data_3C3I # _model_server_result.job_id mFmYJ6d78CjdHUK-EYX43A _model_server_result.datetime_utc '2024-12-02 15:01:37' _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 3c3i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":779}' # _entry.id 3C3I # _exptl.entry_id 3C3I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 388.162 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-DIPHOSPHATE" _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 3C3I _cell.length_a 132.069 _cell.length_b 132.069 _cell.length_c 53.451 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C3I _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_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,E,F,K 1 1,2,3 B,C,D,G,H,I,J,L,M,N 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -66.0345 114.375109 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -132.069 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N # _chem_comp.formula 'C9 H14 N2 O11 P2' _chem_comp.formula_weight 388.162 _chem_comp.id DUD _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-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 N1 C2 DUD sing 70 n n N1 C6 DUD sing 71 n n N1 C1' DUD sing 72 n n C2 N3 DUD sing 73 n n C2 O2 DUD doub 74 n n N3 C4 DUD sing 75 n n N3 HN3 DUD sing 76 n n C4 C5 DUD sing 77 n n C4 O4 DUD doub 78 n n C5 C6 DUD doub 79 n n C5 H5 DUD sing 80 n n C6 H6 DUD sing 81 n n C1' C2' DUD sing 82 n n C1' O4' DUD sing 83 n n C1' H1' DUD sing 84 n n C2' C3' DUD sing 85 n n C2' "H2'1" DUD sing 86 n n C2' "H2'2" DUD sing 87 n n C3' C4' DUD sing 88 n n C3' O3' DUD sing 89 n n C3' H3' DUD sing 90 n n C4' O4' DUD sing 91 n n C4' C5' DUD sing 92 n n C4' H4' DUD sing 93 n n O3' HO3' DUD sing 94 n n C5' O5' DUD sing 95 n n C5' "H5'1" DUD sing 96 n n C5' "H5'2" DUD sing 97 n n O5' PA DUD sing 98 n n PA O1A DUD doub 99 n n PA O2A DUD sing 100 n n PA O3A DUD sing 101 n n O2A HOA2 DUD sing 102 n n O3A PB DUD sing 103 n n PB O1B DUD doub 104 n n PB O2B DUD sing 105 n n PB O3B DUD sing 106 n n O2B HOB2 DUD sing 107 n n O3B HOB3 DUD sing 108 n n # _atom_sites.entry_id 3C3I _atom_sites.fract_transf_matrix[1][1] 0.007572 _atom_sites.fract_transf_matrix[1][2] 0.004372 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008743 _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] 0.018709 _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 MG A 1 998 998 MG MG . F 3 DUD A 1 776 776 DUD DUD . G 3 DUD B 1 777 777 DUD DUD . H 3 DUD B 1 778 778 DUD DUD . I 3 DUD B 1 779 779 DUD DUD . J 2 MG D 1 999 999 MG MG . K 4 HOH A 1 999 7 HOH HOH . K 4 HOH A 2 1000 15 HOH HOH . L 4 HOH B 1 780 9 HOH HOH . L 4 HOH B 2 781 11 HOH HOH . L 4 HOH B 3 782 18 HOH HOH . L 4 HOH B 4 783 19 HOH HOH . M 4 HOH C 1 138 2 HOH HOH . M 4 HOH C 2 139 3 HOH HOH . M 4 HOH C 3 140 4 HOH HOH . M 4 HOH C 4 141 12 HOH HOH . M 4 HOH C 5 142 13 HOH HOH . M 4 HOH C 6 143 16 HOH HOH . M 4 HOH C 7 144 17 HOH HOH . N 4 HOH D 1 1000 1 HOH HOH . N 4 HOH D 2 1001 5 HOH HOH . N 4 HOH D 3 1002 6 HOH HOH . N 4 HOH D 4 1003 8 HOH HOH . N 4 HOH D 5 1004 10 HOH HOH . N 4 HOH D 6 1005 14 HOH HOH . N 4 HOH D 7 1006 20 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 DUD . . . I 3 -29.35 48.492 -3.919 1 41.06 ? N1 DUD 779 B 1 HETATM 2 C C2 DUD . . . I 3 -29.841 48.402 -2.634 1 40.34 ? C2 DUD 779 B 1 HETATM 3 N N3 DUD . . . I 3 -29.937 47.184 -2.035 1 40.41 ? N3 DUD 779 B 1 HETATM 4 C C4 DUD . . . I 3 -29.552 46.039 -2.691 1 39.92 ? C4 DUD 779 B 1 HETATM 5 C C5 DUD . . . I 3 -29.046 46.117 -4.017 1 39.35 ? C5 DUD 779 B 1 HETATM 6 C C6 DUD . . . I 3 -28.957 47.336 -4.602 1 40.1 ? C6 DUD 779 B 1 HETATM 7 O O2 DUD . . . I 3 -30.191 49.396 -2.013 1 38.48 ? O2 DUD 779 B 1 HETATM 8 O O4 DUD . . . I 3 -29.639 44.956 -2.146 1 39.84 ? O4 DUD 779 B 1 HETATM 9 C C1' DUD . . . I 3 -29.224 49.806 -4.597 1 43.33 ? C1' DUD 779 B 1 HETATM 10 C C2' DUD . . . I 3 -27.747 50.049 -4.983 1 44.38 ? C2' DUD 779 B 1 HETATM 11 C C3' DUD . . . I 3 -27.771 50.471 -6.451 1 46.55 ? C3' DUD 779 B 1 HETATM 12 C C4' DUD . . . I 3 -29.254 50.496 -6.852 1 48.04 ? C4' DUD 779 B 1 HETATM 13 O O4' DUD . . . I 3 -29.996 49.81 -5.816 1 44.93 ? O4' DUD 779 B 1 HETATM 14 O O3' DUD . . . I 3 -27.191 51.759 -6.607 1 47.1 ? O3' DUD 779 B 1 HETATM 15 C C5' DUD . . . I 3 -29.453 49.773 -8.169 1 52.67 ? C5' DUD 779 B 1 HETATM 16 O O5' DUD . . . I 3 -30.839 49.797 -8.496 1 58.9 ? O5' DUD 779 B 1 HETATM 17 P PA DUD . . . I 3 -30.996 49.359 -10.041 1 63.32 ? PA DUD 779 B 1 HETATM 18 O O1A DUD . . . I 3 -30.016 48.295 -10.376 1 63.31 ? O1A DUD 779 B 1 HETATM 19 O O2A DUD . . . I 3 -30.759 50.643 -10.989 1 62.22 ? O2A DUD 779 B 1 HETATM 20 O O3A DUD . . . I 3 -32.503 48.81 -10.232 1 65.71 ? O3A DUD 779 B 1 HETATM 21 P PB DUD . . . I 3 -32.492 47.398 -11.031 1 69.43 ? PB DUD 779 B 1 HETATM 22 O O1B DUD . . . I 3 -31.736 46.374 -10.246 1 69.41 ? O1B DUD 779 B 1 HETATM 23 O O2B DUD . . . I 3 -34.008 46.887 -11.226 1 70.17 ? O2B DUD 779 B 1 HETATM 24 O O3B DUD . . . I 3 -31.796 47.591 -12.477 1 70.55 ? O3B DUD 779 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #