data_2C37 # _model_server_result.job_id MHAKnk8qzjsUjUWkZU9Q3g _model_server_result.datetime_utc '2024-10-19 08:23:33' _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 2c37 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":402}' # _entry.id 2C37 # _exptl.entry_id 2C37 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 25 _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 2C37 _cell.length_a 207.02 _cell.length_b 212.94 _cell.length_c 433.09 _cell.Z_PDB 96 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2C37 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS hexameric 6 author_and_software_defined_assembly 1 PQS hexameric 6 author_and_software_defined_assembly 2 PQS hexameric 6 author_and_software_defined_assembly 3 PQS hexameric 6 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA 1 1 G,H,I,J,K,L,JA,KA,LA,MA,NA,OA,PA,QA,RA 2 1 M,N,O,P,Q,R,SA,TA,UA,VA,WA,XA,YA 3 1 S,T,U,V,W,X,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB 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 ? 3 Y N N ? 3 Z N N ? 3 BA N N ? 3 CA N N ? 3 EA N N ? 3 FA N N ? 3 GA N N ? 3 IA N N ? 3 JA N N ? 3 KA N N ? 3 MA N N ? 3 NA N N ? 3 OA N N ? 3 QA N N ? 3 SA N N ? 3 TA N N ? 3 VA N N ? 3 AB N N ? 3 BB N N ? 3 CB N N ? 3 EB N N ? 3 GB N N ? 3 HB N N ? 3 IB N N ? 3 KB 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 Y O3' U5P . A U5P 401 1_555 BA P U5P . B U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? covale ? covale2 Z P U5P . A U5P 402 1_555 BA O3' U5P . B U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.624 ? covale ? covale3 Z O3' U5P . A U5P 402 1_555 CA P U5P . B U5P 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? covale ? covale4 EA O3' U5P . E U5P 401 1_555 FA P U5P . E U5P 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.617 ? covale ? covale5 FA O3' U5P . E U5P 402 1_555 GA P U5P . E U5P 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? covale ? covale6 GA O3' U5P . E U5P 403 1_555 IA P U5P . F U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.621 ? covale ? covale7 JA O3' U5P . G U5P 401 1_555 MA P U5P . H U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.619 ? covale ? covale8 KA P U5P . G U5P 402 1_555 MA O3' U5P . H U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? covale ? covale9 NA O3' U5P . I U5P 401 1_555 QA P U5P . J U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.623 ? covale ? covale10 OA P U5P . I U5P 402 1_555 QA O3' U5P . J U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? covale ? covale11 SA O3' U5P . M U5P 401 1_555 VA P U5P . N U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.62 ? covale ? covale12 TA P U5P . M U5P 402 1_555 VA O3' U5P . N U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? covale ? covale13 AB O3' U5P . U U5P 401 1_555 BB P U5P . U U5P 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? covale ? covale14 BB O3' U5P . U U5P 402 1_555 CB P U5P . U U5P 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale15 CB O3' U5P . U U5P 403 1_555 EB P U5P . V U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? covale ? covale16 GB O3' U5P . W U5P 401 1_555 HB P U5P . W U5P 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.617 ? covale ? covale17 HB O3' U5P . W U5P 402 1_555 IB P U5P . W U5P 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? covale ? covale18 IB O3' U5P . W U5P 403 1_555 KB P U5P . X U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.621 ? metalc ? metalc1 CB O1P U5P . U U5P 403 1_555 FB NA NA . V NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc2 EB O2P U5P . V U5P 302 1_555 FB NA NA . V NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _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 U5P sing 381 n n N1 C6 U5P sing 382 n n N1 C1' U5P sing 383 n n C2 N3 U5P sing 384 n n C2 O2 U5P doub 385 n n N3 C4 U5P sing 386 n n N3 HN3 U5P sing 387 n n C4 C5 U5P sing 388 n n C4 O4 U5P doub 389 n n C5 C6 U5P doub 390 n n C5 H5 U5P sing 391 n n C6 H6 U5P sing 392 n n C1' C2' U5P sing 393 n n C1' O4' U5P sing 394 n n C1' H1' U5P sing 395 n n C2' O2' U5P sing 396 n n C2' C3' U5P sing 397 n n C2' H2' U5P sing 398 n n O2' HO2' U5P sing 399 n n C3' C4' U5P sing 400 n n C3' O3' U5P sing 401 n n C3' H3' U5P sing 402 n n C4' O4' U5P sing 403 n n C4' C5' U5P sing 404 n n C4' H4' U5P sing 405 n n O3' HO3' U5P sing 406 n n C5' O5' U5P sing 407 n n C5' "H5'1" U5P sing 408 n n C5' "H5'2" U5P sing 409 n n O5' P U5P sing 410 n n P O1P U5P doub 411 n n P O2P U5P sing 412 n n P O3P U5P sing 413 n n O2P HOP2 U5P sing 414 n n O3P HOP3 U5P sing 415 n n # _atom_sites.entry_id 2C37 _atom_sites.fract_transf_matrix[1][1] 0.00483 _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] 0.004696 _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] 0.002309 _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 Y 3 U5P A 1 401 401 U5P U5P . Z 3 U5P A 1 402 403 U5P U5P . AA 4 CL B 1 301 301 CL CL . BA 3 U5P B 1 302 402 U5P U5P . CA 3 U5P B 1 303 404 U5P U5P . DA 4 CL D 1 301 301 CL CL . EA 3 U5P E 1 401 401 U5P U5P . FA 3 U5P E 1 402 402 U5P U5P . GA 3 U5P E 1 403 403 U5P U5P . HA 4 CL F 1 301 301 CL CL . IA 3 U5P F 1 302 404 U5P U5P . JA 3 U5P G 1 401 401 U5P U5P . KA 3 U5P G 1 402 403 U5P U5P . LA 4 CL H 1 301 301 CL CL . MA 3 U5P H 1 302 402 U5P U5P . NA 3 U5P I 1 401 401 U5P U5P . OA 3 U5P I 1 402 403 U5P U5P . PA 4 CL J 1 301 301 CL CL . QA 3 U5P J 1 302 402 U5P U5P . RA 4 CL L 1 301 301 CL CL . SA 3 U5P M 1 401 401 U5P U5P . TA 3 U5P M 1 402 403 U5P U5P . UA 4 CL N 1 301 301 CL CL . VA 3 U5P N 1 302 402 U5P U5P . WA 5 RP5 N 1 303 405 RP5 RP5 . XA 4 CL P 1 301 301 CL CL . YA 4 CL R 1 301 301 CL CL . ZA 4 CL T 1 301 301 CL CL . AB 3 U5P U 1 401 401 U5P U5P . BB 3 U5P U 1 402 402 U5P U5P . CB 3 U5P U 1 403 403 U5P U5P . DB 4 CL V 1 301 301 CL CL . EB 3 U5P V 1 302 404 U5P U5P . FB 6 NA V 1 303 501 NA NA . GB 3 U5P W 1 401 401 U5P U5P . HB 3 U5P W 1 402 402 U5P U5P . IB 3 U5P W 1 403 403 U5P U5P . JB 4 CL X 1 301 301 CL CL . KB 3 U5P X 1 302 404 U5P U5P . # 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 U5P . . . Z 3 -31.439 -7.038 -19.097 1 107.09 ? N1 U5P 402 A 1 HETATM 2 C C2 U5P . . . Z 3 -30.799 -7.909 -19.989 1 107.08 ? C2 U5P 402 A 1 HETATM 3 N N3 U5P . . . Z 3 -29.548 -7.484 -20.403 1 107.35 ? N3 U5P 402 A 1 HETATM 4 C C4 U5P . . . Z 3 -28.882 -6.311 -20.04 1 107.74 ? C4 U5P 402 A 1 HETATM 5 C C5 U5P . . . Z 3 -29.609 -5.459 -19.126 1 107.74 ? C5 U5P 402 A 1 HETATM 6 C C6 U5P . . . Z 3 -30.826 -5.849 -18.709 1 107.65 ? C6 U5P 402 A 1 HETATM 7 O O2 U5P . . . Z 3 -31.255 -8.969 -20.389 1 106.78 ? O2 U5P 402 A 1 HETATM 8 O O4 U5P . . . Z 3 -27.761 -6.062 -20.487 1 107.05 ? O4 U5P 402 A 1 HETATM 9 C C1' U5P . . . Z 3 -32.838 -7.274 -18.515 1 106.35 ? C1' U5P 402 A 1 HETATM 10 C C2' U5P . . . Z 3 -33.984 -7.162 -19.54 1 105.53 ? C2' U5P 402 A 1 HETATM 11 O O2' U5P . . . Z 3 -34.693 -5.943 -19.37 1 105.59 ? O2' U5P 402 A 1 HETATM 12 C C3' U5P . . . Z 3 -34.819 -8.417 -19.242 1 104.59 ? C3' U5P 402 A 1 HETATM 13 C C4' U5P . . . Z 3 -34.469 -8.651 -17.774 1 104.34 ? C4' U5P 402 A 1 HETATM 14 O O3' U5P . . . Z 3 -36.23 -8.243 -19.455 1 103.37 ? O3' U5P 402 A 1 HETATM 15 O O4' U5P . . . Z 3 -33.024 -8.503 -17.823 1 105.55 ? O4' U5P 402 A 1 HETATM 16 C C5' U5P . . . Z 3 -34.885 -9.978 -17.17 1 103.36 ? C5' U5P 402 A 1 HETATM 17 O O5' U5P . . . Z 3 -34.835 -11.011 -18.155 1 102.43 ? O5' U5P 402 A 1 HETATM 18 P P U5P . . . Z 3 -35.174 -12.55 -17.837 1 101.76 ? P U5P 402 A 1 HETATM 19 O O1P U5P . . . Z 3 -36.622 -12.693 -17.557 1 101.16 ? O1P U5P 402 A 1 HETATM 20 O O2P U5P . . . Z 3 -34.572 -13.32 -18.948 1 100.61 ? O2P U5P 402 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 69 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #