data_4P00 # _model_server_result.job_id KsYfxYDZPkLmJbfr7Dkzbw _model_server_result.datetime_utc '2024-11-27 13:18:30' _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 4p00 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":918}' # _entry.id 4P00 # _exptl.entry_id 4P00 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 5 _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 4P00 _cell.length_a 67.49 _cell.length_b 216.79 _cell.length_c 219.62 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4P00 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details 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 _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 E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _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 ? 4 2 1 BGC BGC C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BGC BGC C1 O1 . O4 HO4 . sing 3 ? 4 4 3 BGC BGC C1 O1 . O4 HO4 . sing 4 ? 4 5 4 BGC BGC C1 O1 . O4 HO4 . sing 5 ? 4 6 5 BGC BGC C1 O1 . O4 HO4 . sing 6 ? 4 7 6 BGC BGC C1 O1 . O4 HO4 . sing 7 ? 4 8 7 BGC BGC C1 O1 . O4 HO4 . sing 8 ? 4 9 8 BGC BGC C1 O1 . O4 HO4 . sing 9 ? 4 10 9 BGC BGC C1 O1 . O4 HO4 . sing 10 ? 4 11 10 BGC BGC C1 O1 . O4 HO4 . sing 11 ? 4 12 11 BGC BGC C1 O1 . O4 HO4 . sing 12 ? 4 13 12 BGC BGC C1 O1 . O4 HO4 . sing 13 ? 4 14 13 BGC BGC C1 O1 . O4 HO4 . sing 14 ? 4 15 14 BGC BGC C1 O1 . O4 HO4 . sing 15 ? 4 16 15 BGC BGC C1 O1 . O4 HO4 . sing 16 ? 4 17 16 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 4 n D BGC 1 C 1 BGC A 901 BGC 4 n D BGC 2 C 2 BGC A 902 BGC 4 n D BGC 3 C 3 BGC A 903 BGC 4 n D BGC 4 C 4 BGC A 904 BGC 4 n D BGC 5 C 5 BGC A 905 BGC 4 n D BGC 6 C 6 BGC A 906 BGC 4 n D BGC 7 C 7 BGC A 907 BGC 4 n D BGC 8 C 8 BGC A 908 BGC 4 n D BGC 9 C 9 BGC A 909 BGC 4 n D BGC 10 C 10 BGC A 910 BGC 4 n D BGC 11 C 11 BGC A 911 BGC 4 n D BGC 12 C 12 BGC A 912 BGC 4 n D BGC 13 C 13 BGC A 913 BGC 4 n D BGC 14 C 14 BGC A 914 BGC 4 n D BGC 15 C 15 BGC A 915 BGC 4 n D BGC 16 C 16 BGC A 916 BGC 4 n D BGC 17 C 17 BGC A 917 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 163 B CYS 163 1_555 B SG CYS 430 B CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 C C UNK 1 D UNK 169 1_555 C N UNK 2 D UNK 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 C C UNK 2 D UNK 170 1_555 C N UNK 3 D UNK 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 C C UNK 3 D UNK 171 1_555 C N UNK 4 D UNK 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 C C UNK 4 D UNK 172 1_555 C N UNK 5 D UNK 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 C C UNK 5 D UNK 173 1_555 C N UNK 6 D UNK 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 C C UNK 6 D UNK 174 1_555 C N UNK 7 D UNK 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 C C UNK 7 D UNK 175 1_555 C N UNK 8 D UNK 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 C C UNK 8 D UNK 176 1_555 C N UNK 9 D UNK 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale9 D O4 BGC . C BGC 1 1_555 D C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale10 D O4 BGC . C BGC 2 1_555 D C1 BGC . C BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 D O4 BGC . C BGC 3 1_555 D C1 BGC . C BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale12 D O4 BGC . C BGC 4 1_555 D C1 BGC . C BGC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 D O4 BGC . C BGC 5 1_555 D C1 BGC . C BGC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale14 D O4 BGC . C BGC 6 1_555 D C1 BGC . C BGC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale15 D O4 BGC . C BGC 7 1_555 D C1 BGC . C BGC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale16 D O4 BGC . C BGC 8 1_555 D C1 BGC . C BGC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale17 D O4 BGC . C BGC 9 1_555 D C1 BGC . C BGC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale18 D O4 BGC . C BGC 10 1_555 D C1 BGC . C BGC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 D O4 BGC . C BGC 11 1_555 D C1 BGC . C BGC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale20 D O4 BGC . C BGC 12 1_555 D C1 BGC . C BGC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale21 D O4 BGC . C BGC 13 1_555 D C1 BGC . C BGC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale22 D O4 BGC . C BGC 14 1_555 D C1 BGC . C BGC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale23 D O4 BGC . C BGC 15 1_555 D C1 BGC . C BGC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale24 D O4 BGC . C BGC 16 1_555 D C1 BGC . C BGC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? metalc ? metalc1 E O2B UDP . A UDP 918 1_555 H MG MG . A MG 921 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? # _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 ? # 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 UDP sing 694 n n N1 C6 UDP sing 695 n n N1 C1' UDP sing 696 n n C2 N3 UDP sing 697 n n C2 O2 UDP doub 698 n n N3 C4 UDP sing 699 n n N3 HN3 UDP sing 700 n n C4 C5 UDP sing 701 n n C4 O4 UDP doub 702 n n C5 C6 UDP doub 703 n n C5 H5 UDP sing 704 n n C6 H6 UDP sing 705 n n C1' C2' UDP sing 706 n n C1' O4' UDP sing 707 n n C1' H1' UDP sing 708 n n C2' O2' UDP sing 709 n n C2' C3' UDP sing 710 n n C2' H2' UDP sing 711 n n O2' HO2' UDP sing 712 n n C3' C4' UDP sing 713 n n C3' O3' UDP sing 714 n n C3' H3' UDP sing 715 n n C4' O4' UDP sing 716 n n C4' C5' UDP sing 717 n n C4' H4' UDP sing 718 n n O3' HO3' UDP sing 719 n n C5' O5' UDP sing 720 n n C5' "H5'1" UDP sing 721 n n C5' "H5'2" UDP sing 722 n n O5' PA UDP sing 723 n n PA O1A UDP doub 724 n n PA O2A UDP sing 725 n n PA O3A UDP sing 726 n n O2A HOA2 UDP sing 727 n n O3A PB UDP sing 728 n n PB O1B UDP doub 729 n n PB O2B UDP sing 730 n n PB O3B UDP sing 731 n n O2B HOB2 UDP sing 732 n n O3B HOB3 UDP sing 733 n n # _atom_sites.entry_id 4P00 _atom_sites.fract_transf_matrix[1][1] 0.014817 _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] 0.004613 _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] 0.004553 _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 5 UDP A 1 918 918 UDP UDP . F 6 C2E A 1 919 919 C2E C2E . G 6 C2E A 1 920 920 C2E C2E . H 7 MG A 1 921 921 MG MG . I 8 PLC A 1 922 922 PLC PLC . J 9 3PE A 1 923 923 3PE 3PE . # 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 . . . E 5 -38.14 -7.203 -7.854 1 89.01 ? N1 UDP 918 A 1 HETATM 2 C C2 UDP . . . E 5 -38.552 -7.189 -6.535 1 92.53 ? C2 UDP 918 A 1 HETATM 3 N N3 UDP . . . E 5 -39.632 -6.416 -6.156 1 91.49 ? N3 UDP 918 A 1 HETATM 4 C C4 UDP . . . E 5 -40.297 -5.659 -7.097 1 90.86 ? C4 UDP 918 A 1 HETATM 5 C C5 UDP . . . E 5 -39.87 -5.683 -8.417 1 90.45 ? C5 UDP 918 A 1 HETATM 6 C C6 UDP . . . E 5 -38.661 -6.293 -8.726 1 91.55 ? C6 UDP 918 A 1 HETATM 7 O O2 UDP . . . E 5 -37.956 -7.864 -5.698 1 95.27 ? O2 UDP 918 A 1 HETATM 8 O O4 UDP . . . E 5 -41.261 -4.968 -6.772 1 92.25 ? O4 UDP 918 A 1 HETATM 9 C C1' UDP . . . E 5 -36.983 -8.029 -8.247 1 79.63 ? C1' UDP 918 A 1 HETATM 10 C C2' UDP . . . E 5 -37.435 -9.323 -8.903 1 76.49 ? C2' UDP 918 A 1 HETATM 11 O O2' UDP . . . E 5 -37.363 -10.397 -8 1 82.85 ? O2' UDP 918 A 1 HETATM 12 C C3' UDP . . . E 5 -36.466 -9.538 -10.045 1 71.01 ? C3' UDP 918 A 1 HETATM 13 C C4' UDP . . . E 5 -35.704 -8.229 -10.187 1 66.58 ? C4' UDP 918 A 1 HETATM 14 O O4' UDP . . . E 5 -36.191 -7.345 -9.198 1 72.22 ? O4' UDP 918 A 1 HETATM 15 O O3' UDP . . . E 5 -35.581 -10.586 -9.728 1 65.63 ? O3' UDP 918 A 1 HETATM 16 C C5' UDP . . . E 5 -35.922 -7.637 -11.572 1 58.73 ? C5' UDP 918 A 1 HETATM 17 O O5' UDP . . . E 5 -37.139 -8.164 -12.046 1 54.57 ? O5' UDP 918 A 1 HETATM 18 P PA UDP . . . E 5 -37.563 -8.121 -13.595 1 80.92 ? PA UDP 918 A 1 HETATM 19 O O1A UDP . . . E 5 -37.377 -9.474 -14.164 1 86.2 ? O1A UDP 918 A 1 HETATM 20 O O2A UDP . . . E 5 -38.965 -7.675 -13.753 1 81.72 ? O2A UDP 918 A 1 HETATM 21 O O3A UDP . . . E 5 -36.534 -7.1 -14.297 1 126.63 ? O3A UDP 918 A 1 HETATM 22 P PB UDP . . . E 5 -35.617 -7.577 -15.532 1 72.65 ? PB UDP 918 A 1 HETATM 23 O O1B UDP . . . E 5 -36.492 -7.911 -16.679 1 60.07 ? O1B UDP 918 A 1 HETATM 24 O O2B UDP . . . E 5 -34.855 -8.782 -15.13 1 81.41 ? O2B UDP 918 A 1 HETATM 25 O O3B UDP . . . E 5 -34.684 -6.491 -15.912 1 71.23 ? O3B UDP 918 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #