data_4CDR # _model_server_result.job_id 1nCa3_auCkzXERU7LvbE9Q _model_server_result.datetime_utc '2024-11-14 04:28:07' _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 4cdr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"MA","auth_seq_id":1001}' # _entry.id 4CDR # _exptl.entry_id 4CDR _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 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 4CDR _cell.length_a 273.728 _cell.length_b 273.728 _cell.length_c 142.581 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CDR _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 3 2 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 dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression D,H,DA,EA,FA,GA,HA,IA,JA,PA,QA 1 1 C,G,X,Y,Z,AA,BA,CA,OA 2 1 B,F,Q,R,S,T,U,V,W,MA,NA 3 1 A,E,I,J,K,L,M,N,O,P,KA,LA 4 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 KA N N ? 4 MA N N ? 4 OA N N ? 4 PA 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 covale ? covale1 E C ACE 1 E ACE 1 1_555 E N VAL 2 E VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale2 E C VAL 5 E VAL 5 1_555 E N SRZ 6 E SRZ 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale3 E C SRZ 6 E SRZ 6 1_555 E N THR 7 E THR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale4 E CZ SRZ 6 E SRZ 6 1_555 KA O3B UDP . E UDP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale5 E C ALA 8 E ALA 8 1_555 E N NH2 9 E NH2 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale6 F C ACE 1 F ACE 1 1_555 F N VAL 2 F VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale7 F C VAL 5 F VAL 5 1_555 F N SRZ 6 F SRZ 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? covale ? covale8 F C SRZ 6 F SRZ 6 1_555 F N THR 7 F THR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale9 F CZ SRZ 6 F SRZ 6 1_555 MA O3B UDP . F UDP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale10 F C ALA 8 F ALA 8 1_555 F N NH2 9 F NH2 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale11 G C ACE 1 G ACE 1 1_555 G N VAL 2 G VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale12 G C VAL 5 G VAL 5 1_555 G N SRZ 6 G SRZ 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale13 G C SRZ 6 G SRZ 6 1_555 G N THR 7 G THR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale14 G CZ SRZ 6 G SRZ 6 1_555 OA O3B UDP . G UDP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale15 G C ALA 8 G ALA 8 1_555 G N NH2 9 G NH2 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale16 H C ACE 1 H ACE 1 1_555 H N VAL 2 H VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale17 H C VAL 5 H VAL 5 1_555 H N SRZ 6 H SRZ 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? covale ? covale18 H C SRZ 6 H SRZ 6 1_555 H N THR 7 H THR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale19 H CZ SRZ 6 H SRZ 6 1_555 PA O3B UDP . H UDP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale20 H C ALA 8 H ALA 8 1_555 H N NH2 9 H NH2 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? # _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 391 n n N1 C6 UDP sing 392 n n N1 C1' UDP sing 393 n n C2 N3 UDP sing 394 n n C2 O2 UDP doub 395 n n N3 C4 UDP sing 396 n n N3 HN3 UDP sing 397 n n C4 C5 UDP sing 398 n n C4 O4 UDP doub 399 n n C5 C6 UDP doub 400 n n C5 H5 UDP sing 401 n n C6 H6 UDP sing 402 n n C1' C2' UDP sing 403 n n C1' O4' UDP sing 404 n n C1' H1' UDP sing 405 n n C2' O2' UDP sing 406 n n C2' C3' UDP sing 407 n n C2' H2' UDP sing 408 n n O2' HO2' UDP sing 409 n n C3' C4' UDP sing 410 n n C3' O3' UDP sing 411 n n C3' H3' UDP sing 412 n n C4' O4' UDP sing 413 n n C4' C5' UDP sing 414 n n C4' H4' UDP sing 415 n n O3' HO3' UDP sing 416 n n C5' O5' UDP sing 417 n n C5' "H5'1" UDP sing 418 n n C5' "H5'2" UDP sing 419 n n O5' PA UDP sing 420 n n PA O1A UDP doub 421 n n PA O2A UDP sing 422 n n PA O3A UDP sing 423 n n O2A HOA2 UDP sing 424 n n O3A PB UDP sing 425 n n PB O1B UDP doub 426 n n PB O2B UDP sing 427 n n PB O3B UDP sing 428 n n O2B HOB2 UDP sing 429 n n O3B HOB3 UDP sing 430 n n # _atom_sites.entry_id 4CDR _atom_sites.fract_transf_matrix[1][1] 0.003653 _atom_sites.fract_transf_matrix[1][2] 0.002109 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004218 _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] 0.007014 _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 SO4 A 1 2029 2029 SO4 SO4 . J 3 SO4 A 1 2030 2030 SO4 SO4 . K 3 SO4 A 1 2031 2031 SO4 SO4 . L 3 SO4 A 1 2032 2032 SO4 SO4 . M 3 SO4 A 1 2033 2033 SO4 SO4 . N 3 SO4 A 1 2034 2034 SO4 SO4 . O 3 SO4 A 1 2035 2035 SO4 SO4 . P 3 SO4 A 1 2036 2036 SO4 SO4 . Q 3 SO4 B 1 2029 2029 SO4 SO4 . R 3 SO4 B 1 2030 2030 SO4 SO4 . S 3 SO4 B 1 2031 2031 SO4 SO4 . T 3 SO4 B 1 2032 2032 SO4 SO4 . U 3 SO4 B 1 2033 2033 SO4 SO4 . V 3 SO4 B 1 2034 2034 SO4 SO4 . W 3 SO4 B 1 2035 2035 SO4 SO4 . X 3 SO4 C 1 2029 2029 SO4 SO4 . Y 3 SO4 C 1 2030 2030 SO4 SO4 . Z 3 SO4 C 1 2031 2031 SO4 SO4 . AA 3 SO4 C 1 2032 2032 SO4 SO4 . BA 3 SO4 C 1 2033 2033 SO4 SO4 . CA 3 SO4 C 1 2034 2034 SO4 SO4 . DA 3 SO4 D 1 2029 2029 SO4 SO4 . EA 3 SO4 D 1 2030 2030 SO4 SO4 . FA 3 SO4 D 1 2031 2031 SO4 SO4 . GA 3 SO4 D 1 2032 2032 SO4 SO4 . HA 3 SO4 D 1 2033 2033 SO4 SO4 . IA 3 SO4 D 1 2034 2034 SO4 SO4 . JA 3 SO4 D 1 2035 2035 SO4 SO4 . KA 4 UDP E 1 1001 1001 UDP UDP . LA 3 SO4 E 1 1009 1009 SO4 SO4 . MA 4 UDP F 1 1001 1001 UDP UDP . NA 3 SO4 F 1 1009 1009 SO4 SO4 . OA 4 UDP G 1 1001 1001 UDP UDP . PA 4 UDP H 1 1001 1001 UDP UDP . QA 3 SO4 H 1 1009 1009 SO4 SO4 . # 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 . . . MA 4 98.328 27.225 25.574 1 33.93 ? N1 UDP 1001 F 1 HETATM 2 C C2 UDP . . . MA 4 97.689 28.37 25.819 1 35.46 ? C2 UDP 1001 F 1 HETATM 3 N N3 UDP . . . MA 4 96.335 28.515 25.511 1 37.08 ? N3 UDP 1001 F 1 HETATM 4 C C4 UDP . . . MA 4 95.641 27.464 24.918 1 37.27 ? C4 UDP 1001 F 1 HETATM 5 C C5 UDP . . . MA 4 96.311 26.274 24.657 1 36.74 ? C5 UDP 1001 F 1 HETATM 6 C C6 UDP . . . MA 4 97.659 26.164 24.972 1 35.41 ? C6 UDP 1001 F 1 HETATM 7 O O2 UDP . . . MA 4 98.261 29.308 26.367 1 35.9 ? O2 UDP 1001 F 1 HETATM 8 O O4 UDP . . . MA 4 94.447 27.6 24.644 1 38.96 ? O4 UDP 1001 F 1 HETATM 9 C C1' UDP . . . MA 4 99.754 27.129 25.893 1 34.72 ? C1' UDP 1001 F 1 HETATM 10 C C2' UDP . . . MA 4 100.156 25.959 26.709 1 35.82 ? C2' UDP 1001 F 1 HETATM 11 O O2' UDP . . . MA 4 99.933 26.233 28.079 1 37.29 ? O2' UDP 1001 F 1 HETATM 12 C C3' UDP . . . MA 4 101.631 25.967 26.4 1 36.56 ? C3' UDP 1001 F 1 HETATM 13 C C4' UDP . . . MA 4 101.602 26.207 24.919 1 37.48 ? C4' UDP 1001 F 1 HETATM 14 O O4' UDP . . . MA 4 100.312 26.774 24.67 1 36.13 ? O4' UDP 1001 F 1 HETATM 15 O O3' UDP . . . MA 4 102.298 27.102 26.98 1 36.57 ? O3' UDP 1001 F 1 HETATM 16 C C5' UDP . . . MA 4 101.647 24.875 24.167 1 40.18 ? C5' UDP 1001 F 1 HETATM 17 O O5' UDP . . . MA 4 102.854 24.824 23.394 1 42.58 ? O5' UDP 1001 F 1 HETATM 18 P PA UDP . . . MA 4 103.388 23.403 22.855 1 42.83 ? PA UDP 1001 F 1 HETATM 19 O O1A UDP . . . MA 4 102.357 22.905 21.88 1 42.19 ? O1A UDP 1001 F 1 HETATM 20 O O2A UDP . . . MA 4 104.835 23.527 22.482 1 41.65 ? O2A UDP 1001 F 1 HETATM 21 O O3A UDP . . . MA 4 103.231 22.634 24.234 1 40.45 ? O3A UDP 1001 F 1 HETATM 22 P PB UDP . . . MA 4 103.788 21.206 24.558 1 40.44 ? PB UDP 1001 F 1 HETATM 23 O O1B UDP . . . MA 4 102.808 20.669 25.557 1 40.72 ? O1B UDP 1001 F 1 HETATM 24 O O2B UDP . . . MA 4 104.093 20.379 23.372 1 40.35 ? O2B UDP 1001 F 1 HETATM 25 O O3B UDP . . . MA 4 105.199 21.677 25.204 1 39.87 ? O3B UDP 1001 F 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 362 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #