data_5G02 # _model_server_result.job_id 3pgsGYyTlMVTjSFLm0ft6g _model_server_result.datetime_utc '2024-11-28 18:14:32' _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 5g02 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":410}' # _entry.id 5G02 # _exptl.entry_id 5G02 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 381.387 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SINEFUNGIN _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 120 _cell.entry_id 5G02 _cell.length_a 147.994 _cell.length_b 147.994 _cell.length_c 127.69 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5G02 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 127.69 4 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 127.69 5 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 127.69 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 metalc ? metalc1 A OD2 ASP 6 A ASP 73 3_555 G LI LI . A LI 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc2 A OD2 ASP 6 A ASP 73 2_555 G LI LI . A LI 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc3 A OD2 ASP 6 A ASP 73 1_555 G LI LI . A LI 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc4 G LI LI . A LI 1411 1_555 H O HOH . A HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc5 G LI LI . A LI 1411 1_555 H O HOH . A HOH 2001 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc6 G LI LI . A LI 1411 1_555 H O HOH . A HOH 2001 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? # _chem_comp.formula 'C15 H23 N7 O5' _chem_comp.formula_weight 381.387 _chem_comp.id SFG _chem_comp.mon_nstd_flag . _chem_comp.name SINEFUNGIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ADENOSYL-ORNITHINE # 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 N CA SFG sing 324 n n N HN1 SFG sing 325 n n N HN2 SFG sing 326 n n CA C SFG sing 327 n n CA CB SFG sing 328 n n CA HA SFG sing 329 n n C O SFG doub 330 n n C OXT SFG sing 331 n n OXT HXT SFG sing 332 n n CB CG SFG sing 333 n n CB HB1 SFG sing 334 n n CB HB2 SFG sing 335 n n CG CD SFG sing 336 n n CG HG1 SFG sing 337 n n CG HG2 SFG sing 338 n n CD NE SFG sing 339 n n CD C5' SFG sing 340 n n CD HD SFG sing 341 n n NE HNE1 SFG sing 342 n n NE HNE2 SFG sing 343 n n C5' C4' SFG sing 344 n n C5' "H5'1" SFG sing 345 n n C5' "H5'2" SFG sing 346 n n C4' O4' SFG sing 347 n n C4' C3' SFG sing 348 n n C4' H4' SFG sing 349 n n O4' C1' SFG sing 350 n n C3' O3' SFG sing 351 n n C3' C2' SFG sing 352 n n C3' H3' SFG sing 353 n n O3' HO3' SFG sing 354 n n C2' O2' SFG sing 355 n n C2' C1' SFG sing 356 n n C2' H2' SFG sing 357 n n O2' HO2' SFG sing 358 n n C1' N9 SFG sing 359 n n C1' H1' SFG sing 360 n n N9 C8 SFG sing 361 n y N9 C4 SFG sing 362 n y C8 N7 SFG doub 363 n y C8 H8 SFG sing 364 n n N7 C5 SFG sing 365 n y C5 C6 SFG sing 366 n y C5 C4 SFG doub 367 n y C6 N6 SFG sing 368 n n C6 N1 SFG doub 369 n y N6 HN61 SFG sing 370 n n N6 HN62 SFG sing 371 n n N1 C2 SFG sing 372 n y C2 N3 SFG doub 373 n y C2 H2 SFG sing 374 n n N3 C4 SFG sing 375 n y # _atom_sites.entry_id 5G02 _atom_sites.fract_transf_matrix[1][1] 0.006757 _atom_sites.fract_transf_matrix[1][2] 0.003901 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007802 _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] 0.007831 _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 SFG A 1 410 410 SFG SFG . C 3 MES A 1 414 414 MES MES . D 3 MES A 1 415 415 MES MES . E 4 EDO A 1 1409 1409 EDO EDO . F 4 EDO A 1 1410 1410 EDO EDO . G 5 LI A 1 1411 1411 LI LI . H 6 HOH A 1 2001 2001 HOH HOH . H 6 HOH A 2 2002 2002 HOH HOH . H 6 HOH A 3 2003 2003 HOH HOH . H 6 HOH A 4 2004 2004 HOH HOH . H 6 HOH A 5 2005 2005 HOH HOH . H 6 HOH A 6 2006 2006 HOH HOH . H 6 HOH A 7 2007 2007 HOH HOH . H 6 HOH A 8 2008 2008 HOH HOH . H 6 HOH A 9 2009 2009 HOH HOH . H 6 HOH A 10 2010 2010 HOH HOH . H 6 HOH A 11 2011 2011 HOH HOH . H 6 HOH A 12 2012 2012 HOH HOH . H 6 HOH A 13 2013 2013 HOH HOH . H 6 HOH A 14 2014 2014 HOH HOH . H 6 HOH A 15 2015 2015 HOH HOH . H 6 HOH A 16 2016 2016 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 N SFG . . . B 2 2.186 25.858 43.67 1 76.69 ? N SFG 410 A 1 HETATM 2 C CA SFG . . . B 2 1.979 25.875 45.147 1 74.33 ? CA SFG 410 A 1 HETATM 3 C C SFG . . . B 2 2.62 27.033 45.698 1 76.52 ? C SFG 410 A 1 HETATM 4 O O SFG . . . B 2 3.597 27.604 45.04 1 77.5 ? O SFG 410 A 1 HETATM 5 O OXT SFG . . . B 2 2.248 27.557 46.86 1 77.84 ? OXT SFG 410 A 1 HETATM 6 C CB SFG . . . B 2 2.511 24.632 45.844 1 69.64 ? CB SFG 410 A 1 HETATM 7 C CG SFG . . . B 2 3.534 23.751 45.089 1 66.21 ? CG SFG 410 A 1 HETATM 8 C CD SFG . . . B 2 4.084 22.73 45.952 1 62.89 ? CD SFG 410 A 1 HETATM 9 N NE SFG . . . B 2 5.522 22.678 45.8 1 62 ? NE SFG 410 A 1 HETATM 10 C C5' SFG . . . B 2 3.599 21.293 45.671 1 61.17 ? C5' SFG 410 A 1 HETATM 11 C C4' SFG . . . B 2 2.111 21.079 45.704 1 59.03 ? C4' SFG 410 A 1 HETATM 12 O O4' SFG . . . B 2 1.809 20.084 44.69 1 57.29 ? O4' SFG 410 A 1 HETATM 13 C C3' SFG . . . B 2 1.59 20.577 46.96 1 58.01 ? C3' SFG 410 A 1 HETATM 14 O O3' SFG . . . B 2 0.476 21.33 47.394 1 58.11 ? O3' SFG 410 A 1 HETATM 15 C C2' SFG . . . B 2 1.211 19.157 46.698 1 56.87 ? C2' SFG 410 A 1 HETATM 16 O O2' SFG . . . B 2 0.071 18.797 47.389 1 58.16 ? O2' SFG 410 A 1 HETATM 17 C C1' SFG . . . B 2 0.941 19.132 45.272 1 56.49 ? C1' SFG 410 A 1 HETATM 18 N N9 SFG . . . B 2 1.176 17.895 44.65 1 52.98 ? N9 SFG 410 A 1 HETATM 19 C C8 SFG . . . B 2 2.281 17.137 44.712 1 54.08 ? C8 SFG 410 A 1 HETATM 20 N N7 SFG . . . B 2 2.089 16.059 43.961 1 54.6 ? N7 SFG 410 A 1 HETATM 21 C C5 SFG . . . B 2 0.86 16.146 43.409 1 54.57 ? C5 SFG 410 A 1 HETATM 22 C C6 SFG . . . B 2 0.115 15.338 42.529 1 53.43 ? C6 SFG 410 A 1 HETATM 23 N N6 SFG . . . B 2 0.663 14.098 42.042 1 54.6 ? N6 SFG 410 A 1 HETATM 24 N N1 SFG . . . B 2 -1.105 15.725 42.149 1 53.87 ? N1 SFG 410 A 1 HETATM 25 C C2 SFG . . . B 2 -1.633 16.868 42.609 1 54.91 ? C2 SFG 410 A 1 HETATM 26 N N3 SFG . . . B 2 -0.954 17.661 43.443 1 54.8 ? N3 SFG 410 A 1 HETATM 27 C C4 SFG . . . B 2 0.284 17.331 43.853 1 54.53 ? C4 SFG 410 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #