data_4HG6 # _model_server_result.job_id WCt2WfUMT3T-MDGJuCTPTg _model_server_result.datetime_utc '2024-11-21 13:52:04' _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 4hg6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":919}' # _entry.id 4HG6 # _exptl.entry_id 4HG6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-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 90 _cell.entry_id 4HG6 _cell.length_a 103.12 _cell.length_b 103.12 _cell.length_c 468.32 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HG6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 BGC BGC C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BGC BGC C1 O1 . O4 HO4 . sing 3 ? 3 4 3 BGC BGC C1 O1 . O4 HO4 . sing 4 ? 3 5 4 BGC BGC C1 O1 . O4 HO4 . sing 5 ? 3 6 5 BGC BGC C1 O1 . O4 HO4 . sing 6 ? 3 7 6 BGC BGC C1 O1 . O4 HO4 . sing 7 ? 3 8 7 BGC BGC C1 O1 . O4 HO4 . sing 8 ? 3 9 8 BGC BGC C1 O1 . O4 HO4 . sing 9 ? 3 10 9 BGC BGC C1 O1 . O4 HO4 . sing 10 ? 3 11 10 BGC BGC C1 O1 . O4 HO4 . sing 11 ? 3 12 11 BGC BGC C1 O1 . O4 HO4 . sing 12 ? 3 13 12 BGC BGC C1 O1 . O4 HO4 . sing 13 ? 3 14 13 BGC BGC C1 O1 . O4 HO4 . sing 14 ? 3 15 14 BGC BGC C1 O1 . O4 HO4 . sing 15 ? 3 16 15 BGC BGC C1 O1 . O4 HO4 . sing 16 ? 3 17 16 BGC BGC C1 O1 . O4 HO4 . sing 17 ? 3 18 17 BGC BGC C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C BGC 1 C 1 BGC A 901 BGC 3 n C BGC 2 C 2 BGC A 902 BGC 3 n C BGC 3 C 3 BGC A 903 BGC 3 n C BGC 4 C 4 BGC A 904 BGC 3 n C BGC 5 C 5 BGC A 905 BGC 3 n C BGC 6 C 6 BGC A 906 BGC 3 n C BGC 7 C 7 BGC A 907 BGC 3 n C BGC 8 C 8 BGC A 908 BGC 3 n C BGC 9 C 9 BGC A 909 BGC 3 n C BGC 10 C 10 BGC A 910 BGC 3 n C BGC 11 C 11 BGC A 911 BGC 3 n C BGC 12 C 12 BGC A 912 BGC 3 n C BGC 13 C 13 BGC A 913 BGC 3 n C BGC 14 C 14 BGC A 914 BGC 3 n C BGC 15 C 15 BGC A 915 BGC 3 n C BGC 16 C 16 BGC A 916 BGC 3 n C BGC 17 C 17 BGC A 917 BGC 3 n C BGC 18 C 18 BGC A 918 BGC # 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 B SG CYS 145 B CYS 163 1_555 B SG CYS 412 B CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? covale ? covale1 C O4 BGC . C BGC 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 C O4 BGC . C BGC 2 1_555 C C1 BGC . C BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 C O4 BGC . C BGC 3 1_555 C C1 BGC . C BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 C O4 BGC . C BGC 4 1_555 C C1 BGC . C BGC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 C O4 BGC . C BGC 5 1_555 C C1 BGC . C BGC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale6 C O4 BGC . C BGC 6 1_555 C C1 BGC . C BGC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale7 C O4 BGC . C BGC 7 1_555 C C1 BGC . C BGC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale8 C O4 BGC . C BGC 8 1_555 C C1 BGC . C BGC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 C O4 BGC . C BGC 9 1_555 C C1 BGC . C BGC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 C O4 BGC . C BGC 10 1_555 C C1 BGC . C BGC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale11 C O4 BGC . C BGC 11 1_555 C C1 BGC . C BGC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale12 C O4 BGC . C BGC 12 1_555 C C1 BGC . C BGC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale13 C O4 BGC . C BGC 13 1_555 C C1 BGC . C BGC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale14 C O4 BGC . C BGC 14 1_555 C C1 BGC . C BGC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale15 C O4 BGC . C BGC 15 1_555 C C1 BGC . C BGC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale16 C O4 BGC . C BGC 16 1_555 C C1 BGC . C BGC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale17 C O4 BGC . C BGC 17 1_555 C C1 BGC . C BGC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4HG6 _atom_sites.fract_transf_matrix[1][1] 0.009697 _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] 0.009697 _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] 0.002135 _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 4 UDP A 1 919 919 UDP UDP . E 5 LDA A 1 920 920 LDA LDA . F 5 LDA A 1 921 921 LDA LDA . # 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 UDP . . . D 4 -2.999 59.292 50.171 0.5 81.99 ? N1 UDP 919 A 1 HETATM 2 C C2 UDP . . . D 4 -3.714 59.121 49.013 0.5 78.36 ? C2 UDP 919 A 1 HETATM 3 N N3 UDP . . . D 4 -4.549 60.116 48.558 0.5 90.43 ? N3 UDP 919 A 1 HETATM 4 C C4 UDP . . . D 4 -4.658 61.291 49.266 0.5 87.05 ? C4 UDP 919 A 1 HETATM 5 C C5 UDP . . . D 4 -3.931 61.454 50.436 0.5 83.75 ? C5 UDP 919 A 1 HETATM 6 C C6 UDP . . . D 4 -2.965 60.515 50.77 0.5 85.8 ? C6 UDP 919 A 1 HETATM 7 O O2 UDP . . . D 4 -3.604 58.07 48.388 0.5 88.13 ? O2 UDP 919 A 1 HETATM 8 O O4 UDP . . . D 4 -5.399 62.185 48.861 0.5 92.88 ? O4 UDP 919 A 1 HETATM 9 C C1' UDP . . . D 4 -2.123 58.194 50.616 0.5 87.85 ? C1' UDP 919 A 1 HETATM 10 C C2' UDP . . . D 4 -0.874 58.726 51.29 0.5 80.06 ? C2' UDP 919 A 1 HETATM 11 O O2' UDP . . . D 4 0.174 58.78 50.359 0.5 85.35 ? O2' UDP 919 A 1 HETATM 12 C C3' UDP . . . D 4 -0.585 57.699 52.359 0.5 75.47 ? C3' UDP 919 A 1 HETATM 13 C C4' UDP . . . D 4 -1.944 57.115 52.68 0.5 70.99 ? C4' UDP 919 A 1 HETATM 14 O O4' UDP . . . D 4 -2.778 57.378 51.569 0.5 92.23 ? O4' UDP 919 A 1 HETATM 15 O O3' UDP . . . D 4 0.236 56.673 51.843 0.5 83.43 ? O3' UDP 919 A 1 HETATM 16 C C5' UDP . . . D 4 -2.533 57.77 53.92 0.5 57 ? C5' UDP 919 A 1 HETATM 17 O O5' UDP . . . D 4 -1.508 58.431 54.622 0.5 70.89 ? O5' UDP 919 A 1 HETATM 18 P PA UDP . . . D 4 -1.707 59.98 55.012 0.5 98.11 ? PA UDP 919 A 1 HETATM 19 O O1A UDP . . . D 4 -2.566 60.633 53.999 0.5 99.88 ? O1A UDP 919 A 1 HETATM 20 O O2A UDP . . . D 4 -0.425 60.707 55.205 0.5 73.39 ? O2A UDP 919 A 1 HETATM 21 O O3A UDP . . . D 4 -2.482 59.931 56.414 0.5 108.02 ? O3A UDP 919 A 1 HETATM 22 P PB UDP . . . D 4 -3.886 60.704 56.461 0.5 118.08 ? PB UDP 919 A 1 HETATM 23 O O1B UDP . . . D 4 -4.076 61.383 55.158 0.5 113.29 ? O1B UDP 919 A 1 HETATM 24 O O2B UDP . . . D 4 -3.859 61.68 57.577 0.5 100.77 ? O2B UDP 919 A 1 HETATM 25 O O3B UDP . . . D 4 -4.988 59.74 56.66 0.5 131.87 ? O3B UDP 919 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #