data_7FGA # _model_server_result.job_id cfam_CWW2VTKUPz-Qh4ZNg _model_server_result.datetime_utc '2024-10-25 12:20:29' _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 7fga # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 7FGA # _exptl.entry_id 7FGA _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 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 7FGA _cell.length_a 157.712 _cell.length_b 157.712 _cell.length_c 187.803 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7FGA _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,I 1 1 B,F,J 1 2 C,G,K 2 1 D,H,L 2 3 # 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' 5_555 y,-x+y,z+1/6 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 31.3005 3 'crystal symmetry operation' 6_444 x-y-1,x-1,z-1/6 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 -78.856 -136.582598 -31.3005 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L 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 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 Z9N _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 O1 _pdbx_entity_branch_link.leaving_atom_id_2 HO1 _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 E Z9N 1 E 1 Z9N A 402 LIG 2 n E GLC 2 E 2 GLC A 402 LIG 2 n F Z9N 1 F 1 Z9N B 501 LIG 2 n F GLC 2 F 2 GLC B 501 LIG 2 n G Z9N 1 G 1 Z9N C 402 LIG 2 n G GLC 2 G 2 GLC C 402 LIG 2 n H Z9N 1 H 1 Z9N D 501 LIG 2 n H GLC 2 H 2 GLC D 501 LIG # 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 E O2 Z9N . E Z9N 1 1_555 E C1 GLC . E GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale2 F O2 Z9N . F Z9N 1 1_555 F C1 GLC . F GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? covale ? covale3 G O2 Z9N . G Z9N 1 1_555 G C1 GLC . G GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale4 H O2 Z9N . H Z9N 1 1_555 H C1 GLC . H GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? # _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 380 n n N1 C6 UDP sing 381 n n N1 C1' UDP sing 382 n n C2 N3 UDP sing 383 n n C2 O2 UDP doub 384 n n N3 C4 UDP sing 385 n n N3 HN3 UDP sing 386 n n C4 C5 UDP sing 387 n n C4 O4 UDP doub 388 n n C5 C6 UDP doub 389 n n C5 H5 UDP sing 390 n n C6 H6 UDP sing 391 n n C1' C2' UDP sing 392 n n C1' O4' UDP sing 393 n n C1' H1' UDP sing 394 n n C2' O2' UDP sing 395 n n C2' C3' UDP sing 396 n n C2' H2' UDP sing 397 n n O2' HO2' UDP sing 398 n n C3' C4' UDP sing 399 n n C3' O3' UDP sing 400 n n C3' H3' UDP sing 401 n n C4' O4' UDP sing 402 n n C4' C5' UDP sing 403 n n C4' H4' UDP sing 404 n n O3' HO3' UDP sing 405 n n C5' O5' UDP sing 406 n n C5' "H5'1" UDP sing 407 n n C5' "H5'2" UDP sing 408 n n O5' PA UDP sing 409 n n PA O1A UDP doub 410 n n PA O2A UDP sing 411 n n PA O3A UDP sing 412 n n O2A HOA2 UDP sing 413 n n O3A PB UDP sing 414 n n PB O1B UDP doub 415 n n PB O2B UDP sing 416 n n PB O3B UDP sing 417 n n O2B HOB2 UDP sing 418 n n O3B HOB3 UDP sing 419 n n # _atom_sites.entry_id 7FGA _atom_sites.fract_transf_matrix[1][1] 0.006341 _atom_sites.fract_transf_matrix[1][2] 0.003661 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007322 _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] 0.005325 _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 I 3 UDP A 1 401 401 UDP B4H . J 3 UDP B 1 401 401 UDP B4H . K 3 UDP C 1 401 401 UDP B4H . L 3 UDP D 1 401 401 UDP B4H . # 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 . . . J 3 69.296 -38.274 -10.807 1 58.27 ? N1 UDP 401 B 1 HETATM 2 C C2 UDP . . . J 3 69.5 -39.385 -11.58 1 59.65 ? C2 UDP 401 B 1 HETATM 3 N N3 UDP . . . J 3 70.635 -39.778 -11.939 1 64.5 ? N3 UDP 401 B 1 HETATM 4 C C4 UDP . . . J 3 71.703 -39.247 -11.666 1 62.29 ? C4 UDP 401 B 1 HETATM 5 C C5 UDP . . . J 3 71.821 -38.163 -10.94 1 56.99 ? C5 UDP 401 B 1 HETATM 6 C C6 UDP . . . J 3 70.548 -37.651 -10.488 1 56.33 ? C6 UDP 401 B 1 HETATM 7 O O2 UDP . . . J 3 68.557 -40.013 -11.93 1 57.18 ? O2 UDP 401 B 1 HETATM 8 O O4 UDP . . . J 3 72.692 -39.747 -12.085 1 56.41 ? O4 UDP 401 B 1 HETATM 9 C C1' UDP . . . J 3 68.032 -37.804 -10.39 1 57.99 ? C1' UDP 401 B 1 HETATM 10 C C2' UDP . . . J 3 67.559 -38.557 -9.206 1 47.47 ? C2' UDP 401 B 1 HETATM 11 O O2' UDP . . . J 3 66.59 -39.56 -9.629 1 54.44 ? O2' UDP 401 B 1 HETATM 12 C C3' UDP . . . J 3 66.905 -37.616 -8.32 1 47.7 ? C3' UDP 401 B 1 HETATM 13 C C4' UDP . . . J 3 67.17 -36.248 -8.824 1 49.45 ? C4' UDP 401 B 1 HETATM 14 O O4' UDP . . . J 3 68.11 -36.347 -9.999 1 57.74 ? O4' UDP 401 B 1 HETATM 15 O O3' UDP . . . J 3 65.467 -37.868 -8.329 1 54.12 ? O3' UDP 401 B 1 HETATM 16 C C5' UDP . . . J 3 67.802 -35.445 -7.754 1 54.15 ? C5' UDP 401 B 1 HETATM 17 O O5' UDP . . . J 3 67.186 -35.737 -6.532 1 51.31 ? O5' UDP 401 B 1 HETATM 18 P PA UDP . . . J 3 67.268 -34.6 -5.346 1 57.04 ? PA UDP 401 B 1 HETATM 19 O O1A UDP . . . J 3 65.98 -33.944 -5.147 1 62.38 ? O1A UDP 401 B 1 HETATM 20 O O2A UDP . . . J 3 67.485 -35.212 -4.038 1 57.87 ? O2A UDP 401 B 1 HETATM 21 O O3A UDP . . . J 3 68.463 -33.525 -5.711 1 61.55 ? O3A UDP 401 B 1 HETATM 22 P PB UDP . . . J 3 68.192 -31.963 -6.166 1 74.24 ? PB UDP 401 B 1 HETATM 23 O O1B UDP . . . J 3 68.95 -31.642 -7.372 1 59.7 ? O1B UDP 401 B 1 HETATM 24 O O2B UDP . . . J 3 68.564 -30.933 -4.934 1 67.37 ? O2B UDP 401 B 1 HETATM 25 O O3B UDP . . . J 3 66.822 -31.762 -6.632 1 57.88 ? O3B UDP 401 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #