data_6KIH # _model_server_result.job_id n2g2JviQjGR8iKKllYlJ1w _model_server_result.datetime_utc '2024-10-19 00:44:31' _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 6kih # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"EA","auth_seq_id":701}' # _entry.id 6KIH # _exptl.entry_id 6KIH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.43 _cell.angle_gamma 90 _cell.entry_id 6KIH _cell.length_a 116.662 _cell.length_b 170.835 _cell.length_c 160.546 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KIH _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 PISA monomeric 1 author_and_software_defined_assembly 5 PISA monomeric 1 author_and_software_defined_assembly 6 PISA monomeric 1 author_and_software_defined_assembly 7 PISA monomeric 1 author_and_software_defined_assembly 8 PISA monomeric 1 author_and_software_defined_assembly 9 PISA monomeric 1 author_and_software_defined_assembly 10 PISA monomeric 1 author_and_software_defined_assembly 11 PISA monomeric 1 author_and_software_defined_assembly 12 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,M,V 1 1 B,W 2 1 C,N,X 3 1 D,O,Y 4 1 E,P,Z 5 1 F,Q,AA 6 1 G,BA 7 1 H,R,CA 8 1 I,S,DA 9 1 J,EA 10 1 K,T,FA 11 1 L,U,GA 12 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 ? 3 V N N ? 3 W N N ? 3 X N N ? 3 Y N N ? 3 Z N N ? 3 AA N N ? 3 BA N N ? 3 CA N N ? 3 DA N N ? 3 EA N N ? 3 FA N N ? 3 GA N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 F6P _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 2 n M GLC 1 M 1 GLC A 601 SUP 2 n M F6P 2 M 2 F6P A 601 SUP 2 n N GLC 1 N 1 GLC N 601 SUP 2 n N F6P 2 N 2 F6P N 601 SUP 2 n O GLC 1 O 1 GLC O 601 SUP 2 n O F6P 2 O 2 F6P O 601 SUP 2 n P GLC 1 P 1 GLC P 601 SUP 2 n P F6P 2 P 2 F6P P 601 SUP 2 n Q GLC 1 Q 1 GLC Q 601 SUP 2 n Q F6P 2 Q 2 F6P Q 601 SUP 2 n R GLC 1 R 1 GLC S 601 SUP 2 n R F6P 2 R 2 F6P S 601 SUP 2 n S GLC 1 S 1 GLC T 601 SUP 2 n S F6P 2 S 2 F6P T 601 SUP 2 n T GLC 1 T 1 GLC V 601 SUP 2 n T F6P 2 T 2 F6P V 601 SUP 2 n U GLC 1 U 1 GLC W 601 SUP 2 n U F6P 2 U 2 F6P W 601 SUP # 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 covale ? covale1 M C1 GLC . M GLC 1 1_555 M O2 F6P . M F6P 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 sing covale ? covale2 N C1 GLC . N GLC 1 1_555 N O2 F6P . N F6P 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 sing covale ? covale3 O C1 GLC . O GLC 1 1_555 O O2 F6P . O F6P 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 sing covale ? covale4 P C1 GLC . P GLC 1 1_555 P O2 F6P . P F6P 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 sing covale ? covale5 Q C1 GLC . Q GLC 1 1_555 Q O2 F6P . Q F6P 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 sing covale ? covale6 R C1 GLC . R GLC 1 1_555 R O2 F6P . R F6P 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 sing covale ? covale7 S C1 GLC . S GLC 1 1_555 S O2 F6P . S F6P 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 sing covale ? covale8 T C1 GLC . T GLC 1 1_555 T O2 F6P . T F6P 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 sing covale ? covale9 U C1 GLC . U GLC 1 1_555 U O2 F6P . U F6P 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 sing # _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 409 n n N1 C6 UDP sing 410 n n N1 C1' UDP sing 411 n n C2 N3 UDP sing 412 n n C2 O2 UDP doub 413 n n N3 C4 UDP sing 414 n n N3 HN3 UDP sing 415 n n C4 C5 UDP sing 416 n n C4 O4 UDP doub 417 n n C5 C6 UDP doub 418 n n C5 H5 UDP sing 419 n n C6 H6 UDP sing 420 n n C1' C2' UDP sing 421 n n C1' O4' UDP sing 422 n n C1' H1' UDP sing 423 n n C2' O2' UDP sing 424 n n C2' C3' UDP sing 425 n n C2' H2' UDP sing 426 n n O2' HO2' UDP sing 427 n n C3' C4' UDP sing 428 n n C3' O3' UDP sing 429 n n C3' H3' UDP sing 430 n n C4' O4' UDP sing 431 n n C4' C5' UDP sing 432 n n C4' H4' UDP sing 433 n n O3' HO3' UDP sing 434 n n C5' O5' UDP sing 435 n n C5' "H5'1" UDP sing 436 n n C5' "H5'2" UDP sing 437 n n O5' PA UDP sing 438 n n PA O1A UDP doub 439 n n PA O2A UDP sing 440 n n PA O3A UDP sing 441 n n O2A HOA2 UDP sing 442 n n O3A PB UDP sing 443 n n PB O1B UDP doub 444 n n PB O2B UDP sing 445 n n PB O3B UDP sing 446 n n O2B HOB2 UDP sing 447 n n O3B HOB3 UDP sing 448 n n # _atom_sites.entry_id 6KIH _atom_sites.fract_transf_matrix[1][1] 0.008572 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000966 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005854 _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] 0.006268 _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 V 3 UDP A 1 602 701 UDP UDP . W 3 UDP B 1 701 701 UDP UDP . X 3 UDP C 1 602 701 UDP UDP . Y 3 UDP D 1 602 701 UDP UDP . Z 3 UDP E 1 602 701 UDP UDP . AA 3 UDP F 1 602 701 UDP UDP . BA 3 UDP G 1 701 701 UDP UDP . CA 3 UDP H 1 602 701 UDP UDP . DA 3 UDP I 1 602 701 UDP UDP . EA 3 UDP J 1 701 701 UDP UDP . FA 3 UDP K 1 602 701 UDP UDP . GA 3 UDP L 1 602 701 UDP UDP . # 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 . . . EA 3 48.154 11.998 98.44 1 75.29 ? N1 UDP 701 J 1 HETATM 2 C C2 UDP . . . EA 3 46.891 11.864 98.909 1 79.55 ? C2 UDP 701 J 1 HETATM 3 N N3 UDP . . . EA 3 45.89 12.288 98.289 1 82.41 ? N3 UDP 701 J 1 HETATM 4 C C4 UDP . . . EA 3 45.916 12.864 97.211 1 78.86 ? C4 UDP 701 J 1 HETATM 5 C C5 UDP . . . EA 3 47.007 13.118 96.532 1 79.39 ? C5 UDP 701 J 1 HETATM 6 C C6 UDP . . . EA 3 48.208 12.664 97.183 1 75.16 ? C6 UDP 701 J 1 HETATM 7 O O2 UDP . . . EA 3 46.747 11.314 99.953 1 80.46 ? O2 UDP 701 J 1 HETATM 8 O O4 UDP . . . EA 3 44.884 13.21 96.748 1 75.29 ? O4 UDP 701 J 1 HETATM 9 C C1' UDP . . . EA 3 49.255 11.525 99.119 1 72.07 ? C1' UDP 701 J 1 HETATM 10 C C2' UDP . . . EA 3 49.862 10.437 98.34 1 71.34 ? C2' UDP 701 J 1 HETATM 11 O O2' UDP . . . EA 3 49.212 9.158 98.637 1 69.58 ? O2' UDP 701 J 1 HETATM 12 C C3' UDP . . . EA 3 51.219 10.46 98.818 1 73.52 ? C3' UDP 701 J 1 HETATM 13 C C4' UDP . . . EA 3 51.557 11.885 99.09 1 78.47 ? C4' UDP 701 J 1 HETATM 14 O O4' UDP . . . EA 3 50.252 12.641 99.148 1 76.46 ? O4' UDP 701 J 1 HETATM 15 O O3' UDP . . . EA 3 51.225 9.753 100.099 1 74.38 ? O3' UDP 701 J 1 HETATM 16 C C5' UDP . . . EA 3 52.502 12.557 98.135 1 76.91 ? C5' UDP 701 J 1 HETATM 17 O O5' UDP . . . EA 3 53.111 11.736 97.171 1 71.09 ? O5' UDP 701 J 1 HETATM 18 P PA UDP . . . EA 3 54.76 11.7 97.087 1 72.43 ? PA UDP 701 J 1 HETATM 19 O O1A UDP . . . EA 3 55.206 10.553 96.3 1 75.88 ? O1A UDP 701 J 1 HETATM 20 O O2A UDP . . . EA 3 55.404 11.553 98.384 1 68.5 -1 O2A UDP 701 J 1 HETATM 21 O O3A UDP . . . EA 3 55.381 13.059 96.449 1 84.75 ? O3A UDP 701 J 1 HETATM 22 P PB UDP . . . EA 3 55.394 14.374 97.404 1 83.29 ? PB UDP 701 J 1 HETATM 23 O O1B UDP . . . EA 3 54.111 15.008 97.046 1 75.74 -1 O1B UDP 701 J 1 HETATM 24 O O2B UDP . . . EA 3 56.793 15.232 97.187 1 77.24 -1 O2B UDP 701 J 1 HETATM 25 O O3B UDP . . . EA 3 55.215 14.077 98.822 1 70.66 ? O3B UDP 701 J 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 115 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #