data_4KY4 # _model_server_result.job_id rzRgk6qv8DEKLgyY2kOH2Q _model_server_result.datetime_utc '2024-11-23 12:22:25' _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 4ky4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"KA","auth_seq_id":701}' # _entry.id 4KY4 # _exptl.entry_id 4KY4 _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 89.97 _cell.angle_beta 89.95 _cell.angle_gamma 89.89 _cell.entry_id 4KY4 _cell.length_a 53.539 _cell.length_b 145.122 _cell.length_c 176.159 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KY4 _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 529 n n N1 C6 UMP sing 530 n n N1 C1' UMP sing 531 n n C2 N3 UMP sing 532 n n C2 O2 UMP doub 533 n n N3 C4 UMP sing 534 n n N3 HN3 UMP sing 535 n n C4 C5 UMP sing 536 n n C4 O4 UMP doub 537 n n C5 C6 UMP doub 538 n n C5 H5 UMP sing 539 n n C6 H6 UMP sing 540 n n C1' C2' UMP sing 541 n n C1' O4' UMP sing 542 n n C1' H1' UMP sing 543 n n C2' C3' UMP sing 544 n n C2' H2' UMP sing 545 n n C2' "H2''" UMP sing 546 n n C3' C4' UMP sing 547 n n C3' O3' UMP sing 548 n n C3' H3' UMP sing 549 n n C4' O4' UMP sing 550 n n C4' C5' UMP sing 551 n n C4' H4' UMP sing 552 n n O3' HO3' UMP sing 553 n n C5' O5' UMP sing 554 n n C5' H5' UMP sing 555 n n C5' "H5''" UMP sing 556 n n O5' P UMP sing 557 n n P OP1 UMP doub 558 n n P OP2 UMP sing 559 n n P OP3 UMP sing 560 n n OP2 HOP2 UMP sing 561 n n OP3 HOP3 UMP sing 562 n n # _atom_sites.entry_id 4KY4 _atom_sites.fract_transf_matrix[1][1] 0.018678 _atom_sites.fract_transf_matrix[1][2] -0.000035 _atom_sites.fract_transf_matrix[1][3] -0.000017 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006891 _atom_sites.fract_transf_matrix[2][3] -0.000003 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.005677 _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 1 701 703 UMP UMP . J 3 04J A 1 702 705 04J MTX . K 4 NDP A 1 703 706 NDP NDP . L 5 1UE A 1 704 707 1UE CP2 . M 2 UMP B 1 701 703 UMP UMP . N 3 04J B 1 702 705 04J MTX . O 4 NDP B 1 703 706 NDP NDP . P 5 1UE B 1 704 707 1UE CP2 . Q 2 UMP C 1 701 703 UMP UMP . R 3 04J C 1 702 705 04J MTX . S 4 NDP C 1 703 706 NDP NDP . T 5 1UE C 1 704 707 1UE CP2 . U 2 UMP D 1 701 703 UMP UMP . V 3 04J D 1 702 705 04J MTX . W 4 NDP D 1 703 706 NDP NDP . X 5 1UE D 1 704 707 1UE CP2 . Y 2 UMP E 1 701 703 UMP UMP . Z 3 04J E 1 702 705 04J MTX . AA 4 NDP E 1 703 706 NDP NDP . BA 5 1UE E 1 704 707 1UE CP2 . CA 2 UMP F 1 701 703 UMP UMP . DA 3 04J F 1 702 705 04J MTX . EA 4 NDP F 1 703 706 NDP NDP . FA 5 1UE F 1 704 707 1UE CP2 . GA 2 UMP G 1 701 703 UMP UMP . HA 3 04J G 1 702 705 04J MTX . IA 4 NDP G 1 703 706 NDP NDP . JA 5 1UE G 1 704 707 1UE CP2 . KA 2 UMP H 1 701 703 UMP UMP . LA 3 04J H 1 702 705 04J MTX . MA 4 NDP H 1 703 706 NDP NDP . NA 5 1UE H 1 704 707 1UE CP2 . # 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 . . . KA 2 13.832 -56.16 46.496 1 138.03 ? N1 UMP 701 H 1 HETATM 2 C C2 UMP . . . KA 2 14.947 -56.024 45.765 1 133.17 ? C2 UMP 701 H 1 HETATM 3 N N3 UMP . . . KA 2 16.141 -55.651 46.359 1 132.81 ? N3 UMP 701 H 1 HETATM 4 C C4 UMP . . . KA 2 16.196 -55.41 47.717 1 130.5 ? C4 UMP 701 H 1 HETATM 5 C C5 UMP . . . KA 2 15.057 -55.541 48.481 1 135.42 ? C5 UMP 701 H 1 HETATM 6 C C6 UMP . . . KA 2 13.874 -55.91 47.865 1 133.75 ? C6 UMP 701 H 1 HETATM 7 O O2 UMP . . . KA 2 14.939 -56.229 44.559 1 118.46 ? O2 UMP 701 H 1 HETATM 8 O O4 UMP . . . KA 2 17.252 -55.078 48.236 1 132.92 ? O4 UMP 701 H 1 HETATM 9 C C1' UMP . . . KA 2 12.534 -56.55 45.881 1 133.39 ? C1' UMP 701 H 1 HETATM 10 C C2' UMP . . . KA 2 12.656 -57.647 44.857 1 129.62 ? C2' UMP 701 H 1 HETATM 11 C C3' UMP . . . KA 2 11.268 -58.25 44.851 1 128.11 ? C3' UMP 701 H 1 HETATM 12 C C4' UMP . . . KA 2 10.561 -57.449 45.902 1 132.44 ? C4' UMP 701 H 1 HETATM 13 O O3' UMP . . . KA 2 10.655 -57.991 43.603 1 118.07 ? O3' UMP 701 H 1 HETATM 14 O O4' UMP . . . KA 2 11.624 -57.158 46.797 1 133.5 ? O4' UMP 701 H 1 HETATM 15 C C5' UMP . . . KA 2 9.407 -58.262 46.504 1 138.08 ? C5' UMP 701 H 1 HETATM 16 O O5' UMP . . . KA 2 9.853 -59.376 47.267 1 131.6 ? O5' UMP 701 H 1 HETATM 17 P P UMP . . . KA 2 9.139 -60.742 47.121 1 116.12 ? P UMP 701 H 1 HETATM 18 O OP1 UMP . . . KA 2 10.202 -61.645 47.537 1 107.12 ? OP1 UMP 701 H 1 HETATM 19 O OP2 UMP . . . KA 2 7.978 -60.652 47.984 1 138.59 ? OP2 UMP 701 H 1 HETATM 20 O OP3 UMP . . . KA 2 8.826 -60.776 45.694 1 123.67 ? OP3 UMP 701 H 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #