data_2Q7T
#
_model_server_result.job_id            7v3GFmFNoEPY_e6fmvKKKA 
_model_server_result.datetime_utc      '2024-12-26 23:46:26' 
_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          2q7t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":2001}' 
#
_entry.id    2Q7T 
#
_exptl.entry_id    2Q7T 
_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-5'-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            2Q7T 
_cell.length_a            44.888 
_cell.length_b            88.259 
_cell.length_c            127.293 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Q7T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,F 1 1 
B,D,E,G 2 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 
#
_struct_conn.conn_type_id                   metalc 
_struct_conn.details                        ? 
_struct_conn.id                             metalc1 
_struct_conn.ptnr1_label_asym_id            B 
_struct_conn.ptnr1_label_atom_id            NE2 
_struct_conn.ptnr1_label_comp_id            HIS 
_struct_conn.ptnr1_label_seq_id             159 
_struct_conn.ptnr1_auth_asym_id             B 
_struct_conn.ptnr1_auth_comp_id             HIS 
_struct_conn.ptnr1_auth_seq_id              1159 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            D 
_struct_conn.ptnr2_label_atom_id            MG 
_struct_conn.ptnr2_label_comp_id            MG 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             B 
_struct_conn.ptnr2_auth_comp_id             MG 
_struct_conn.ptnr2_auth_seq_id              5002 
_struct_conn.ptnr2_symmetry                 1_555 
_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                2.483 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C10 H15 N2 O8 P' 
_chem_comp.formula_weight    322.208 
_chem_comp.id                TMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-5'-PHOSPHATE" 
_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
P O1P TMP doub 293 n n 
P O2P TMP sing 294 n n 
P O3P TMP sing 295 n n 
P O5' TMP sing 296 n n 
O2P HOP2 TMP sing 297 n n 
O3P HOP3 TMP sing 298 n n 
O5' C5' TMP sing 299 n n 
C5' C4' TMP sing 300 n n 
C5' "H5'1" TMP sing 301 n n 
C5' "H5'2" TMP sing 302 n n 
C4' O4' TMP sing 303 n n 
C4' C3' TMP sing 304 n n 
C4' H4' TMP sing 305 n n 
O4' C1' TMP sing 306 n n 
C3' O3' TMP sing 307 n n 
C3' C2' TMP sing 308 n n 
C3' H3' TMP sing 309 n n 
O3' HO3' TMP sing 310 n n 
C2' C1' TMP sing 311 n n 
C2' "H2'1" TMP sing 312 n n 
C2' "H2'2" TMP sing 313 n n 
C1' N1 TMP sing 314 n n 
C1' H1' TMP sing 315 n n 
N1 C2 TMP sing 316 n n 
N1 C6 TMP sing 317 n n 
C2 O2 TMP doub 318 n n 
C2 N3 TMP sing 319 n n 
N3 C4 TMP sing 320 n n 
N3 HN3 TMP sing 321 n n 
C4 O4 TMP doub 322 n n 
C4 C5 TMP sing 323 n n 
C5 C5M TMP sing 324 n n 
C5 C6 TMP doub 325 n n 
C5M H51 TMP sing 326 n n 
C5M H52 TMP sing 327 n n 
C5M H53 TMP sing 328 n n 
C6 H6 TMP sing 329 n n 
#
_atom_sites.entry_id                     2Q7T 
_atom_sites.fract_transf_matrix[1][1]    0.022278 
_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]    0.01133 
_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]    0.007856 
_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
C 2 MG A 1 5001 5001 MG MG2 . 
D 2 MG B 1 5002 5002 MG MG2 . 
E 3 TMP B 1 2001 2001 TMP THY . 
F 4 HOH A 1 6006 6006 HOH HOH . 
F 4 HOH A 2 6008 6008 HOH HOH . 
F 4 HOH A 3 6009 6009 HOH HOH . 
F 4 HOH A 4 6010 6010 HOH HOH . 
F 4 HOH A 5 6012 6012 HOH HOH . 
F 4 HOH A 6 6013 6013 HOH HOH . 
F 4 HOH A 7 6014 6014 HOH HOH . 
F 4 HOH A 8 6015 6015 HOH HOH . 
F 4 HOH A 9 6019 6019 HOH HOH . 
F 4 HOH A 10 6021 6021 HOH HOH . 
F 4 HOH A 11 6022 6022 HOH HOH . 
F 4 HOH A 12 6023 6023 HOH HOH . 
F 4 HOH A 13 6024 6024 HOH HOH . 
F 4 HOH A 14 6025 6025 HOH HOH . 
F 4 HOH A 15 6027 6027 HOH HOH . 
F 4 HOH A 16 6028 6028 HOH HOH . 
F 4 HOH A 17 6029 6029 HOH HOH . 
F 4 HOH A 18 6030 6030 HOH HOH . 
F 4 HOH A 19 6032 6032 HOH HOH . 
F 4 HOH A 20 6033 6033 HOH HOH . 
F 4 HOH A 21 6034 6034 HOH HOH . 
F 4 HOH A 22 6037 6037 HOH HOH . 
F 4 HOH A 23 6038 6038 HOH HOH . 
F 4 HOH A 24 6040 6040 HOH HOH . 
F 4 HOH A 25 6042 6042 HOH HOH . 
F 4 HOH A 26 6043 6043 HOH HOH . 
F 4 HOH A 27 6045 6045 HOH HOH . 
F 4 HOH A 28 6046 6046 HOH HOH . 
F 4 HOH A 29 6047 6047 HOH HOH . 
F 4 HOH A 30 6048 6048 HOH HOH . 
F 4 HOH A 31 6051 6051 HOH HOH . 
F 4 HOH A 32 6052 6052 HOH HOH . 
F 4 HOH A 33 6056 6056 HOH HOH . 
F 4 HOH A 34 6061 6061 HOH HOH . 
F 4 HOH A 35 6062 6062 HOH HOH . 
F 4 HOH A 36 6063 6063 HOH HOH . 
F 4 HOH A 37 6067 6067 HOH HOH . 
F 4 HOH A 38 6068 6068 HOH HOH . 
F 4 HOH A 39 6071 6071 HOH HOH . 
F 4 HOH A 40 6073 6073 HOH HOH . 
F 4 HOH A 41 6074 6074 HOH HOH . 
F 4 HOH A 42 6075 6075 HOH HOH . 
F 4 HOH A 43 6081 6081 HOH HOH . 
F 4 HOH A 44 6085 6085 HOH HOH . 
F 4 HOH A 45 6086 6086 HOH HOH . 
F 4 HOH A 46 6087 6087 HOH HOH . 
F 4 HOH A 47 6088 6088 HOH HOH . 
F 4 HOH A 48 6092 6092 HOH HOH . 
F 4 HOH A 49 6093 6093 HOH HOH . 
F 4 HOH A 50 6094 6094 HOH HOH . 
F 4 HOH A 51 6095 6095 HOH HOH . 
F 4 HOH A 52 6096 6096 HOH HOH . 
F 4 HOH A 53 6103 6103 HOH HOH . 
F 4 HOH A 54 6104 6104 HOH HOH . 
F 4 HOH A 55 6106 6106 HOH HOH . 
F 4 HOH A 56 6111 6111 HOH HOH . 
F 4 HOH A 57 6113 6113 HOH HOH . 
F 4 HOH A 58 6115 6115 HOH HOH . 
F 4 HOH A 59 6116 6116 HOH HOH . 
F 4 HOH A 60 6118 6118 HOH HOH . 
F 4 HOH A 61 6119 6119 HOH HOH . 
F 4 HOH A 62 6120 6120 HOH HOH . 
F 4 HOH A 63 6121 6121 HOH HOH . 
F 4 HOH A 64 6123 6123 HOH HOH . 
F 4 HOH A 65 6124 6124 HOH HOH . 
F 4 HOH A 66 6127 6127 HOH HOH . 
F 4 HOH A 67 6128 6128 HOH HOH . 
F 4 HOH A 68 6129 6129 HOH HOH . 
F 4 HOH A 69 6130 6130 HOH HOH . 
F 4 HOH A 70 6132 6132 HOH HOH . 
F 4 HOH A 71 6133 6133 HOH HOH . 
F 4 HOH A 72 6134 6134 HOH HOH . 
F 4 HOH A 73 6135 6135 HOH HOH . 
F 4 HOH A 74 6136 6136 HOH HOH . 
F 4 HOH A 75 6137 6137 HOH HOH . 
F 4 HOH A 76 6138 6138 HOH HOH . 
F 4 HOH A 77 6139 6139 HOH HOH . 
F 4 HOH A 78 6140 6140 HOH HOH . 
F 4 HOH A 79 6142 6142 HOH HOH . 
F 4 HOH A 80 6143 6143 HOH HOH . 
F 4 HOH A 81 6144 6144 HOH HOH . 
F 4 HOH A 82 6145 6145 HOH HOH . 
F 4 HOH A 83 6146 6146 HOH HOH . 
F 4 HOH A 84 6151 6151 HOH HOH . 
F 4 HOH A 85 6152 6152 HOH HOH . 
F 4 HOH A 86 6154 6154 HOH HOH . 
F 4 HOH A 87 6155 6155 HOH HOH . 
F 4 HOH A 88 6156 6156 HOH HOH . 
F 4 HOH A 89 6158 6158 HOH HOH . 
G 4 HOH B 1 6002 6002 HOH HOH . 
G 4 HOH B 2 6004 6004 HOH HOH . 
G 4 HOH B 3 6005 6005 HOH HOH . 
G 4 HOH B 4 6007 6007 HOH HOH . 
G 4 HOH B 5 6011 6011 HOH HOH . 
G 4 HOH B 6 6016 6016 HOH HOH . 
G 4 HOH B 7 6017 6017 HOH HOH . 
G 4 HOH B 8 6018 6018 HOH HOH . 
G 4 HOH B 9 6020 6020 HOH HOH . 
G 4 HOH B 10 6026 6026 HOH HOH . 
G 4 HOH B 11 6031 6031 HOH HOH . 
G 4 HOH B 12 6035 6035 HOH HOH . 
G 4 HOH B 13 6036 6036 HOH HOH . 
G 4 HOH B 14 6039 6039 HOH HOH . 
G 4 HOH B 15 6041 6041 HOH HOH . 
G 4 HOH B 16 6044 6044 HOH HOH . 
G 4 HOH B 17 6049 6049 HOH HOH . 
G 4 HOH B 18 6050 6050 HOH HOH . 
G 4 HOH B 19 6053 6053 HOH HOH . 
G 4 HOH B 20 6054 6054 HOH HOH . 
G 4 HOH B 21 6055 6055 HOH HOH . 
G 4 HOH B 22 6057 6057 HOH HOH . 
G 4 HOH B 23 6058 6058 HOH HOH . 
G 4 HOH B 24 6059 6059 HOH HOH . 
G 4 HOH B 25 6060 6060 HOH HOH . 
G 4 HOH B 26 6064 6064 HOH HOH . 
G 4 HOH B 27 6065 6065 HOH HOH . 
G 4 HOH B 28 6066 6066 HOH HOH . 
G 4 HOH B 29 6069 6069 HOH HOH . 
G 4 HOH B 30 6070 6070 HOH HOH . 
G 4 HOH B 31 6072 6072 HOH HOH . 
G 4 HOH B 32 6076 6076 HOH HOH . 
G 4 HOH B 33 6077 6077 HOH HOH . 
G 4 HOH B 34 6078 6078 HOH HOH . 
G 4 HOH B 35 6079 6079 HOH HOH . 
G 4 HOH B 36 6080 6080 HOH HOH . 
G 4 HOH B 37 6082 6082 HOH HOH . 
G 4 HOH B 38 6083 6083 HOH HOH . 
G 4 HOH B 39 6084 6084 HOH HOH . 
G 4 HOH B 40 6089 6089 HOH HOH . 
G 4 HOH B 41 6090 6090 HOH HOH . 
G 4 HOH B 42 6091 6091 HOH HOH . 
G 4 HOH B 43 6097 6097 HOH HOH . 
G 4 HOH B 44 6098 6098 HOH HOH . 
G 4 HOH B 45 6099 6099 HOH HOH . 
G 4 HOH B 46 6100 6100 HOH HOH . 
G 4 HOH B 47 6101 6101 HOH HOH . 
G 4 HOH B 48 6102 6102 HOH HOH . 
G 4 HOH B 49 6105 6105 HOH HOH . 
G 4 HOH B 50 6107 6107 HOH HOH . 
G 4 HOH B 51 6108 6108 HOH HOH . 
G 4 HOH B 52 6109 6109 HOH HOH . 
G 4 HOH B 53 6110 6110 HOH HOH . 
G 4 HOH B 54 6112 6112 HOH HOH . 
G 4 HOH B 55 6114 6114 HOH HOH . 
G 4 HOH B 56 6117 6117 HOH HOH . 
G 4 HOH B 57 6122 6122 HOH HOH . 
G 4 HOH B 58 6125 6125 HOH HOH . 
G 4 HOH B 59 6126 6126 HOH HOH . 
G 4 HOH B 60 6131 6131 HOH HOH . 
G 4 HOH B 61 6141 6141 HOH HOH . 
G 4 HOH B 62 6147 6147 HOH HOH . 
G 4 HOH B 63 6148 6148 HOH HOH . 
G 4 HOH B 64 6149 6149 HOH HOH . 
G 4 HOH B 65 6150 6150 HOH HOH . 
G 4 HOH B 66 6153 6153 HOH HOH . 
G 4 HOH B 67 6157 6157 HOH HOH . 
G 4 HOH B 68 6159 6159 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 TMP . . . E 3 -7.032 34.507 40.085 1 107.94 ? P TMP 2001 B 1 
HETATM 2 O O1P TMP . . . E 3 -6.332 33.201 39.962 1 107.2 ? O1P TMP 2001 B 1 
HETATM 3 O O2P TMP . . . E 3 -7.368 35.288 38.862 1 106.81 ? O2P TMP 2001 B 1 
HETATM 4 O O5' TMP . . . E 3 -6.191 35.436 41.07 1 106.16 ? O5' TMP 2001 B 1 
HETATM 5 C C5' TMP . . . E 3 -4.912 35.953 40.709 1 104.28 ? C5' TMP 2001 B 1 
HETATM 6 C C4' TMP . . . E 3 -4.736 37.348 41.268 1 103.29 ? C4' TMP 2001 B 1 
HETATM 7 O O4' TMP . . . E 3 -5.32 38.368 40.408 1 103.02 ? O4' TMP 2001 B 1 
HETATM 8 C C3' TMP . . . E 3 -5.02 37.784 42.71 1 102.84 ? C3' TMP 2001 B 1 
HETATM 9 O O3' TMP . . . E 3 -3.853 37.725 43.525 1 101.51 ? O3' TMP 2001 B 1 
HETATM 10 C C2' TMP . . . E 3 -5.511 39.223 42.572 1 102.51 ? C2' TMP 2001 B 1 
HETATM 11 C C1' TMP . . . E 3 -6.151 39.204 41.186 1 102.34 ? C1' TMP 2001 B 1 
HETATM 12 N N1 TMP . . . E 3 -7.631 39.175 41.025 1 101.27 ? N1 TMP 2001 B 1 
HETATM 13 C C2 TMP . . . E 3 -8.288 40.231 40.412 1 100.95 ? C2 TMP 2001 B 1 
HETATM 14 O O2 TMP . . . E 3 -7.719 41.231 39.993 1 101.15 ? O2 TMP 2001 B 1 
HETATM 15 N N3 TMP . . . E 3 -9.65 40.078 40.317 1 100.94 ? N3 TMP 2001 B 1 
HETATM 16 C C4 TMP . . . E 3 -10.41 39.017 40.775 1 100.89 ? C4 TMP 2001 B 1 
HETATM 17 O O4 TMP . . . E 3 -11.635 39.074 40.714 1 101.32 ? O4 TMP 2001 B 1 
HETATM 18 C C5 TMP . . . E 3 -9.66 37.95 41.404 1 100.62 ? C5 TMP 2001 B 1 
HETATM 19 C C5M TMP . . . E 3 -10.384 36.726 41.873 1 99.31 ? C5M TMP 2001 B 1 
HETATM 20 C C6 TMP . . . E 3 -8.33 38.084 41.498 1 100.66 ? C6 TMP 2001 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           341 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           20 
#