data_3NYN # _model_server_result.job_id dME0PElxa59clFLfXOvQ-g _model_server_result.datetime_utc '2024-11-01 17:25:56' _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 3nyn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":577}' # _entry.id 3NYN # _exptl.entry_id 3NYN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.278 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SANGIVAMYCIN _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 3NYN _cell.length_a 154.59 _cell.length_b 154.59 _cell.length_c 207.914 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NYN _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,U 1 1 B,L,M,N,O,P,Q,R,S,T,V 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V 3 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 ? 2 C N N ? 2 L N N # _chem_comp.formula 'C12 H15 N5 O5' _chem_comp.formula_weight 309.278 _chem_comp.id SGV _chem_comp.mon_nstd_flag . _chem_comp.name SANGIVAMYCIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 4-amino-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide # 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 SGV doub 311 n y N1 C6 SGV sing 312 n y C2 N3 SGV sing 313 n y N3 C4 SGV doub 314 n y C4 C5 SGV sing 315 n y C4 N9 SGV sing 316 n y C5 C6 SGV doub 317 n y C5 C7 SGV sing 318 n y C6 N6 SGV sing 319 n n C7 C8 SGV doub 320 n y C7 C10 SGV sing 321 n n C8 N9 SGV sing 322 n y N9 C1' SGV sing 323 n n C1' C2' SGV sing 324 n n C1' O4' SGV sing 325 n n C10 N11 SGV sing 326 n n C10 O12 SGV doub 327 n n C2' O2' SGV sing 328 n n C2' C3' SGV sing 329 n n C3' O3' SGV sing 330 n n C3' C4' SGV sing 331 n n C4' O4' SGV sing 332 n n C4' C5' SGV sing 333 n n C5' O5' SGV sing 334 n n C2 H2 SGV sing 335 n n N6 HN6 SGV sing 336 n n N6 HN6A SGV sing 337 n n C8 H8 SGV sing 338 n n C1' H1' SGV sing 339 n n N11 HN11 SGV sing 340 n n N11 HN1A SGV sing 341 n n C2' H2' SGV sing 342 n n O2' HO2' SGV sing 343 n n C3' H3' SGV sing 344 n n O3' HO3' SGV sing 345 n n C4' H4' SGV sing 346 n n C5' H5' SGV sing 347 n n C5' "H5'A" SGV sing 348 n n O5' HO5' SGV sing 349 n n # _atom_sites.entry_id 3NYN _atom_sites.fract_transf_matrix[1][1] 0.006469 _atom_sites.fract_transf_matrix[1][2] 0.003735 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007469 _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] 0.00481 _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 SGV A 1 577 577 SGV SGV . D 3 SO4 A 1 578 578 SO4 SO4 . E 3 SO4 A 1 579 579 SO4 SO4 . F 3 SO4 A 1 580 580 SO4 SO4 . G 3 SO4 A 1 581 581 SO4 SO4 . H 3 SO4 A 1 582 582 SO4 SO4 . I 4 BU3 A 1 583 583 BU3 BU3 . J 3 SO4 A 1 584 584 SO4 SO4 . K 3 SO4 A 1 585 585 SO4 SO4 . L 2 SGV B 1 577 577 SGV SGV . M 3 SO4 B 1 578 578 SO4 SO4 . N 3 SO4 B 1 579 579 SO4 SO4 . O 3 SO4 B 1 580 580 SO4 SO4 . P 3 SO4 B 1 581 581 SO4 SO4 . Q 3 SO4 B 1 582 582 SO4 SO4 . R 4 BU3 B 1 583 583 BU3 BU3 . S 3 SO4 B 1 584 584 SO4 SO4 . T 3 SO4 B 1 585 585 SO4 SO4 . U 5 HOH A 1 558 1 HOH HOH . U 5 HOH A 2 559 2 HOH HOH . U 5 HOH A 3 560 3 HOH HOH . U 5 HOH A 4 561 4 HOH HOH . U 5 HOH A 5 562 5 HOH HOH . U 5 HOH A 6 563 6 HOH HOH . U 5 HOH A 7 564 7 HOH HOH . V 5 HOH B 1 558 1 HOH HOH . V 5 HOH B 2 559 2 HOH HOH . V 5 HOH B 3 560 3 HOH HOH . V 5 HOH B 4 561 4 HOH HOH . V 5 HOH B 5 562 6 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 SGV . . . C 2 -71.04 17.485 19.279 1 85.37 ? N1 SGV 577 A 1 HETATM 2 C C2 SGV . . . C 2 -70.873 16.187 19.608 1 86.8 ? C2 SGV 577 A 1 HETATM 3 N N3 SGV . . . C 2 -71.727 15.507 20.403 1 86.97 ? N3 SGV 577 A 1 HETATM 4 C C4 SGV . . . C 2 -72.828 16.1 20.925 1 86.5 ? C4 SGV 577 A 1 HETATM 5 C C5 SGV . . . C 2 -73.075 17.515 20.608 1 85.57 ? C5 SGV 577 A 1 HETATM 6 C C6 SGV . . . C 2 -72.093 18.197 19.73 1 85 ? C6 SGV 577 A 1 HETATM 7 N N6 SGV . . . C 2 -72.219 19.489 19.377 1 84.84 ? N6 SGV 577 A 1 HETATM 8 C C7 SGV . . . C 2 -74.325 17.792 21.338 1 85.86 ? C7 SGV 577 A 1 HETATM 9 C C8 SGV . . . C 2 -74.705 16.636 21.98 1 86.68 ? C8 SGV 577 A 1 HETATM 10 N N9 SGV . . . C 2 -73.814 15.658 21.721 1 87.05 ? N9 SGV 577 A 1 HETATM 11 C C1' SGV . . . C 2 -73.883 14.268 22.241 1 88.13 ? C1' SGV 577 A 1 HETATM 12 C C10 SGV . . . C 2 -74.942 19.144 21.291 1 85.71 ? C10 SGV 577 A 1 HETATM 13 N N11 SGV . . . C 2 -76.263 19.241 21.346 1 86.33 ? N11 SGV 577 A 1 HETATM 14 O O12 SGV . . . C 2 -74.243 20.136 21.211 1 85.41 ? O12 SGV 577 A 1 HETATM 15 C C2' SGV . . . C 2 -72.932 14.199 23.417 1 88.3 ? C2' SGV 577 A 1 HETATM 16 O O2' SGV . . . C 2 -72.383 12.88 23.533 1 89.07 ? O2' SGV 577 A 1 HETATM 17 C C3' SGV . . . C 2 -73.823 14.568 24.576 1 88.03 ? C3' SGV 577 A 1 HETATM 18 O O3' SGV . . . C 2 -73.352 13.984 25.787 1 88.96 ? O3' SGV 577 A 1 HETATM 19 C C4' SGV . . . C 2 -75.198 14.04 24.179 1 88.8 ? C4' SGV 577 A 1 HETATM 20 O O4' SGV . . . C 2 -75.182 13.941 22.752 1 88.48 ? O4' SGV 577 A 1 HETATM 21 C C5' SGV . . . C 2 -76.378 14.895 24.658 1 89.18 ? C5' SGV 577 A 1 HETATM 22 O O5' SGV . . . C 2 -75.999 15.771 25.74 1 89.91 ? O5' SGV 577 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 22 #