data_4UXI
#
_model_server_result.job_id            66WzqlYygW18GgAcKU6qXw 
_model_server_result.datetime_utc      '2024-11-24 21:34:19' 
_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          4uxi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1183}' 
#
_entry.id    4UXI 
#
_exptl.entry_id    4UXI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              242.229 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            THYMIDINE 
_entity.pdbx_number_of_molecules    2 
_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            4UXI 
_cell.length_a            121.149 
_cell.length_b            121.149 
_cell.length_c            116.22 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4UXI 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,F,G,H,I,J 
_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' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -60.5745 104.918112 -19.37 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 G 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
metalc ? metalc1 A SG CYS 141 A CYS 140 1_555 E ZN ZN . A ZN 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? 
metalc ? metalc2 A SG CYS 144 A CYS 143 1_555 E ZN ZN . A ZN 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? 
metalc ? metalc3 A SG CYS 174 A CYS 173 1_555 E ZN ZN . A ZN 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc4 A SG CYS 177 A CYS 176 1_555 E ZN ZN . A ZN 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc5 B SG CYS 141 B CYS 140 1_555 H ZN ZN . B ZN 1183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc6 B SG CYS 144 B CYS 143 1_555 H ZN ZN . B ZN 1183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc7 B SG CYS 174 B CYS 173 1_555 H ZN ZN . B ZN 1183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc8 B SG CYS 177 B CYS 176 1_555 H ZN ZN . B ZN 1183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
#
_chem_comp.formula           'C10 H14 N2 O5' 
_chem_comp.formula_weight    242.229 
_chem_comp.id                THM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              THYMIDINE 
_chem_comp.type              'dna oh 5 prime terminus' 
_chem_comp.pdbx_synonyms     "DEOXYTHYMIDINE;2'-DEOXYTHYMIDINE" 
#
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
O5' C5' THM sing 294 n n 
O5' HO5' THM sing 295 n n 
C5' C4' THM sing 296 n n 
C5' "H5'1" THM sing 297 n n 
C5' "H5'2" THM sing 298 n n 
C4' O4' THM sing 299 n n 
C4' C3' THM sing 300 n n 
C4' H4' THM sing 301 n n 
O4' C1' THM sing 302 n n 
C3' O3' THM sing 303 n n 
C3' C2' THM sing 304 n n 
C3' H3' THM sing 305 n n 
O3' HO3' THM sing 306 n n 
C2' C1' THM sing 307 n n 
C2' "H2'1" THM sing 308 n n 
C2' "H2'2" THM sing 309 n n 
C1' N1 THM sing 310 n n 
C1' H1' THM sing 311 n n 
N1 C2 THM sing 312 n n 
N1 C6 THM sing 313 n n 
C2 O2 THM doub 314 n n 
C2 N3 THM sing 315 n n 
N3 C4 THM sing 316 n n 
N3 HN3 THM sing 317 n n 
C4 O4 THM doub 318 n n 
C4 C5 THM sing 319 n n 
C5 C5M THM sing 320 n n 
C5 C6 THM doub 321 n n 
C5M HM51 THM sing 322 n n 
C5M HM52 THM sing 323 n n 
C5M HM53 THM sing 324 n n 
C6 H6 THM sing 325 n n 
#
_atom_sites.entry_id                     4UXI 
_atom_sites.fract_transf_matrix[1][1]    0.008254 
_atom_sites.fract_transf_matrix[1][2]    0.004766 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009531 
_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]    0.008604 
_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 PO4 A 1 1182 1182 PO4 PO4 . 
D 3 THM A 1 1183 1183 THM THM . 
E 4 ZN A 1 1184 1184 ZN ZN . 
F 2 PO4 B 1 1181 1181 PO4 PO4 . 
G 3 THM B 1 1182 1182 THM THM . 
H 4 ZN B 1 1183 1183 ZN ZN . 
I 5 HOH A 1 2001 2001 HOH HOH . 
I 5 HOH A 2 2002 2002 HOH HOH . 
I 5 HOH A 3 2003 2003 HOH HOH . 
I 5 HOH A 4 2004 2004 HOH HOH . 
I 5 HOH A 5 2005 2005 HOH HOH . 
I 5 HOH A 6 2006 2006 HOH HOH . 
I 5 HOH A 7 2007 2007 HOH HOH . 
I 5 HOH A 8 2008 2008 HOH HOH . 
I 5 HOH A 9 2009 2009 HOH HOH . 
I 5 HOH A 10 2010 2010 HOH HOH . 
J 5 HOH B 1 2001 2001 HOH HOH . 
J 5 HOH B 2 2002 2002 HOH HOH . 
J 5 HOH B 3 2003 2003 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 O O5' THM . . . D 3 -26.579 34.964 5.313 1 66.24 ? O5' THM 1183 A 1 
HETATM 2 C C5' THM . . . D 3 -27.824 34.592 5.912 1 61.37 ? C5' THM 1183 A 1 
HETATM 3 C C4' THM . . . D 3 -27.61 34.101 7.342 1 58.04 ? C4' THM 1183 A 1 
HETATM 4 O O4' THM . . . D 3 -28.361 34.913 8.254 1 53.94 ? O4' THM 1183 A 1 
HETATM 5 C C3' THM . . . D 3 -28.091 32.658 7.542 1 55.38 ? C3' THM 1183 A 1 
HETATM 6 O O3' THM . . . D 3 -27.026 31.802 7.964 1 51.41 ? O3' THM 1183 A 1 
HETATM 7 C C2' THM . . . D 3 -29.189 32.722 8.591 1 52.19 ? C2' THM 1183 A 1 
HETATM 8 C C1' THM . . . D 3 -28.923 34.054 9.263 1 51.14 ? C1' THM 1183 A 1 
HETATM 9 N N1 THM . . . D 3 -30.137 34.648 9.825 1 47.61 ? N1 THM 1183 A 1 
HETATM 10 C C2 THM . . . D 3 -30.288 34.694 11.232 1 52.57 ? C2 THM 1183 A 1 
HETATM 11 O O2 THM . . . D 3 -29.389 34.195 11.971 1 52.98 ? O2 THM 1183 A 1 
HETATM 12 N N3 THM . . . D 3 -31.389 35.248 11.781 1 49.73 ? N3 THM 1183 A 1 
HETATM 13 C C4 THM . . . D 3 -32.358 35.771 11.019 1 46.35 ? C4 THM 1183 A 1 
HETATM 14 O O4 THM . . . D 3 -33.379 36.292 11.52 1 45.53 ? O4 THM 1183 A 1 
HETATM 15 C C5 THM . . . D 3 -32.212 35.738 9.553 1 45.99 ? C5 THM 1183 A 1 
HETATM 16 C C5M THM . . . D 3 -33.289 36.338 8.672 1 47.48 ? C5M THM 1183 A 1 
HETATM 17 C C6 THM . . . D 3 -31.07 35.159 9.019 1 45.73 ? C6 THM 1183 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           17 
#