data_2VF0 # _model_server_result.job_id YX8r99yiYnzI32cjmNZxIw _model_server_result.datetime_utc '2024-12-22 11:37:28' _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 2vf0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1265}' # _entry.id 2VF0 # _exptl.entry_id 2VF0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 355.195 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE" _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 2VF0 _cell.length_a 127.16 _cell.length_b 127.16 _cell.length_c 67.95 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VF0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PQS _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,F,G,H,I _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 A C CXM 1 A CXM 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale2 A SG CYS 146 A CYS 146 1_555 C C6 NDU . A NDU 1265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? covale ? covale3 B C CXM 1 B CXM 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale4 B SG CYS 146 B CYS 146 1_555 E C6 NDU . B NDU 1265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? # _chem_comp.formula 'C9 H14 N3 O10 P' _chem_comp.formula_weight 355.195 _chem_comp.id NDU _chem_comp.mon_nstd_flag n _chem_comp.name "2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _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 OP1 NDU doub 324 n n P OP2 NDU sing 325 n n P OP3 NDU sing 326 n n P O5' NDU sing 327 n n O5' C5' NDU sing 328 n n C5' C4' NDU sing 329 n n C4' C3' NDU sing 330 n n C4' O4' NDU sing 331 n n C3' O3' NDU sing 332 n n C3' C2' NDU sing 333 n n C2' C1' NDU sing 334 n n C1' O4' NDU sing 335 n n C1' N1 NDU sing 336 n n N1 C2 NDU sing 337 n n N1 C6 NDU sing 338 n n C2 O2 NDU doub 339 n n C2 N3 NDU sing 340 n n N3 C4 NDU sing 341 n n C4 O4 NDU doub 342 n n C4 C5 NDU sing 343 n n C5 C6 NDU sing 344 n n C5 N5 NDU sing 345 n n N5 O51 NDU sing 346 n n N5 O52 NDU doub 347 n n OP2 HP2 NDU sing 348 n n OP3 HP3 NDU sing 349 n n C5' H51' NDU sing 350 n n C5' H52' NDU sing 351 n n C4' H4' NDU sing 352 n n C3' H3' NDU sing 353 n n O3' HA NDU sing 354 n n C2' H21' NDU sing 355 n n C2' H22' NDU sing 356 n n C1' H1' NDU sing 357 n n C6 H611 NDU sing 358 n n C6 H612 NDU sing 359 n n N3 H3 NDU sing 360 n n C5 H5 NDU sing 361 n n # _atom_sites.entry_id 2VF0 _atom_sites.fract_transf_matrix[1][1] 0.007864 _atom_sites.fract_transf_matrix[1][2] 0.00454 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009081 _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] 0.014717 _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 NDU A 1 1265 1265 NDU NDU . D 3 F89 A 1 1266 1266 F89 F89 . E 2 NDU B 1 1265 1265 NDU NDU . F 3 F89 B 1 1266 1266 F89 F89 . G 4 SO4 B 1 1268 1268 SO4 SO4 . H 5 HOH A 1 2001 2001 HOH HOH . H 5 HOH A 2 2002 2002 HOH HOH . H 5 HOH A 3 2003 2003 HOH HOH . H 5 HOH A 4 2004 2004 HOH HOH . H 5 HOH A 5 2005 2005 HOH HOH . H 5 HOH A 6 2006 2006 HOH HOH . H 5 HOH A 7 2007 2007 HOH HOH . H 5 HOH A 8 2008 2008 HOH HOH . H 5 HOH A 9 2009 2009 HOH HOH . H 5 HOH A 10 2010 2010 HOH HOH . H 5 HOH A 11 2011 2011 HOH HOH . H 5 HOH A 12 2012 2012 HOH HOH . H 5 HOH A 13 2013 2013 HOH HOH . I 5 HOH B 1 2001 2001 HOH HOH . I 5 HOH B 2 2002 2002 HOH HOH . I 5 HOH B 3 2003 2003 HOH HOH . I 5 HOH B 4 2004 2004 HOH HOH . I 5 HOH B 5 2005 2005 HOH HOH . I 5 HOH B 6 2006 2006 HOH HOH . I 5 HOH B 7 2007 2007 HOH HOH . I 5 HOH B 8 2008 2008 HOH HOH . I 5 HOH B 9 2009 2009 HOH HOH . I 5 HOH B 10 2010 2010 HOH HOH . I 5 HOH B 11 2011 2011 HOH HOH . I 5 HOH B 12 2012 2012 HOH HOH . I 5 HOH B 13 2013 2013 HOH HOH . I 5 HOH B 14 2014 2014 HOH HOH . I 5 HOH B 15 2015 2015 HOH HOH . I 5 HOH B 16 2016 2016 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 NDU . . . E 2 46.374 27.94 24.414 1 42.04 ? P NDU 1265 B 1 HETATM 2 O OP1 NDU . . . E 2 47.273 26.786 24.744 1 42.63 ? OP1 NDU 1265 B 1 HETATM 3 O OP2 NDU . . . E 2 45.286 28.064 25.416 1 43.27 ? OP2 NDU 1265 B 1 HETATM 4 O OP3 NDU . . . E 2 45.834 27.901 23.018 1 42.42 ? OP3 NDU 1265 B 1 HETATM 5 O O5' NDU . . . E 2 47.092 29.348 24.55 1 41.99 ? O5' NDU 1265 B 1 HETATM 6 C C5' NDU . . . E 2 46.756 30.593 23.949 1 41.51 ? C5' NDU 1265 B 1 HETATM 7 C C4' NDU . . . E 2 46.862 31.871 24.787 1 39.46 ? C4' NDU 1265 B 1 HETATM 8 C C3' NDU . . . E 2 46.444 32.017 26.244 1 38.09 ? C3' NDU 1265 B 1 HETATM 9 O O3' NDU . . . E 2 47.476 32.585 27.024 1 37.48 ? O3' NDU 1265 B 1 HETATM 10 C C2' NDU . . . E 2 45.124 32.794 26.223 1 36.5 ? C2' NDU 1265 B 1 HETATM 11 C C1' NDU . . . E 2 45.28 33.69 24.985 1 35.16 ? C1' NDU 1265 B 1 HETATM 12 O O4' NDU . . . E 2 46.169 32.967 24.12 1 37.69 ? O4' NDU 1265 B 1 HETATM 13 N N1 NDU . . . E 2 43.955 34.234 24.491 1 32.38 ? N1 NDU 1265 B 1 HETATM 14 C C2 NDU . . . E 2 43.169 35.304 25.03 1 30.98 ? C2 NDU 1265 B 1 HETATM 15 O O2 NDU . . . E 2 43.205 35.571 26.19 1 30.06 ? O2 NDU 1265 B 1 HETATM 16 N N3 NDU . . . E 2 42.343 36.028 24.164 1 30.62 ? N3 NDU 1265 B 1 HETATM 17 C C4 NDU . . . E 2 42.103 35.787 22.795 1 31.79 ? C4 NDU 1265 B 1 HETATM 18 O O4 NDU . . . E 2 41.373 36.525 22.154 1 31.53 ? O4 NDU 1265 B 1 HETATM 19 C C5 NDU . . . E 2 42.833 34.529 22.123 1 32.8 ? C5 NDU 1265 B 1 HETATM 20 C C6 NDU . . . E 2 43.648 33.519 23.078 1 30.64 ? C6 NDU 1265 B 1 HETATM 21 N N5 NDU . . . E 2 42.846 34.247 20.754 1 35.45 ? N5 NDU 1265 B 1 HETATM 22 O O51 NDU . . . E 2 42.012 34.725 19.96 1 37.15 ? O51 NDU 1265 B 1 HETATM 23 O O52 NDU . . . E 2 43.647 33.503 20.147 1 36.34 ? O52 NDU 1265 B 1 # _model_server_stats.io_time_ms 105 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 23 #