data_4WTF # _model_server_result.job_id JLmu4NLXRzpX5xaEwXIRCQ _model_server_result.datetime_utc '2024-11-09 02:22:26' _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 4wtf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":605}' # _entry.id 4WTF # _exptl.entry_id 4WTF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 418.188 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-C-methyluridine 5'-(trihydrogen diphosphate)" _entity.pdbx_number_of_molecules 1 _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 4WTF _cell.length_a 141.65 _cell.length_b 141.65 _cell.length_c 91.64 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WTF _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B O3' U 8 P U 6 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc2 C OD2 ASP 222 A ASP 220 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc3 C OD1 ASP 222 A ASP 220 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc4 C O THR 223 A THR 221 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc5 C OE2 GLU 239 A GLU 237 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc6 C ND1 HIS 256 A HIS 254 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc7 C OD1 ASP 320 A ASP 318 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc8 C OD2 ASP 320 A ASP 318 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc9 C OD1 ASP 321 A ASP 319 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc10 D MN MN . A MN 601 1_555 H O2A 5GS . A 5GS 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc11 D MN MN . A MN 601 1_555 K O HOH . A HOH 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc12 E MN MN . A MN 602 1_555 H O2B 5GS . A 5GS 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc13 E MN MN . A MN 602 1_555 H O2A 5GS . A 5GS 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc14 E MN MN . A MN 602 1_555 K O HOH . A HOH 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? hydrog WATSON-CRICK hydrog1 A N1 A 3 T A 3 1_555 B N3 U 8 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N6 A 3 T A 3 1_555 B O4 U 8 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 A 4 T A 4 1_555 B N3 U 7 P U 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N6 A 4 T A 4 1_555 B O4 U 7 P U 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N1 A 5 T A 5 1_555 B N3 U 6 P U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N6 A 5 T A 5 1_555 B O4 U 6 P U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 U 6 T U 6 1_555 B N1 A 5 P A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O4 U 6 T U 6 1_555 B N6 A 5 P A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 U 7 T U 7 1_555 B N1 A 4 P A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O4 U 7 T U 7 1_555 B N6 A 4 P A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N2 O12 P2' _chem_comp.formula_weight 418.188 _chem_comp.id 5GS _chem_comp.mon_nstd_flag . _chem_comp.name "2'-C-methyluridine 5'-(trihydrogen diphosphate)" _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 O2B PB 5GS sing 1 n n O1B PB 5GS doub 2 n n PB O3B 5GS sing 3 n n PB O3A 5GS sing 4 n n O2A PA 5GS sing 5 n n O3' C3' 5GS sing 6 n n C5' C4' 5GS sing 7 n n C5' O5' 5GS sing 8 n n O3A PA 5GS sing 9 n n PA O5' 5GS sing 10 n n PA O1A 5GS doub 11 n n C4' C3' 5GS sing 12 n n C4' O4' 5GS sing 13 n n C3' C2' 5GS sing 14 n n O2' C2' 5GS sing 15 n n O4' C1' 5GS sing 16 n n C2' C1' 5GS sing 17 n n C2' C2M 5GS sing 18 n n C1' N1 5GS sing 19 n n N1 C6 5GS sing 20 n n N1 C2 5GS sing 21 n n C6 C5 5GS doub 22 n n O2 C2 5GS doub 23 n n C2 N3 5GS sing 24 n n C5 C4 5GS sing 25 n n N3 C4 5GS sing 26 n n C4 O4 5GS doub 27 n n C5 H1 5GS sing 28 n n N3 H2 5GS sing 29 n n C6 H3 5GS sing 30 n n O2B H4 5GS sing 31 n n O3B H5 5GS sing 32 n n O2A H8 5GS sing 33 n n C5' H9 5GS sing 34 n n C5' H10 5GS sing 35 n n C4' H11 5GS sing 36 n n C3' H12 5GS sing 37 n n O3' H13 5GS sing 38 n n C2M H14 5GS sing 39 n n C2M H15 5GS sing 40 n n C2M H16 5GS sing 41 n n O2' H17 5GS sing 42 n n C1' H18 5GS sing 43 n n # _atom_sites.entry_id 4WTF _atom_sites.fract_transf_matrix[1][1] 0.00706 _atom_sites.fract_transf_matrix[1][2] 0.004076 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008152 _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] 0.010912 _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 D 3 MN A 1 601 1 MN MN . E 3 MN A 1 602 2 MN MN . F 3 MN A 1 603 3 MN MN . G 4 CL A 1 604 1 CL CL . H 5 5GS A 1 605 1 5GS 475 . I 6 HOH T 1 101 55 HOH HOH . I 6 HOH T 2 102 65 HOH HOH . J 6 HOH P 1 101 44 HOH HOH . J 6 HOH P 2 102 60 HOH HOH . J 6 HOH P 3 103 61 HOH HOH . K 6 HOH A 1 701 11 HOH HOH . K 6 HOH A 2 702 26 HOH HOH . K 6 HOH A 3 703 34 HOH HOH . K 6 HOH A 4 704 15 HOH HOH . K 6 HOH A 5 705 3 HOH HOH . K 6 HOH A 6 706 10 HOH HOH . K 6 HOH A 7 707 14 HOH HOH . K 6 HOH A 8 708 45 HOH HOH . K 6 HOH A 9 709 71 HOH HOH . K 6 HOH A 10 710 70 HOH HOH . K 6 HOH A 11 711 12 HOH HOH . K 6 HOH A 12 712 50 HOH HOH . K 6 HOH A 13 713 80 HOH HOH . K 6 HOH A 14 714 1 HOH HOH . K 6 HOH A 15 715 2 HOH HOH . K 6 HOH A 16 716 4 HOH HOH . K 6 HOH A 17 717 5 HOH HOH . K 6 HOH A 18 718 6 HOH HOH . K 6 HOH A 19 719 7 HOH HOH . K 6 HOH A 20 720 8 HOH HOH . K 6 HOH A 21 721 9 HOH HOH . K 6 HOH A 22 722 13 HOH HOH . K 6 HOH A 23 723 16 HOH HOH . K 6 HOH A 24 724 17 HOH HOH . K 6 HOH A 25 725 18 HOH HOH . K 6 HOH A 26 726 19 HOH HOH . K 6 HOH A 27 727 20 HOH HOH . K 6 HOH A 28 728 21 HOH HOH . K 6 HOH A 29 729 22 HOH HOH . K 6 HOH A 30 730 23 HOH HOH . K 6 HOH A 31 731 24 HOH HOH . K 6 HOH A 32 732 25 HOH HOH . K 6 HOH A 33 733 27 HOH HOH . K 6 HOH A 34 734 28 HOH HOH . K 6 HOH A 35 735 29 HOH HOH . K 6 HOH A 36 736 30 HOH HOH . K 6 HOH A 37 737 31 HOH HOH . K 6 HOH A 38 738 32 HOH HOH . K 6 HOH A 39 739 33 HOH HOH . K 6 HOH A 40 740 35 HOH HOH . K 6 HOH A 41 741 36 HOH HOH . K 6 HOH A 42 742 37 HOH HOH . K 6 HOH A 43 743 38 HOH HOH . K 6 HOH A 44 744 39 HOH HOH . K 6 HOH A 45 745 40 HOH HOH . K 6 HOH A 46 746 41 HOH HOH . K 6 HOH A 47 747 42 HOH HOH . K 6 HOH A 48 748 43 HOH HOH . K 6 HOH A 49 749 46 HOH HOH . K 6 HOH A 50 750 47 HOH HOH . K 6 HOH A 51 751 48 HOH HOH . K 6 HOH A 52 752 49 HOH HOH . K 6 HOH A 53 753 51 HOH HOH . K 6 HOH A 54 754 52 HOH HOH . K 6 HOH A 55 755 53 HOH HOH . K 6 HOH A 56 756 54 HOH HOH . K 6 HOH A 57 757 56 HOH HOH . K 6 HOH A 58 758 57 HOH HOH . K 6 HOH A 59 759 58 HOH HOH . K 6 HOH A 60 760 59 HOH HOH . K 6 HOH A 61 761 62 HOH HOH . K 6 HOH A 62 762 63 HOH HOH . K 6 HOH A 63 763 64 HOH HOH . K 6 HOH A 64 764 66 HOH HOH . K 6 HOH A 65 765 67 HOH HOH . K 6 HOH A 66 766 68 HOH HOH . K 6 HOH A 67 767 69 HOH HOH . K 6 HOH A 68 768 72 HOH HOH . K 6 HOH A 69 769 73 HOH HOH . K 6 HOH A 70 770 74 HOH HOH . K 6 HOH A 71 771 75 HOH HOH . K 6 HOH A 72 772 76 HOH HOH . K 6 HOH A 73 773 77 HOH HOH . K 6 HOH A 74 774 78 HOH HOH . K 6 HOH A 75 775 79 HOH HOH . K 6 HOH A 76 776 81 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 C C2 5GS . . . H 5 39.568 -46.582 8.664 1 57.82 ? C2 5GS 605 A 1 HETATM 2 C C5 5GS . . . H 5 42.069 -45.451 8.742 1 54.04 ? C5 5GS 605 A 1 HETATM 3 C C4 5GS . . . H 5 41.229 -45.505 9.877 1 58.67 ? C4 5GS 605 A 1 HETATM 4 N N3 5GS . . . H 5 39.989 -46.063 9.831 1 54.43 ? N3 5GS 605 A 1 HETATM 5 N N1 5GS . . . H 5 40.39 -46.567 7.482 1 56.44 ? N1 5GS 605 A 1 HETATM 6 C C6 5GS . . . H 5 41.624 -45.998 7.535 1 54.93 ? C6 5GS 605 A 1 HETATM 7 O O4 5GS . . . H 5 41.627 -44.981 11.064 1 56.32 ? O4 5GS 605 A 1 HETATM 8 O O2 5GS . . . H 5 38.332 -47.131 8.652 1 58.94 ? O2 5GS 605 A 1 HETATM 9 O O2B 5GS . . . H 5 42.955 -44.218 1.364 1 39.71 ? O2B 5GS 605 A 1 HETATM 10 P PB 5GS . . . H 5 42.857 -43.164 2.468 1 54.79 ? PB 5GS 605 A 1 HETATM 11 O O3B 5GS . . . H 5 41.44 -42.939 2.973 1 55.57 ? O3B 5GS 605 A 1 HETATM 12 O O1B 5GS . . . H 5 43.543 -41.816 2.247 1 51.3 ? O1B 5GS 605 A 1 HETATM 13 O O3A 5GS . . . H 5 43.669 -43.762 3.735 1 52.9 ? O3A 5GS 605 A 1 HETATM 14 P PA 5GS . . . H 5 44.353 -45.22 3.859 1 50.12 ? PA 5GS 605 A 1 HETATM 15 O O1A 5GS . . . H 5 45.226 -45.204 5.069 1 60.04 ? O1A 5GS 605 A 1 HETATM 16 O O2A 5GS . . . H 5 44.918 -45.732 2.544 1 51.6 ? O2A 5GS 605 A 1 HETATM 17 O O5' 5GS . . . H 5 43.083 -46.074 4.334 1 56.39 ? O5' 5GS 605 A 1 HETATM 18 C C5' 5GS . . . H 5 42.191 -46.775 3.447 1 55.81 ? C5' 5GS 605 A 1 HETATM 19 C C4' 5GS . . . H 5 40.804 -46.904 4.071 1 53.2 ? C4' 5GS 605 A 1 HETATM 20 C C3' 5GS . . . H 5 40.201 -45.558 4.43 1 52.97 ? C3' 5GS 605 A 1 HETATM 21 O O3' 5GS . . . H 5 39.692 -44.781 3.335 1 50.01 ? O3' 5GS 605 A 1 HETATM 22 C C2' 5GS . . . H 5 39.145 -45.982 5.452 1 55.92 ? C2' 5GS 605 A 1 HETATM 23 C C2M 5GS . . . H 5 38.852 -44.726 6.263 1 59.74 ? C2M 5GS 605 A 1 HETATM 24 O O2' 5GS . . . H 5 37.911 -46.507 4.859 1 52.34 ? O2' 5GS 605 A 1 HETATM 25 O O4' 5GS . . . H 5 40.799 -47.645 5.323 1 57.25 ? O4' 5GS 605 A 1 HETATM 26 C C1' 5GS . . . H 5 39.835 -47.117 6.237 1 53.07 ? C1' 5GS 605 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #