data_9EVL # _model_server_result.job_id oHp4EODSjYKPlbVwBrvxNQ _model_server_result.datetime_utc '2025-09-05 01:17:58' _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 9evl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":710}' # _entry.id 9EVL # _exptl.entry_id 9EVL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _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 90 _cell.entry_id 9EVL _cell.length_a 220.187 _cell.length_b 220.187 _cell.length_c 220.187 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9EVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z _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 ? 4 L N N ? 4 W 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 disulf ? disulf1 A SG CYS 201 A CYS 228 1_555 A SG CYS 256 A CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 B SG CYS 201 B CYS 228 1_555 B SG CYS 256 B CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A OD1 ASP 141 A ASP 168 1_555 O CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc2 A OD2 ASP 141 A ASP 168 1_555 O CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc3 A SG CYS 176 A CYS 203 1_555 D HG HG . A HG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.075 ? metalc ? metalc4 A SG CYS 246 A CYS 273 1_555 C HG HG . A HG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc5 A SD MET 253 A MET 280 1_555 C HG HG . A HG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? metalc ? metalc6 A ND1 HIS 271 A HIS 298 1_555 S HG HG . B HG 704 19_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc7 A NE2 HIS 283 A HIS 310 1_555 F HG HG . A HG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc8 A O CYS 342 A CYS 369 1_555 G HG HG . A HG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? metalc ? metalc9 A SG CYS 342 A CYS 369 1_555 G HG HG . A HG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? metalc ? metalc10 A SG CYS 385 A CYS 412 1_555 E HG HG . A HG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc11 A OE2 GLU 408 A GLU 435 1_555 E HG HG . A HG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc12 A O PHE 413 A PHE 440 1_555 F HG HG . A HG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.161 ? metalc ? metalc13 L O1A GDU . A GDU 710 1_555 O CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc14 L O1B GDU . A GDU 710 1_555 O CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc15 O CA CA . A CA 713 1_555 Y O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.01 ? metalc ? metalc16 B OD1 ASP 141 B ASP 168 1_555 X CA CA . B CA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc17 B OD2 ASP 141 B ASP 168 1_555 X CA CA . B CA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc18 B SG CYS 176 B CYS 203 1_555 Q HG HG . B HG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.02 ? metalc ? metalc19 B SG CYS 246 B CYS 273 1_555 P HG HG . B HG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc20 B SD MET 253 B MET 280 1_555 P HG HG . B HG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc21 B ND1 HIS 271 B HIS 298 1_555 S HG HG . B HG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc22 B SG CYS 342 B CYS 369 1_555 R HG HG . B HG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc23 W O1A GDU . B GDU 708 1_555 X CA CA . B CA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc24 W O2B GDU . B GDU 708 1_555 X CA CA . B CA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id GDU _chem_comp.mon_nstd_flag . _chem_comp.name "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms UDP-D-GALACTOPYRANOSE # 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 GDU sing 83 n n N1 C6 GDU sing 84 n n N1 C1D GDU sing 85 n n C2 N3 GDU sing 86 n n C2 O2 GDU doub 87 n n N3 C4 GDU sing 88 n n N3 HN3 GDU sing 89 n n C4 C5 GDU sing 90 n n C4 O4 GDU doub 91 n n C5 C6 GDU doub 92 n n C5 H5 GDU sing 93 n n C6 H6 GDU sing 94 n n C1D C2D GDU sing 95 n n C1D O4D GDU sing 96 n n C1D H1D GDU sing 97 n n C2D O2D GDU sing 98 n n C2D C3D GDU sing 99 n n C2D H2D GDU sing 100 n n O2D HO2' GDU sing 101 n n C3D C4D GDU sing 102 n n C3D O3D GDU sing 103 n n C3D H3D GDU sing 104 n n C4D O4D GDU sing 105 n n C4D C5D GDU sing 106 n n C4D H4D GDU sing 107 n n O3D HO3' GDU sing 108 n n C5D O5D GDU sing 109 n n C5D "H5'1" GDU sing 110 n n C5D "H5'2" GDU sing 111 n n O5D PA GDU sing 112 n n PA O1A GDU doub 113 n n PA O2A GDU sing 114 n n PA O3A GDU sing 115 n n O2A HOA2 GDU sing 116 n n O3A PB GDU sing 117 n n PB O1B GDU doub 118 n n PB O2B GDU sing 119 n n PB O3B GDU sing 120 n n O2B HOB2 GDU sing 121 n n O3B C1' GDU sing 122 n n C1' C2' GDU sing 123 n n C1' O5' GDU sing 124 n n C1' H1' GDU sing 125 n n C2' C3' GDU sing 126 n n C2' O2' GDU sing 127 n n C2' H2' GDU sing 128 n n C3' C4' GDU sing 129 n n C3' O3' GDU sing 130 n n C3' H3' GDU sing 131 n n C4' C5' GDU sing 132 n n C4' O4' GDU sing 133 n n C4' H4' GDU sing 134 n n C5' C6' GDU sing 135 n n C5' O5' GDU sing 136 n n C5' H5' GDU sing 137 n n C6' O6' GDU sing 138 n n C6' "H6'1" GDU sing 139 n n C6' "H6'2" GDU sing 140 n n O2' HO2A GDU sing 141 n n O3' HO3A GDU sing 142 n n O4' HO4' GDU sing 143 n n O6' HO6' GDU sing 144 n n # _atom_sites.entry_id 9EVL _atom_sites.fract_transf_matrix[1][1] 0.004542 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004542 _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] 0.004542 _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 HG A 1 701 4 HG HG . D 2 HG A 1 702 5 HG HG . E 2 HG A 1 703 8 HG HG . F 2 HG A 1 704 12 HG HG . G 2 HG A 1 705 18 HG HG . H 3 CL A 1 706 2 CL CL . I 3 CL A 1 707 3 CL CL . J 3 CL A 1 708 4 CL CL . K 3 CL A 1 709 9 CL CL . L 4 GDU A 1 710 600 GDU GDU . M 5 MES A 1 711 611 MES MES . N 5 MES A 1 712 613 MES MES . O 6 CA A 1 713 1 CA CA . P 2 HG B 1 701 1 HG HG . Q 2 HG B 1 702 2 HG HG . R 2 HG B 1 703 17 HG HG . S 2 HG B 1 704 19 HG HG . T 3 CL B 1 705 5 CL CL . U 3 CL B 1 706 6 CL CL . V 3 CL B 1 707 7 CL CL . W 4 GDU B 1 708 600 GDU GDU . X 6 CA B 1 709 2 CA CA . Y 7 HOH A 1 801 2 HOH HOH . Y 7 HOH A 2 802 6 HOH HOH . Z 7 HOH B 1 801 1 HOH HOH . Z 7 HOH B 2 802 5 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 GDU . . . L 4 47.813 54.913 92.234 1 62.34 ? N1 GDU 710 A 1 HETATM 2 C C2 GDU . . . L 4 47.979 53.474 92.658 1 71.96 ? C2 GDU 710 A 1 HETATM 3 N N3 GDU . . . L 4 49.064 53.069 93.606 1 53.84 ? N3 GDU 710 A 1 HETATM 4 C C4 GDU . . . L 4 49.981 54.094 94.105 1 85.62 ? C4 GDU 710 A 1 HETATM 5 C C5 GDU . . . L 4 49.823 55.512 93.669 1 75.37 ? C5 GDU 710 A 1 HETATM 6 C C6 GDU . . . L 4 48.74 55.912 92.726 1 56.79 ? C6 GDU 710 A 1 HETATM 7 O O2 GDU . . . L 4 47.236 52.626 92.262 1 82.16 ? O2 GDU 710 A 1 HETATM 8 O O4 GDU . . . L 4 50.851 53.786 94.863 1 82.57 ? O4 GDU 710 A 1 HETATM 9 C C1D GDU . . . L 4 46.757 55.275 91.275 1 75.9 ? C1D GDU 710 A 1 HETATM 10 C C2D GDU . . . L 4 45.51 56.036 91.833 1 78.67 ? C2D GDU 710 A 1 HETATM 11 O O2D GDU . . . L 4 44.609 55.201 92.417 1 70.2 ? O2D GDU 710 A 1 HETATM 12 C C3D GDU . . . L 4 44.923 56.627 90.553 1 73.68 ? C3D GDU 710 A 1 HETATM 13 C C4D GDU . . . L 4 45.964 56.842 89.739 1 64.36 ? C4D GDU 710 A 1 HETATM 14 O O4D GDU . . . L 4 47.238 56.123 90.403 1 76.43 ? O4D GDU 710 A 1 HETATM 15 O O3D GDU . . . L 4 43.992 55.674 89.888 1 66.76 ? O3D GDU 710 A 1 HETATM 16 C C5D GDU . . . L 4 46.241 58.325 89.651 1 80.93 ? C5D GDU 710 A 1 HETATM 17 O O5D GDU . . . L 4 46.688 58.75 90.965 1 94.66 ? O5D GDU 710 A 1 HETATM 18 P PA GDU . . . L 4 45.885 59.981 91.722 1 71.55 ? PA GDU 710 A 1 HETATM 19 O O1A GDU . . . L 4 44.549 60.234 91.076 1 75.1 ? O1A GDU 710 A 1 HETATM 20 O O2A GDU . . . L 4 45.701 59.66 93.188 1 74.38 ? O2A GDU 710 A 1 HETATM 21 O O3A GDU . . . L 4 46.873 61.295 91.544 1 68.12 ? O3A GDU 710 A 1 HETATM 22 P PB GDU . . . L 4 46.442 62.633 90.683 1 72.52 ? PB GDU 710 A 1 HETATM 23 O O1B GDU . . . L 4 44.975 62.941 90.989 1 73.6 ? O1B GDU 710 A 1 HETATM 24 O O2B GDU . . . L 4 47.358 63.778 91.132 1 74.64 ? O2B GDU 710 A 1 HETATM 25 O O3B GDU . . . L 4 46.6 62.433 89.029 1 95.89 ? O3B GDU 710 A 1 HETATM 26 C C1' GDU . . . L 4 47.632 61.78 88.413 1 76.41 ? C1' GDU 710 A 1 HETATM 27 C C2' GDU . . . L 4 49.011 62.169 88.946 1 79.27 ? C2' GDU 710 A 1 HETATM 28 C C3' GDU . . . L 4 50.111 61.86 87.985 1 78.83 ? C3' GDU 710 A 1 HETATM 29 C C4' GDU . . . L 4 49.746 60.868 86.925 1 91.52 ? C4' GDU 710 A 1 HETATM 30 C C5' GDU . . . L 4 48.5 61.329 86.134 1 93.46 ? C5' GDU 710 A 1 HETATM 31 C C6' GDU . . . L 4 47.807 60.159 85.519 1 90.89 ? C6' GDU 710 A 1 HETATM 32 O O2' GDU . . . L 4 49.015 63.586 89.157 1 103.93 ? O2' GDU 710 A 1 HETATM 33 O O3' GDU . . . L 4 51.285 61.366 88.707 1 69.17 ? O3' GDU 710 A 1 HETATM 34 O O4' GDU . . . L 4 49.567 59.558 87.481 1 64.68 ? O4' GDU 710 A 1 HETATM 35 O O5' GDU . . . L 4 47.553 62.113 86.955 1 76.93 ? O5' GDU 710 A 1 HETATM 36 O O6' GDU . . . L 4 47.111 59.423 86.508 1 86.84 ? O6' GDU 710 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #