOH A 29 1032 29 HOH HOH . 
F 4 HOH A 30 1033 30 HOH HOH . 
F 4 HOH A 31 1034 31 HOH HOH . 
F 4 HOH A 32 1035 32 HOH HOH . 
F 4 HOH A 33 1036 33 HOH HOH . 
F 4 HOH A 34 1037 34 HOH HOH . 
F 4 HOH A 35 1038 35 HOH HOH . 
F 4 HOH A 36 1039 36 HOH HOH . 
F 4 HOH A 37 1040 37 HOH HOH . 
F 4 HOH A 38 1041 38 HOH HOH . 
F 4 HOH A 39 1042 39 HOH HOH . 
F 4 HOH A 40 1043 40 HOH HOH . 
F 4 HOH A 41 1044 41 HOH HOH . 
F 4 HOH A 42 1045 42 HOH HOH . 
F 4 HOH A 43 1046 43 HOH HOH . 
F 4 HOH A 44 1047 44 HOH HOH . 
F 4 HOH A 45 1048 45 HOH HOH . 
F 4 HOH A 46 1049 46 HOH HOH . 
F 4 HOH A 47 1050 47 HOH HOH . 
F 4 HOH A 48 1051 48 HOH HOH . 
F 4 HOH A 49 1052 49 HOH HOH . 
F 4 HOH A 50 1053 50 HOH HOH . 
F 4 HOH A 51 1054 51 HOH HOH . 
F 4 HOH A 52 1055 52 HOH HOH . 
F 4 HOH A 53 1056 53 HOH HOH . 
F 4 HOH A 54 1057 54 HOH HOH . 
F 4 HOH A 55 1058 55 HOH HOH . 
F 4 HOH A 56 1059 56 HOH HOH . 
F 4 HOH A 57 1060 57 HOH HOH . 
F 4 HOH A 58 1061 58 HOH HOH . 
F 4 HOH A 59 1062 59 HOH HOH . 
F 4 HOH A 60 1063 60 HOH HOH . 
F 4 HOH A 61 1064 61 HOH HOH . 
F 4 HOH A 62 1065 62 HOH HOH . 
F 4 HOH A 63 1066 63 HOH HOH . 
F 4 HOH A 64 1067 64 HOH HOH . 
F 4 HOH A 65 1068 65 HOH HOH . 
F 4 HOH A 66 1069 66 HOH HOH . 
F 4 HOH A 67 1070 67 HOH HOH . 
F 4 HOH A 68 1071 68 HOH HOH . 
F 4 HOH A 69 1072 69 HOH HOH . 
F 4 HOH A 70 1073 70 HOH HOH . 
F 4 HOH A 71 1074 71 HOH HOH . 
F 4 HOH A 72 1075 72 HOH HOH . 
F 4 HOH A 73 1076 73 HOH HOH . 
F 4 HOH A 74 1077 74 HOH HOH . 
F 4 HOH A 75 1078 75 HOH HOH . 
F 4 HOH A 76 1079 76 HOH HOH . 
F 4 HOH A 77 1080 77 HOH HOH . 
F 4 HOH A 78 1081 78 HOH HOH . 
F 4 HOH A 79 1082 79 HOH HOH . 
F 4 HOH A 80 1083 80 HOH HOH . 
F 4 HOH A 81 1084 81 HOH HOH . 
F 4 HOH A 82 1085 82 HOH HOH . 
F 4 HOH A 83 1086 83 HOH HOH . 
F 4 HOH A 84 1087 84 HOH HOH . 
F 4 HOH A 85 1088 85 HOH HOH . 
F 4 HOH A 86 1089 86 HOH HOH . 
F 4 HOH A 87 1090 87 HOH HOH . 
F 4 HOH A 88 1091 88 HOH HOH . 
F 4 HOH A 89 1092 89 HOH HOH . 
F 4 HOH A 90 1093 90 HOH HOH . 
F 4 HOH A 91 1094 91 HOH HOH . 
F 4 HOH A 92 1095 92 HOH HOH . 
F 4 HOH A 93 1096 93 HOH HOH . 
F 4 HOH A 94 1097 94 HOH HOH . 
F 4 HOH A 95 1098 95 HOH HOH . 
F 4 HOH A 96 1099 96 HOH HOH . 
F 4 HOH A 97 1100 97 HOH HOH . 
F 4 HOH A 98 1101 98 HOH HOH . 
F 4 HOH A 99 1102 99 HOH HOH . 
F 4 HOH A 100 1103 100 HOH HOH . 
F 4 HOH A 101 1104 101 HOH HOH . 
F 4 HOH A 102 1105 102 HOH HOH . 
F 4 HOH A 103 1106 103 HOH HOH . 
F 4 HOH A 104 1107 104 HOH HOH . 
F 4 HOH A 105 1108 105 HOH HOH . 
F 4 HOH A 106 1109 106 HOH HOH . 
F 4 HOH A 107 1110 107 HOH HOH . 
F 4 HOH A 108 1111 108 HOH HOH . 
F 4 HOH A 109 1112 109 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 P P T3P . . . E 3 38.075 17.632 43.872 0.6 46.11 ? P T3P 600 A 1 
HETATM 2 O OP1 T3P . . . E 3 38.708 16.569 43.081 0.6 46.32 ? OP1 T3P 600 A 1 
HETATM 3 O OP2 T3P . . . E 3 36.731 17.637 44.465 0.6 46.05 ? OP2 T3P 600 A 1 
HETATM 4 O OP3 T3P . . . E 3 39.095 17.959 45.049 0.6 45.8 ? OP3 T3P 600 A 1 
HETATM 5 O O5' T3P . . . E 3 38.196 23.394 41.55 0.6 52.42 ? O5' T3P 600 A 1 
HETATM 6 C C5' T3P . . . E 3 38.397 22.457 42.587 0.6 53.1 ? C5' T3P 600 A 1 
HETATM 7 C C4' T3P . . . E 3 38.658 21.105 41.952 0.6 52.87 ? C4' T3P 600 A 1 
HETATM 8 O O4' T3P . . . E 3 39.839 21.166 41.126 0.6 54.13 ? O4' T3P 600 A 1 
HETATM 9 C C3' T3P . . . E 3 38.895 20.05 43.014 0.6 52.24 ? C3' T3P 600 A 1 
HETATM 10 O O3' T3P . . . E 3 38.088 18.871 42.814 0.6 49.11 ? O3' T3P 600 A 1 
HETATM 11 C C2' T3P . . . E 3 40.359 19.717 42.97 0.6 52.68 ? C2' T3P 600 A 1 
HETATM 12 C C1' T3P . . . E 3 40.798 20.214 41.598 0.6 53.5 ? C1' T3P 600 A 1 
HETATM 13 N N1 T3P . . . E 3 42.182 20.76 41.774 0.6 53.25 ? N1 T3P 600 A 1 
HETATM 14 C C2 T3P . . . E 3 43.184 20.221 40.929 0.6 53.27 ? C2 T3P 600 A 1 
HETATM 15 O O2 T3P . . . E 3 42.996 19.352 40.075 0.6 53.01 ? O2 T3P 600 A 1 
HETATM 16 N N3 T3P . . . E 3 44.452 20.72 41.097 0.6 52.95 ? N3 T3P 600 A 1 
HETATM 17 C C4 T3P . . . E 3 44.831 21.69 42.005 0.6 52.2 ? C4 T3P 600 A 1 
HETATM 18 O O4 T3P . . . E 3 46.01 22.018 42.021 0.6 52.6 ? O4 T3P 600 A 1 
HETATM 19 C C5 T3P . . . E 3 43.772 22.228 42.865 0.6 52.11 ? C5 T3P 600 A 1 
HETATM 20 C C5M T3P . . . E 3 44.11 23.313 43.91 0.6 50.63 ? C5M T3P 600 A 1 
HETATM 21 C C6 T3P . . . E 3 42.499 21.759 42.728 0.6 51.9 ? C6 T3P 600 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           21 
#