data_3S04 # _model_server_result.job_id 2mhUh_Ly7UoiA-Fvum9C9A _model_server_result.datetime_utc '2024-10-18 16:28:07' _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 3s04 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":8}' # _entry.id 3S04 # _exptl.entry_id 3S04 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 164.156 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description alpha-L-rhamnopyranose _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 90 _cell.entry_id 3S04 _cell.length_a 72.01 _cell.length_b 72.01 _cell.length_c 262.57 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S04 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA tetrameric 4 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,D,G,H,I 1 1 B,C,E,F,J 2 1 A,D,G,H,I 3 1 B,C,E,F,J 3 2 # 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' 6_555 x+1/2,-y+1/2,-z+1/4 1 0 0 0 -1 0 0 0 -1 36.005 36.005 65.6425 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G 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 disulf ? disulf1 A SG CYS 97 A CYS 171 1_555 A SG CYS 103 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 E C 02U . I 02U 1 1_555 C N DSE 1 I DSE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale2 C C DSE 1 I DSE 2 1_555 C N DAL 2 I DAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 C C DAL 2 I DAL 3 1_555 C N GLY 3 I GLY 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.484 ? covale ? covale4 C C GLY 3 I GLY 4 1_555 C N 02V 4 I 02V 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale5 C C 02V 4 I 02V 5 1_555 C N ALA 5 I ALA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale6 C C22 02V 4 I 02V 5 1_555 C CE1 TYR 6 I TYR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale7 C C24 02V 4 I 02V 5 1_555 F O1 RAM . I RAM 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.37 ? covale ? covale8 H C 02U . J 02U 1 1_555 D N DSE 1 J DSE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? covale ? covale9 D C DSE 1 J DSE 2 1_555 D N DAL 2 J DAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale10 D C DAL 2 J DAL 3 1_555 D N GLY 3 J GLY 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale11 D C GLY 3 J GLY 4 1_555 D N 02V 4 J 02V 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale12 D C 02V 4 J 02V 5 1_555 D N ALA 5 J ALA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale13 D C22 02V 4 J 02V 5 1_555 D CE1 TYR 6 J TYR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale14 D C24 02V 4 J 02V 5 1_555 G O1 RAM . J RAM 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.368 ? # _chem_comp.formula 'C6 H12 O5' _chem_comp.formula_weight 164.156 _chem_comp.id RAM _chem_comp.mon_nstd_flag . _chem_comp.name alpha-L-rhamnopyranose _chem_comp.type 'l-saccharide, alpha linking' _chem_comp.pdbx_synonyms alpha-L-rhamnose;6-deoxy-alpha-L-mannopyranose;L-rhamnose;rhamnose # 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 C1 C2 RAM sing 380 n n C1 O1 RAM sing 381 n n C1 O5 RAM sing 382 n n C1 H1 RAM sing 383 n n C2 C3 RAM sing 384 n n C2 O2 RAM sing 385 n n C2 H2 RAM sing 386 n n C3 C4 RAM sing 387 n n C3 O3 RAM sing 388 n n C3 H3 RAM sing 389 n n C4 C5 RAM sing 390 n n C4 O4 RAM sing 391 n n C4 H4 RAM sing 392 n n C5 C6 RAM sing 393 n n C5 O5 RAM sing 394 n n C5 H5 RAM sing 395 n n C6 H61 RAM sing 396 n n C6 H62 RAM sing 397 n n C6 H63 RAM sing 398 n n O1 HO1 RAM sing 399 n n O2 HO2 RAM sing 400 n n O3 HO3 RAM sing 401 n n O4 HO4 RAM sing 402 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version RAM LRhapa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 RAM a-L-rhamnopyranose 'COMMON NAME' GMML 1 RAM a-L-Rhap 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 RAM Rha 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3S04 _atom_sites.fract_transf_matrix[1][1] 0.013887 _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] 0.013887 _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] 0.003809 _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 E 3 02U I 1 1 1 02U 02U . F 4 RAM I 1 8 8 RAM RAM . G 4 RAM J 1 8 8 RAM RAM . H 3 02U J 1 1 1 02U 02U . I 5 HOH A 1 1 1 HOH HOH . I 5 HOH A 2 4 4 HOH HOH . I 5 HOH A 3 8 8 HOH HOH . I 5 HOH A 4 9 9 HOH HOH . I 5 HOH A 5 11 11 HOH HOH . I 5 HOH A 6 13 13 HOH HOH . I 5 HOH A 7 14 14 HOH HOH . I 5 HOH A 8 19 19 HOH HOH . I 5 HOH A 9 21 21 HOH HOH . I 5 HOH A 10 22 22 HOH HOH . I 5 HOH A 11 23 23 HOH HOH . I 5 HOH A 12 26 26 HOH HOH . I 5 HOH A 13 28 28 HOH HOH . I 5 HOH A 14 29 29 HOH HOH . I 5 HOH A 15 30 30 HOH HOH . I 5 HOH A 16 31 31 HOH HOH . I 5 HOH A 17 35 35 HOH HOH . I 5 HOH A 18 36 36 HOH HOH . I 5 HOH A 19 38 38 HOH HOH . I 5 HOH A 20 39 39 HOH HOH . I 5 HOH A 21 40 40 HOH HOH . I 5 HOH A 22 41 41 HOH HOH . I 5 HOH A 23 42 42 HOH HOH . I 5 HOH A 24 43 43 HOH HOH . I 5 HOH A 25 44 44 HOH HOH . I 5 HOH A 26 45 45 HOH HOH . I 5 HOH A 27 46 46 HOH HOH . I 5 HOH A 28 50 50 HOH HOH . I 5 HOH A 29 52 52 HOH HOH . I 5 HOH A 30 53 53 HOH HOH . I 5 HOH A 31 54 54 HOH HOH . I 5 HOH A 32 57 57 HOH HOH . J 5 HOH B 1 2 2 HOH HOH . J 5 HOH B 2 3 3 HOH HOH . J 5 HOH B 3 5 5 HOH HOH . J 5 HOH B 4 6 6 HOH HOH . J 5 HOH B 5 7 7 HOH HOH . J 5 HOH B 6 10 10 HOH HOH . J 5 HOH B 7 12 12 HOH HOH . J 5 HOH B 8 15 15 HOH HOH . J 5 HOH B 9 16 16 HOH HOH . J 5 HOH B 10 17 17 HOH HOH . J 5 HOH B 11 18 18 HOH HOH . J 5 HOH B 12 20 20 HOH HOH . J 5 HOH B 13 24 24 HOH HOH . J 5 HOH B 14 25 25 HOH HOH . J 5 HOH B 15 27 27 HOH HOH . J 5 HOH B 16 32 32 HOH HOH . J 5 HOH B 17 33 33 HOH HOH . J 5 HOH B 18 34 34 HOH HOH . J 5 HOH B 19 37 37 HOH HOH . J 5 HOH B 20 47 47 HOH HOH . J 5 HOH B 21 48 48 HOH HOH . J 5 HOH B 22 49 49 HOH HOH . J 5 HOH B 23 51 51 HOH HOH . J 5 HOH B 24 55 55 HOH HOH . J 5 HOH B 25 56 56 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 C C1 RAM . . . G 4 10.963 -12.719 44.294 1 57.59 ? C1 RAM 8 J 1 HETATM 2 C C2 RAM . . . G 4 11.971 -12.988 43.173 1 58.42 ? C2 RAM 8 J 1 HETATM 3 C C3 RAM . . . G 4 11.257 -12.921 41.818 1 58.86 ? C3 RAM 8 J 1 HETATM 4 C C4 RAM . . . G 4 10.472 -11.613 41.68 1 59.34 ? C4 RAM 8 J 1 HETATM 5 C C5 RAM . . . G 4 9.543 -11.396 42.879 1 59.2 ? C5 RAM 8 J 1 HETATM 6 C C6 RAM . . . G 4 8.875 -10.023 42.765 1 59.49 ? C6 RAM 8 J 1 HETATM 7 O O1 RAM . . . G 4 10.054 -13.812 44.462 1 55.77 ? O1 RAM 8 J 1 HETATM 8 O O2 RAM . . . G 4 13.018 -12.014 43.234 1 57.36 ? O2 RAM 8 J 1 HETATM 9 O O3 RAM . . . G 4 12.215 -13.022 40.761 1 58.92 ? O3 RAM 8 J 1 HETATM 10 O O4 RAM . . . G 4 9.696 -11.648 40.478 1 59.26 ? O4 RAM 8 J 1 HETATM 11 O O5 RAM . . . G 4 10.273 -11.47 44.114 1 58.04 ? O5 RAM 8 J 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 11 #