data_2YAZ # _model_server_result.job_id ITkG0Bnz9hau2Hw9SW3kmQ _model_server_result.datetime_utc '2024-11-29 09:18:06' _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 2yaz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1265}' # _entry.id 2YAZ # _exptl.entry_id 2YAZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 2YAZ _cell.length_a 109.11 _cell.length_b 109.11 _cell.length_c 309.311 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YAZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,E,F,G,H,I,P,Q 1 1 C,D,J,K,L,M,N,O,R,S 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 I N N ? 2 J N N ? 2 N 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 OE1 GLU 51 A GLU 48 1_555 G MG MG . A MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc2 A OE1 GLU 79 A GLU 76 1_555 G MG MG . A MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc3 A OE2 GLU 79 A GLU 76 1_555 G MG MG . A MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc4 A OD2 ASP 82 A ASP 79 1_555 G MG MG . A MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc5 C OD2 ASP 82 D ASP 79 1_555 K MG MG . D MG 1266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc6 D OE1 GLU 51 E GLU 48 1_555 O MG MG . E MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc7 D OE2 GLU 79 E GLU 76 1_555 O MG MG . E MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc8 N OP3 UMP . E UMP 1266 1_555 O MG MG . E MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 N1 C2 UMP sing 362 n n N1 C6 UMP sing 363 n n N1 C1' UMP sing 364 n n C2 N3 UMP sing 365 n n C2 O2 UMP doub 366 n n N3 C4 UMP sing 367 n n N3 HN3 UMP sing 368 n n C4 C5 UMP sing 369 n n C4 O4 UMP doub 370 n n C5 C6 UMP doub 371 n n C5 H5 UMP sing 372 n n C6 H6 UMP sing 373 n n C1' C2' UMP sing 374 n n C1' O4' UMP sing 375 n n C1' H1' UMP sing 376 n n C2' C3' UMP sing 377 n n C2' H2' UMP sing 378 n n C2' "H2''" UMP sing 379 n n C3' C4' UMP sing 380 n n C3' O3' UMP sing 381 n n C3' H3' UMP sing 382 n n C4' O4' UMP sing 383 n n C4' C5' UMP sing 384 n n C4' H4' UMP sing 385 n n O3' HO3' UMP sing 386 n n C5' O5' UMP sing 387 n n C5' H5' UMP sing 388 n n C5' "H5''" UMP sing 389 n n O5' P UMP sing 390 n n P OP1 UMP doub 391 n n P OP2 UMP sing 392 n n P OP3 UMP sing 393 n n OP2 HOP2 UMP sing 394 n n OP3 HOP3 UMP sing 395 n n # _atom_sites.entry_id 2YAZ _atom_sites.fract_transf_matrix[1][1] 0.009165 _atom_sites.fract_transf_matrix[1][2] 0.005291 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010583 _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] 0.003233 _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 E 2 UMP A 1 1265 1265 UMP UMP . F 3 SO4 A 1 1266 1266 SO4 SO4 . G 4 MG A 1 1267 1267 MG MG . H 3 SO4 A 1 1268 1268 SO4 SO4 . I 2 UMP B 1 1265 1265 UMP UMP . J 2 UMP D 1 1265 1265 UMP UMP . K 4 MG D 1 1266 1266 MG MG . L 3 SO4 D 1 1267 1267 SO4 SO4 . M 3 SO4 E 1 1265 1265 SO4 SO4 . N 2 UMP E 1 1266 1266 UMP UMP . O 4 MG E 1 1267 1267 MG MG . P 5 HOH A 1 2001 2001 HOH HOH . P 5 HOH A 2 2002 2002 HOH HOH . P 5 HOH A 3 2003 2003 HOH HOH . P 5 HOH A 4 2004 2004 HOH HOH . P 5 HOH A 5 2005 2005 HOH HOH . P 5 HOH A 6 2006 2006 HOH HOH . P 5 HOH A 7 2007 2007 HOH HOH . P 5 HOH A 8 2008 2008 HOH HOH . P 5 HOH A 9 2009 2009 HOH HOH . P 5 HOH A 10 2010 2010 HOH HOH . P 5 HOH A 11 2011 2011 HOH HOH . P 5 HOH A 12 2012 2012 HOH HOH . Q 5 HOH B 1 2001 2001 HOH HOH . Q 5 HOH B 2 2002 2002 HOH HOH . Q 5 HOH B 3 2003 2003 HOH HOH . Q 5 HOH B 4 2004 2004 HOH HOH . Q 5 HOH B 5 2005 2005 HOH HOH . Q 5 HOH B 6 2006 2006 HOH HOH . R 5 HOH D 1 2001 2001 HOH HOH . R 5 HOH D 2 2002 2002 HOH HOH . R 5 HOH D 3 2003 2003 HOH HOH . R 5 HOH D 4 2004 2004 HOH HOH . R 5 HOH D 5 2005 2005 HOH HOH . R 5 HOH D 6 2006 2006 HOH HOH . R 5 HOH D 7 2007 2007 HOH HOH . R 5 HOH D 8 2008 2008 HOH HOH . R 5 HOH D 9 2009 2009 HOH HOH . R 5 HOH D 10 2010 2010 HOH HOH . R 5 HOH D 11 2011 2011 HOH HOH . S 5 HOH E 1 2001 2001 HOH HOH . S 5 HOH E 2 2002 2002 HOH HOH . S 5 HOH E 3 2003 2003 HOH HOH . S 5 HOH E 4 2004 2004 HOH HOH . S 5 HOH E 5 2005 2005 HOH HOH . S 5 HOH E 6 2006 2006 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 N N1 UMP . . . I 2 -16.007 66.23 -16.917 1 36.81 ? N1 UMP 1265 B 1 HETATM 2 C C2 UMP . . . I 2 -16.13 67.533 -16.445 1 35.96 ? C2 UMP 1265 B 1 HETATM 3 N N3 UMP . . . I 2 -17.344 68.174 -16.447 1 33.45 ? N3 UMP 1265 B 1 HETATM 4 C C4 UMP . . . I 2 -18.481 67.547 -16.928 1 33.72 ? C4 UMP 1265 B 1 HETATM 5 C C5 UMP . . . I 2 -18.374 66.237 -17.403 1 31.59 ? C5 UMP 1265 B 1 HETATM 6 C C6 UMP . . . I 2 -17.126 65.583 -17.405 1 33.07 ? C6 UMP 1265 B 1 HETATM 7 O O2 UMP . . . I 2 -15.156 68.141 -16.012 1 50.55 ? O2 UMP 1265 B 1 HETATM 8 O O4 UMP . . . I 2 -19.568 68.145 -16.912 1 42.36 ? O4 UMP 1265 B 1 HETATM 9 C C1' UMP . . . I 2 -14.66 65.617 -16.904 1 31.95 ? C1' UMP 1265 B 1 HETATM 10 C C2' UMP . . . I 2 -14.169 65.289 -15.506 1 32.74 ? C2' UMP 1265 B 1 HETATM 11 C C3' UMP . . . I 2 -13.198 64.142 -15.723 1 38.13 ? C3' UMP 1265 B 1 HETATM 12 C C4' UMP . . . I 2 -13.464 63.669 -17.132 1 46.68 ? C4' UMP 1265 B 1 HETATM 13 O O3' UMP . . . I 2 -11.84 64.513 -15.634 1 46.44 ? O3' UMP 1265 B 1 HETATM 14 O O4' UMP . . . I 2 -14.552 64.422 -17.63 1 42.13 ? O4' UMP 1265 B 1 HETATM 15 C C5' UMP . . . I 2 -13.801 62.178 -17.071 1 53.14 ? C5' UMP 1265 B 1 HETATM 16 O O5' UMP . . . I 2 -14.226 61.742 -18.341 1 58.75 ? O5' UMP 1265 B 1 HETATM 17 P P UMP . . . I 2 -13.726 60.324 -18.897 1 65.2 ? P UMP 1265 B 1 HETATM 18 O OP1 UMP . . . I 2 -12.224 60.331 -19.138 1 68.6 ? OP1 UMP 1265 B 1 HETATM 19 O OP2 UMP . . . I 2 -14.472 60.087 -20.177 1 60.8 ? OP2 UMP 1265 B 1 HETATM 20 O OP3 UMP . . . I 2 -14.019 59.286 -17.883 1 62.57 ? OP3 UMP 1265 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #