data_6H0N # _model_server_result.job_id u5cCcAVjrJqIgh9evFYSrg _model_server_result.datetime_utc '2024-12-22 02:15:34' _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 6h0n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 6H0N # _exptl.entry_id 6H0N _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 2 _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 6H0N _cell.length_a 146.028 _cell.length_b 146.028 _cell.length_c 132.845 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6H0N _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,E,F,G,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G N N # _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 437 n n N1 C6 UDP sing 438 n n N1 C1' UDP sing 439 n n C2 N3 UDP sing 440 n n C2 O2 UDP doub 441 n n N3 C4 UDP sing 442 n n N3 HN3 UDP sing 443 n n C4 C5 UDP sing 444 n n C4 O4 UDP doub 445 n n C5 C6 UDP doub 446 n n C5 H5 UDP sing 447 n n C6 H6 UDP sing 448 n n C1' C2' UDP sing 449 n n C1' O4' UDP sing 450 n n C1' H1' UDP sing 451 n n C2' O2' UDP sing 452 n n C2' C3' UDP sing 453 n n C2' H2' UDP sing 454 n n O2' HO2' UDP sing 455 n n C3' C4' UDP sing 456 n n C3' O3' UDP sing 457 n n C3' H3' UDP sing 458 n n C4' O4' UDP sing 459 n n C4' C5' UDP sing 460 n n C4' H4' UDP sing 461 n n O3' HO3' UDP sing 462 n n C5' O5' UDP sing 463 n n C5' "H5'1" UDP sing 464 n n C5' "H5'2" UDP sing 465 n n O5' PA UDP sing 466 n n PA O1A UDP doub 467 n n PA O2A UDP sing 468 n n PA O3A UDP sing 469 n n O2A HOA2 UDP sing 470 n n O3A PB UDP sing 471 n n PB O1B UDP doub 472 n n PB O2B UDP sing 473 n n PB O3B UDP sing 474 n n O2B HOB2 UDP sing 475 n n O3B HOB3 UDP sing 476 n n # _atom_sites.entry_id 6H0N _atom_sites.fract_transf_matrix[1][1] 0.006848 _atom_sites.fract_transf_matrix[1][2] 0.003954 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007907 _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] 0.007528 _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 C 2 NAD A 1 401 800 NAD NAD . D 3 UDP A 1 402 900 UDP UDP . E 4 PO4 A 1 403 902 PO4 PO4 . F 2 NAD B 1 401 800 NAD NAD . G 3 UDP B 1 402 900 UDP UDP . H 4 PO4 B 1 403 902 PO4 PO4 . I 5 HOH A 1 501 112 HOH HOH . I 5 HOH A 2 502 24 HOH HOH . I 5 HOH A 3 503 52 HOH HOH . I 5 HOH A 4 504 20 HOH HOH . I 5 HOH A 5 505 31 HOH HOH . I 5 HOH A 6 506 23 HOH HOH . I 5 HOH A 7 507 29 HOH HOH . I 5 HOH A 8 508 32 HOH HOH . I 5 HOH A 9 509 13 HOH HOH . I 5 HOH A 10 510 12 HOH HOH . I 5 HOH A 11 511 33 HOH HOH . I 5 HOH A 12 512 14 HOH HOH . J 5 HOH B 1 501 95 HOH HOH . J 5 HOH B 2 502 34 HOH HOH . J 5 HOH B 3 503 28 HOH HOH . J 5 HOH B 4 504 15 HOH HOH . J 5 HOH B 5 505 11 HOH HOH . J 5 HOH B 6 506 13 HOH HOH . J 5 HOH B 7 507 37 HOH HOH . J 5 HOH B 8 508 25 HOH HOH . J 5 HOH B 9 509 12 HOH HOH . J 5 HOH B 10 510 11 HOH HOH . J 5 HOH B 11 511 9 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 N N1 UDP . . . D 3 1.367 65.078 71.154 1 80.16 ? N1 UDP 402 A 1 HETATM 2 C C2 UDP . . . D 3 2.502 65.343 71.967 1 83.53 ? C2 UDP 402 A 1 HETATM 3 N N3 UDP . . . D 3 2.856 64.561 72.999 1 87.85 ? N3 UDP 402 A 1 HETATM 4 C C4 UDP . . . D 3 2.139 63.492 73.334 1 91.8 ? C4 UDP 402 A 1 HETATM 5 C C5 UDP . . . D 3 1.008 63.196 72.583 1 92.99 ? C5 UDP 402 A 1 HETATM 6 C C6 UDP . . . D 3 0.64 64.01 71.504 1 88.64 ? C6 UDP 402 A 1 HETATM 7 O O2 UDP . . . D 3 3.246 66.31 71.749 1 89 ? O2 UDP 402 A 1 HETATM 8 O O4 UDP . . . D 3 2.484 62.787 74.313 1 96.45 ? O4 UDP 402 A 1 HETATM 9 C C1' UDP . . . D 3 0.967 65.965 70.011 1 80.51 ? C1' UDP 402 A 1 HETATM 10 C C2' UDP . . . D 3 0.665 65.342 68.634 1 77.43 ? C2' UDP 402 A 1 HETATM 11 O O2' UDP . . . D 3 1.804 65.277 67.79 1 74.75 ? O2' UDP 402 A 1 HETATM 12 C C3' UDP . . . D 3 -0.374 66.294 68.039 1 77.73 ? C3' UDP 402 A 1 HETATM 13 C C4' UDP . . . D 3 -1.156 66.804 69.246 1 75 ? C4' UDP 402 A 1 HETATM 14 O O4' UDP . . . D 3 -0.233 66.703 70.35 1 80.46 ? O4' UDP 402 A 1 HETATM 15 O O3' UDP . . . D 3 0.197 67.425 67.372 1 74.89 ? O3' UDP 402 A 1 HETATM 16 C C5' UDP . . . D 3 -2.424 65.999 69.541 1 69.53 ? C5' UDP 402 A 1 HETATM 17 O O5' UDP . . . D 3 -2.218 64.657 69.093 1 68.87 ? O5' UDP 402 A 1 HETATM 18 P PA UDP . . . D 3 -3.182 63.439 69.41 1 66 ? PA UDP 402 A 1 HETATM 19 O O1A UDP . . . D 3 -2.295 62.202 69.422 1 68.4 ? O1A UDP 402 A 1 HETATM 20 O O2A UDP . . . D 3 -4.082 63.755 70.61 1 60.59 ? O2A UDP 402 A 1 HETATM 21 O O3A UDP . . . D 3 -4.101 63.398 68.064 1 69.62 ? O3A UDP 402 A 1 HETATM 22 P PB UDP . . . D 3 -4.292 64.422 66.805 1 70.08 ? PB UDP 402 A 1 HETATM 23 O O1B UDP . . . D 3 -5.251 63.679 65.898 1 69.31 ? O1B UDP 402 A 1 HETATM 24 O O2B UDP . . . D 3 -4.931 65.705 67.283 1 61.55 ? O2B UDP 402 A 1 HETATM 25 O O3B UDP . . . D 3 -2.867 64.533 66.273 1 76.27 ? O3B UDP 402 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 25 #