data_4KYA # _model_server_result.job_id ScmvM3Us3aVC7i2ZCg9ePQ _model_server_result.datetime_utc '2024-11-12 21:13:19' _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 4kya # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":701}' # _entry.id 4KYA # _exptl.entry_id 4KYA _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 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90.07 _cell.angle_beta 89.96 _cell.angle_gamma 90.07 _cell.entry_id 4KYA _cell.length_a 53.531 _cell.length_b 145.079 _cell.length_c 176.614 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KYA _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,K,L,M,N,O,P 1 1 C,D,Q,R,S,T,U,V,W,X 2 1 E,F,Y,Z,AA,BA,CA,DA,EA,FA 3 1 G,H,GA,HA,IA,JA,KA,LA,MA,NA 4 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 I N N ? 2 M N N ? 2 Q N N ? 2 U N N ? 2 Y N N ? 2 CA N N ? 2 GA N N ? 2 KA N N # _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 535 n n N1 C6 UMP sing 536 n n N1 C1' UMP sing 537 n n C2 N3 UMP sing 538 n n C2 O2 UMP doub 539 n n N3 C4 UMP sing 540 n n N3 HN3 UMP sing 541 n n C4 C5 UMP sing 542 n n C4 O4 UMP doub 543 n n C5 C6 UMP doub 544 n n C5 H5 UMP sing 545 n n C6 H6 UMP sing 546 n n C1' C2' UMP sing 547 n n C1' O4' UMP sing 548 n n C1' H1' UMP sing 549 n n C2' C3' UMP sing 550 n n C2' H2' UMP sing 551 n n C2' "H2''" UMP sing 552 n n C3' C4' UMP sing 553 n n C3' O3' UMP sing 554 n n C3' H3' UMP sing 555 n n C4' O4' UMP sing 556 n n C4' C5' UMP sing 557 n n C4' H4' UMP sing 558 n n O3' HO3' UMP sing 559 n n C5' O5' UMP sing 560 n n C5' H5' UMP sing 561 n n C5' "H5''" UMP sing 562 n n O5' P UMP sing 563 n n P OP1 UMP doub 564 n n P OP2 UMP sing 565 n n P OP3 UMP sing 566 n n OP2 HOP2 UMP sing 567 n n OP3 HOP3 UMP sing 568 n n # _atom_sites.entry_id 4KYA _atom_sites.fract_transf_matrix[1][1] 0.018681 _atom_sites.fract_transf_matrix[1][2] 0.000023 _atom_sites.fract_transf_matrix[1][3] -0.000013 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006893 _atom_sites.fract_transf_matrix[2][3] 0.000008 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.005662 _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 I 2 UMP A 1 701 701 UMP UMP . J 3 1UG A 1 702 702 1UG 1UG . K 4 FOL A 1 703 703 FOL FOL . L 5 NDP A 1 704 704 NDP NDP . M 2 UMP B 1 701 701 UMP UMP . N 3 1UG B 1 702 702 1UG 1UG . O 4 FOL B 1 703 703 FOL FOL . P 5 NDP B 1 704 704 NDP NDP . Q 2 UMP C 1 701 701 UMP UMP . R 3 1UG C 1 702 702 1UG 1UG . S 4 FOL C 1 703 703 FOL FOL . T 5 NDP C 1 704 704 NDP NDP . U 2 UMP D 1 701 701 UMP UMP . V 3 1UG D 1 702 702 1UG 1UG . W 4 FOL D 1 703 703 FOL FOL . X 5 NDP D 1 704 704 NDP NDP . Y 2 UMP E 1 701 701 UMP UMP . Z 3 1UG E 1 702 702 1UG 1UG . AA 4 FOL E 1 703 703 FOL FOL . BA 5 NDP E 1 704 704 NDP NDP . CA 2 UMP F 1 701 701 UMP UMP . DA 3 1UG F 1 702 702 1UG 1UG . EA 4 FOL F 1 703 703 FOL FOL . FA 5 NDP F 1 704 704 NDP NDP . GA 2 UMP G 1 701 701 UMP UMP . HA 3 1UG G 1 702 702 1UG 1UG . IA 4 FOL G 1 703 703 FOL FOL . JA 5 NDP G 1 704 704 NDP NDP . KA 2 UMP H 1 701 701 UMP UMP . LA 3 1UG H 1 702 702 1UG 1UG . MA 4 FOL H 1 703 703 FOL FOL . NA 5 NDP H 1 704 704 NDP NDP . # 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 . . . Y 2 7.331 -79.941 -34.464 1 69.51 ? N1 UMP 701 E 1 HETATM 2 C C2 UMP . . . Y 2 6.714 -79.884 -35.758 1 56.18 ? C2 UMP 701 E 1 HETATM 3 N N3 UMP . . . Y 2 5.465 -80.268 -35.91 1 57.62 ? N3 UMP 701 E 1 HETATM 4 C C4 UMP . . . Y 2 4.75 -80.715 -34.881 1 63.25 ? C4 UMP 701 E 1 HETATM 5 C C5 UMP . . . Y 2 5.313 -80.792 -33.588 1 74.34 ? C5 UMP 701 E 1 HETATM 6 C C6 UMP . . . Y 2 6.631 -80.393 -33.414 1 78.64 ? C6 UMP 701 E 1 HETATM 7 O O2 UMP . . . Y 2 7.299 -79.48 -36.791 1 47.82 ? O2 UMP 701 E 1 HETATM 8 O O4 UMP . . . Y 2 3.588 -81.065 -35.063 1 63.29 ? O4 UMP 701 E 1 HETATM 9 C C1' UMP . . . Y 2 8.71 -79.54 -34.225 1 73.77 ? C1' UMP 701 E 1 HETATM 10 C C2' UMP . . . Y 2 9.048 -78.12 -34.612 1 51.29 ? C2' UMP 701 E 1 HETATM 11 C C3' UMP . . . Y 2 10.28 -77.825 -33.762 1 47.54 ? C3' UMP 701 E 1 HETATM 12 C C4' UMP . . . Y 2 10.229 -78.826 -32.641 1 59.07 ? C4' UMP 701 E 1 HETATM 13 O O3' UMP . . . Y 2 11.421 -78.24 -34.487 1 50.53 ? O3' UMP 701 E 1 HETATM 14 O O4' UMP . . . Y 2 9.046 -79.622 -32.828 1 75.91 ? O4' UMP 701 E 1 HETATM 15 C C5' UMP . . . Y 2 10.475 -78.247 -31.236 1 57.63 ? C5' UMP 701 E 1 HETATM 16 O O5' UMP . . . Y 2 9.617 -77.23 -30.863 1 58.7 ? O5' UMP 701 E 1 HETATM 17 P P UMP . . . Y 2 10.123 -75.733 -30.449 1 51.94 ? P UMP 701 E 1 HETATM 18 O OP1 UMP . . . Y 2 9.906 -75.071 -31.756 1 34.56 ? OP1 UMP 701 E 1 HETATM 19 O OP2 UMP . . . Y 2 9.155 -75.373 -29.313 1 39.72 ? OP2 UMP 701 E 1 HETATM 20 O OP3 UMP . . . Y 2 11.537 -75.713 -30.036 1 57.19 ? OP3 UMP 701 E 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 59 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #