data_4RVF # _model_server_result.job_id YWhRm_ptpDWKRGBcqY6SKw _model_server_result.datetime_utc '2025-02-20 13:54:27' _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 4rvf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 4RVF # _exptl.entry_id 4RVF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-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 4RVF _cell.length_a 134.214 _cell.length_b 134.214 _cell.length_c 132.293 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RVF _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A C CYS 348 A CYS 348 1_555 A N CSO 349 A CSO 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C CSO 349 A CSO 349 1_555 A N ASP 350 A ASP 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A SG CYS 13 A CYS 13 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc2 A SG CYS 16 A CYS 16 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc3 A SG CYS 56 A CYS 56 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc4 A SG CYS 59 A CYS 59 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _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 PA O1A TYD doub 348 n n PA O2A TYD sing 349 n n PA O3A TYD sing 350 n n PA O5' TYD sing 351 n n O2A HOA2 TYD sing 352 n n O3A PB TYD sing 353 n n PB O1B TYD doub 354 n n PB O2B TYD sing 355 n n PB O3B TYD sing 356 n n O2B HOB2 TYD sing 357 n n O3B HOB3 TYD sing 358 n n O5' C5' TYD sing 359 n n C5' C4' TYD sing 360 n n C5' "H5'1" TYD sing 361 n n C5' "H5'2" TYD sing 362 n n C4' O4' TYD sing 363 n n C4' C3' TYD sing 364 n n C4' H4' TYD sing 365 n n O4' C1' TYD sing 366 n n C3' O3' TYD sing 367 n n C3' C2' TYD sing 368 n n C3' H3' TYD sing 369 n n O3' HO3' TYD sing 370 n n C2' C1' TYD sing 371 n n C2' "H2'1" TYD sing 372 n n C2' "H2'2" TYD sing 373 n n C1' N1 TYD sing 374 n n C1' H1' TYD sing 375 n n N1 C2 TYD sing 376 n y N1 C6 TYD sing 377 n y C2 O2 TYD doub 378 n n C2 N3 TYD sing 379 n y N3 C4 TYD sing 380 n y N3 HN3 TYD sing 381 n n C4 O4 TYD doub 382 n n C4 C5 TYD sing 383 n y C5 C5M TYD sing 384 n n C5 C6 TYD doub 385 n y C5M H51 TYD sing 386 n n C5M H52 TYD sing 387 n n C5M H53 TYD sing 388 n n C6 H6 TYD sing 389 n n # _atom_sites.entry_id 4RVF _atom_sites.fract_transf_matrix[1][1] 0.007451 _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] 0.007451 _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] 0.007559 _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 B 2 ZN A 1 501 500 ZN ZN . C 3 TYD A 1 502 507 TYD TYD . D 4 HOH A 1 601 1 HOH HOH . D 4 HOH A 2 602 2 HOH HOH . D 4 HOH A 3 603 4 HOH HOH . D 4 HOH A 4 604 5 HOH HOH . D 4 HOH A 5 605 8 HOH HOH . D 4 HOH A 6 606 10 HOH HOH . D 4 HOH A 7 607 12 HOH HOH . D 4 HOH A 8 608 16 HOH HOH . # 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 P PA TYD . . . C 3 -21.221 5.19 11.703 1 77.97 ? PA TYD 502 A 1 HETATM 2 O O1A TYD . . . C 3 -21.017 5.124 10.202 1 76.16 ? O1A TYD 502 A 1 HETATM 3 O O2A TYD . . . C 3 -21.966 6.348 12.327 1 72.5 ? O2A TYD 502 A 1 HETATM 4 O O3A TYD . . . C 3 -22.027 3.867 12.139 1 80.9 ? O3A TYD 502 A 1 HETATM 5 P PB TYD . . . C 3 -21.322 2.423 12.126 1 84.89 ? PB TYD 502 A 1 HETATM 6 O O1B TYD . . . C 3 -20.528 2.395 10.836 1 79.31 ? O1B TYD 502 A 1 HETATM 7 O O2B TYD . . . C 3 -20.491 2.453 13.391 1 84.8 ? O2B TYD 502 A 1 HETATM 8 O O3B TYD . . . C 3 -22.49 1.464 12.169 0.5 81.83 ? O3B TYD 502 A 1 HETATM 9 O O5' TYD . . . C 3 -19.793 5.005 12.442 1 71.76 ? O5' TYD 502 A 1 HETATM 10 C C5' TYD . . . C 3 -18.53 5.256 11.813 1 66.46 ? C5' TYD 502 A 1 HETATM 11 C C4' TYD . . . C 3 -17.926 6.564 12.335 1 62.43 ? C4' TYD 502 A 1 HETATM 12 O O4' TYD . . . C 3 -16.669 6.308 12.981 1 58.64 ? O4' TYD 502 A 1 HETATM 13 C C3' TYD . . . C 3 -17.649 7.593 11.242 1 60.59 ? C3' TYD 502 A 1 HETATM 14 O O3' TYD . . . C 3 -18.18 8.875 11.61 1 58.95 ? O3' TYD 502 A 1 HETATM 15 C C2' TYD . . . C 3 -16.137 7.676 11.129 1 58.87 ? C2' TYD 502 A 1 HETATM 16 C C1' TYD . . . C 3 -15.636 7.163 12.471 1 57.17 ? C1' TYD 502 A 1 HETATM 17 N N1 TYD . . . C 3 -14.336 6.472 12.366 1 54.36 ? N1 TYD 502 A 1 HETATM 18 C C2 TYD . . . C 3 -13.129 7.194 12.583 1 51.91 ? C2 TYD 502 A 1 HETATM 19 O O2 TYD . . . C 3 -13.16 8.411 12.849 1 50.56 ? O2 TYD 502 A 1 HETATM 20 N N3 TYD . . . C 3 -11.929 6.6 12.507 1 51.82 ? N3 TYD 502 A 1 HETATM 21 C C4 TYD . . . C 3 -11.818 5.297 12.224 1 51.94 ? C4 TYD 502 A 1 HETATM 22 O O4 TYD . . . C 3 -10.687 4.76 12.157 1 50.3 ? O4 TYD 502 A 1 HETATM 23 C C5 TYD . . . C 3 -13.057 4.512 11.99 1 51.11 ? C5 TYD 502 A 1 HETATM 24 C C5M TYD . . . C 3 -12.995 3.045 11.665 1 51.02 ? C5M TYD 502 A 1 HETATM 25 C C6 TYD . . . C 3 -14.284 5.159 12.079 1 52.47 ? C6 TYD 502 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 25 #