data_6WKB # _model_server_result.job_id aI94bzfjOvRcFqUa6RdoVQ _model_server_result.datetime_utc '2024-11-23 05:05:16' _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 6wkb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6WKB # _exptl.entry_id 6WKB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 228.202 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-deoxyuridine" _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 6WKB _cell.length_a 144.191 _cell.length_b 144.191 _cell.length_c 188.196 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WKB _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA _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 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 covale ? covale1 C C5' U4P . A U4P 401 1_555 F SD MET . B MET 502 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.839 ? covale ? covale2 D SD MED . A MED 402 1_555 G C5' U4P . B U4P 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? # _chem_comp.formula 'C9 H12 N2 O5' _chem_comp.formula_weight 228.202 _chem_comp.id U4P _chem_comp.mon_nstd_flag . _chem_comp.name "5'-deoxyuridine" _chem_comp.type non-polymer _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 CAK CAG U4P doub 386 n n CAK CAL U4P sing 387 n n CAG NAR U4P sing 388 n n O2' C2' U4P sing 389 n n OAB CAL U4P doub 390 n n CAL NAI U4P sing 391 n n NAR C1' U4P sing 392 n n NAR CAM U4P sing 393 n n C1' C2' U4P sing 394 n n C1' O4' U4P sing 395 n n C2' C3' U4P sing 396 n n O4' C4' U4P sing 397 n n NAI CAM U4P sing 398 n n CAM OAC U4P doub 399 n n C4' C3' U4P sing 400 n n C4' C5' U4P sing 401 n n C3' O3' U4P sing 402 n n NAI H1 U4P sing 403 n n CAK H2 U4P sing 404 n n CAG H3 U4P sing 405 n n C1' H4 U4P sing 406 n n C4' H5 U4P sing 407 n n C5' H6 U4P sing 408 n n C5' H7 U4P sing 409 n n C5' H8 U4P sing 410 n n C3' H9 U4P sing 411 n n O3' H10 U4P sing 412 n n C2' H11 U4P sing 413 n n O2' H12 U4P sing 414 n n # _atom_sites.entry_id 6WKB _atom_sites.fract_transf_matrix[1][1] 0.006935 _atom_sites.fract_transf_matrix[1][2] 0.004004 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008008 _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] 0.005314 _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 U4P A 1 401 601 U4P DRG . D 3 MED A 1 402 601 MED DRG . E 4 EDO B 1 501 501 EDO EDO . F 5 MET B 1 502 601 MET DRG . G 2 U4P B 1 503 601 U4P DRG . H 6 HOH A 1 501 30 HOH HOH . H 6 HOH A 2 502 1 HOH HOH . H 6 HOH A 3 503 9 HOH HOH . H 6 HOH A 4 504 7 HOH HOH . H 6 HOH A 5 505 12 HOH HOH . H 6 HOH A 6 506 4 HOH HOH . H 6 HOH A 7 507 10 HOH HOH . I 6 HOH B 1 601 26 HOH HOH . I 6 HOH B 2 602 28 HOH HOH . I 6 HOH B 3 603 20 HOH HOH . I 6 HOH B 4 604 24 HOH HOH . I 6 HOH B 5 605 27 HOH HOH . I 6 HOH B 6 606 14 HOH HOH . I 6 HOH B 7 607 8 HOH HOH . I 6 HOH B 8 608 17 HOH HOH . I 6 HOH B 9 609 31 HOH HOH . I 6 HOH B 10 610 3 HOH HOH . I 6 HOH B 11 611 21 HOH HOH . I 6 HOH B 12 612 5 HOH HOH . I 6 HOH B 13 613 23 HOH HOH . I 6 HOH B 14 614 18 HOH HOH . I 6 HOH B 15 615 2 HOH HOH . I 6 HOH B 16 616 32 HOH HOH . I 6 HOH B 17 617 6 HOH HOH . I 6 HOH B 18 618 33 HOH HOH . I 6 HOH B 19 619 25 HOH HOH . I 6 HOH B 20 620 15 HOH HOH . I 6 HOH B 21 621 29 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 OAC U4P . B . C 2 2.75 -56.622 25.466 0.68 115.1 ? OAC U4P 401 A 1 HETATM 2 C CAM U4P . B . C 2 2.726 -57.284 24.229 0.68 117.56 ? CAM U4P 401 A 1 HETATM 3 N NAI U4P . B . C 2 1.868 -58.447 24.08 0.68 123.23 ? NAI U4P 401 A 1 HETATM 4 C CAL U4P . B . C 2 1.812 -59.128 22.9 0.68 116.89 ? CAL U4P 401 A 1 HETATM 5 O OAB U4P . B . C 2 0.986 -60.255 22.753 0.68 124.05 ? OAB U4P 401 A 1 HETATM 6 C CAK U4P . B . C 2 2.602 -58.691 21.786 0.68 117.27 ? CAK U4P 401 A 1 HETATM 7 C CAG U4P . B . C 2 3.433 -57.566 21.916 0.68 114.67 ? CAG U4P 401 A 1 HETATM 8 N NAR U4P . B . C 2 3.499 -56.853 23.135 0.68 117.8 ? NAR U4P 401 A 1 HETATM 9 C C1' U4P . B . C 2 4.36 -55.734 23.182 0.68 122.27 ? C1' U4P 401 A 1 HETATM 10 O O4' U4P . B . C 2 5.616 -56.025 24.071 0.68 123.97 ? O4' U4P 401 A 1 HETATM 11 C C4' U4P . B . C 2 5.688 -54.662 24.813 0.68 118.08 ? C4' U4P 401 A 1 HETATM 12 C C5' U4P . B . C 2 6.285 -54.823 26.162 0.68 125.04 ? C5' U4P 401 A 1 HETATM 13 C C3' U4P . B . C 2 4.305 -54.199 24.936 0.68 119.29 ? C3' U4P 401 A 1 HETATM 14 O O3' U4P . B . C 2 4.239 -52.746 25.175 0.68 127.51 ? O3' U4P 401 A 1 HETATM 15 C C2' U4P . B . C 2 3.714 -54.516 23.684 0.68 125.29 ? C2' U4P 401 A 1 HETATM 16 O O2' U4P . B . C 2 3.996 -53.405 22.734 0.68 121.61 ? O2' U4P 401 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #