data_3RUL # _model_server_result.job_id 6YIqIDxgJbj80lXERgHPLA _model_server_result.datetime_utc '2024-11-26 20:23:24' _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 3rul # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":8}' # _entry.id 3RUL # _exptl.entry_id 3RUL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 193.155 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '2-amino-2-deoxy-beta-D-glucopyranuronic acid' _entity.pdbx_number_of_molecules 4 _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 3RUL _cell.length_a 53.3 _cell.length_b 86.25 _cell.length_c 107.19 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RUL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 ? dimeric 2 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I,J,N,O,P,Z 1 1 B,F,K,L,M,Q,R,S,AA 2 1 C,G,T,U,V,BA,DA 3 1 D,H,W,X,Y,CA,EA 4 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 ? 5 N N N ? 5 Q N N ? 5 T N N ? 5 W 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 covale ? covale1 A C LYS 77 A LYS 77 1_555 A N DAL 78 A DAL 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C DAL 78 A DAL 78 1_555 A N DAL 79 A DAL 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 B C LYS 77 B LYS 77 1_555 B N DAL 78 B DAL 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 B C DAL 78 B DAL 78 1_555 B N DAL 79 B DAL 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 C C LYS 77 C LYS 77 1_555 C N DAL 78 C DAL 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 C C DAL 78 C DAL 78 1_555 C N DAL 79 C DAL 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 D C LYS 77 D LYS 77 1_555 D N DAL 78 D DAL 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 D C DAL 78 D DAL 78 1_555 D N DAL 79 D DAL 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 E C HGM 1 E HGM 1 1_555 E N DTY 2 E DTY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale10 E C3 HGM 1 E HGM 1 1_555 E O4 HCL 3 E HCL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.365 ? covale ? covale11 E C DTY 2 E DTY 2 1_555 E N HCL 3 E HCL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale12 E OH DTY 2 E DTY 2 1_555 E C3 GHP 4 E GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.392 ? covale ? covale13 E C HCL 3 E HCL 3 1_555 E N GHP 4 E GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale14 E C GHP 4 E GHP 4 1_555 E N GHP 5 E GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale15 E C5 GHP 4 E GHP 4 1_555 E OCZ OMY 6 E OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale16 E O4 GHP 4 E GHP 4 1_555 N C1 N1L . E N1L 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.382 ? covale ? covale17 E C GHP 5 E GHP 5 1_555 E N OMY 6 E OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale18 E C3 GHP 5 E GHP 5 1_555 E C6 HG7 7 E HG7 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale19 E C OMY 6 E OMY 6 1_555 E N HG7 7 E HG7 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale20 E C5 HG7 7 E HG7 7 1_555 O O1 MAN . E MAN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale21 N N2 N1L . E N1L 8 1_555 P C1 M12 . E M12 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale22 F C HGM 1 F HGM 1 1_555 F N DTY 2 F DTY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale23 F C3 HGM 1 F HGM 1 1_555 F O4 HCL 3 F HCL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.364 ? covale ? covale24 F C DTY 2 F DTY 2 1_555 F N HCL 3 F HCL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale25 F OH DTY 2 F DTY 2 1_555 F C3 GHP 4 F GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale26 F C HCL 3 F HCL 3 1_555 F N GHP 4 F GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale27 F C GHP 4 F GHP 4 1_555 F N GHP 5 F GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale28 F C5 GHP 4 F GHP 4 1_555 F OCZ OMY 6 F OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale29 F O4 GHP 4 F GHP 4 1_555 Q C1 N1L . F N1L 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale30 F C GHP 5 F GHP 5 1_555 F N OMY 6 F OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale31 F C3 GHP 5 F GHP 5 1_555 F C6 HG7 7 F HG7 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale32 F C OMY 6 F OMY 6 1_555 F N HG7 7 F HG7 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale33 F C5 HG7 7 F HG7 7 1_555 R O1 MAN . F MAN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale34 Q N2 N1L . F N1L 8 1_555 S C1 M12 . F M12 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.198 ? covale ? covale35 G C HGM 1 G HGM 1 1_555 G N DTY 2 G DTY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale36 G C3 HGM 1 G HGM 1 1_555 G O4 HCL 3 G HCL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.361 ? covale ? covale37 G C DTY 2 G DTY 2 1_555 G N HCL 3 G HCL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale38 G OH DTY 2 G DTY 2 1_555 G C3 GHP 4 G GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale39 G C HCL 3 G HCL 3 1_555 G N GHP 4 G GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale40 G C GHP 4 G GHP 4 1_555 G N GHP 5 G GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale41 G C5 GHP 4 G GHP 4 1_555 G OCZ OMY 6 G OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale42 G O4 GHP 4 G GHP 4 1_555 T C1 N1L . G N1L 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale43 G C GHP 5 G GHP 5 1_555 G N OMY 6 G OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.315 ? covale ? covale44 G C3 GHP 5 G GHP 5 1_555 G C6 HG7 7 G HG7 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? covale ? covale45 G C OMY 6 G OMY 6 1_555 G N HG7 7 G HG7 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale46 G C5 HG7 7 G HG7 7 1_555 U O1 MAN . G MAN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale47 T N2 N1L . G N1L 8 1_555 V C1 M12 . G M12 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.269 ? covale ? covale48 H C HGM 1 H HGM 1 1_555 H N DTY 2 H DTY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale49 H C3 HGM 1 H HGM 1 1_555 H O4 HCL 3 H HCL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.358 ? covale ? covale50 H C DTY 2 H DTY 2 1_555 H N HCL 3 H HCL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale51 H OH DTY 2 H DTY 2 1_555 H C3 GHP 4 H GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale52 H C HCL 3 H HCL 3 1_555 H N GHP 4 H GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale53 H C GHP 4 H GHP 4 1_555 H N GHP 5 H GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale54 H C5 GHP 4 H GHP 4 1_555 H OCZ OMY 6 H OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale55 H O4 GHP 4 H GHP 4 1_555 W C1 N1L . H N1L 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale56 H C GHP 5 H GHP 5 1_555 H N OMY 6 H OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale57 H C3 GHP 5 H GHP 5 1_555 H C6 HG7 7 H HG7 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale58 H C OMY 6 H OMY 6 1_555 H N HG7 7 H HG7 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale59 H C5 HG7 7 H HG7 7 1_555 X O1 MAN . H MAN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale60 W N2 N1L . H N1L 8 1_555 Y C1 M12 . H M12 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.158 ? # _chem_comp.formula 'C6 H11 N O6' _chem_comp.formula_weight 193.155 _chem_comp.id N1L _chem_comp.mon_nstd_flag . _chem_comp.name '2-amino-2-deoxy-beta-D-glucopyranuronic acid' _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms '2-amino-2-deoxy-beta-D-glucuronic acid;2-amino-2-deoxy-D-glucuronic acid;2-amino-2-deoxy-glucuronic acid' # 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 N1L sing 446 n n C1 O5 N1L sing 447 n n C1 O1 N1L sing 448 n n C2 C3 N1L sing 449 n n C2 N2 N1L sing 450 n n C3 C4 N1L sing 451 n n C3 O3 N1L sing 452 n n C4 C5 N1L sing 453 n n C4 O4 N1L sing 454 n n C5 C6 N1L sing 455 n n C5 O5 N1L sing 456 n n C6 O6B N1L sing 457 n n C6 O6A N1L doub 458 n n C1 H1 N1L sing 459 n n C2 H2 N1L sing 460 n n O1 HO1 N1L sing 461 n n C3 H3 N1L sing 462 n n N2 H21N N1L sing 463 n n N2 H22N N1L sing 464 n n C4 H4 N1L sing 465 n n O3 HO3 N1L sing 466 n n C5 H5 N1L sing 467 n n O4 HO4 N1L sing 468 n n O6B HO6B N1L sing 469 n n # _pdbx_chem_comp_identifier.comp_id N1L _pdbx_chem_comp_identifier.identifier b-D-GlcpAN _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 3RUL _atom_sites.fract_transf_matrix[1][1] 0.018762 _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] 0.011594 _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] 0.009329 _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 I 3 TLA A 1 101 101 TLA TLA . J 3 TLA A 1 102 102 TLA TLA . K 3 TLA B 1 101 101 TLA TLA . L 3 TLA B 1 102 102 TLA TLA . M 4 CL B 1 103 103 CL CL . N 5 N1L E 1 8 8 N1L N1L . O 6 MAN E 1 9 9 MAN MAN . P 7 M12 E 1 10 10 M12 M12 . Q 5 N1L F 1 8 8 N1L N1L . R 6 MAN F 1 9 9 MAN MAN . S 7 M12 F 1 10 10 M12 M12 . T 5 N1L G 1 8 8 N1L N1L . U 6 MAN G 1 9 9 MAN MAN . V 7 M12 G 1 10 10 M12 M12 . W 5 N1L H 1 8 8 N1L N1L . X 6 MAN H 1 9 9 MAN MAN . Y 7 M12 H 1 10 10 M12 M12 . Z 8 HOH A 1 201 201 HOH HOH . Z 8 HOH A 2 202 202 HOH HOH . Z 8 HOH A 3 203 203 HOH HOH . Z 8 HOH A 4 204 204 HOH HOH . AA 8 HOH B 1 201 201 HOH HOH . AA 8 HOH B 2 202 202 HOH HOH . BA 8 HOH C 1 101 101 HOH HOH . BA 8 HOH C 2 102 102 HOH HOH . CA 8 HOH D 1 101 101 HOH HOH . CA 8 HOH D 2 102 102 HOH HOH . CA 8 HOH D 3 103 103 HOH HOH . DA 8 HOH G 1 201 201 HOH HOH . EA 8 HOH H 1 201 201 HOH HOH . EA 8 HOH H 2 202 202 HOH HOH . EA 8 HOH H 3 203 203 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 N1L . . . T 5 20.988 -35.524 31.295 1 70.93 ? C1 N1L 8 G 1 HETATM 2 C C2 N1L . . . T 5 21.624 -34.796 30.078 1 66.99 ? C2 N1L 8 G 1 HETATM 3 C C3 N1L . . . T 5 22.076 -33.408 30.548 1 71.43 ? C3 N1L 8 G 1 HETATM 4 C C4 N1L . . . T 5 20.859 -32.641 31.059 1 75.92 ? C4 N1L 8 G 1 HETATM 5 C C5 N1L . . . T 5 20.225 -33.434 32.217 1 68.77 ? C5 N1L 8 G 1 HETATM 6 C C6 N1L . . . T 5 18.998 -32.676 32.741 1 83.52 ? C6 N1L 8 G 1 HETATM 7 N N2 N1L . . . T 5 22.791 -35.543 29.574 1 52.13 ? N2 N1L 8 G 1 HETATM 8 O O3 N1L . . . T 5 22.73 -32.662 29.512 1 69.74 ? O3 N1L 8 G 1 HETATM 9 O O4 N1L . . . T 5 21.27 -31.342 31.501 1 84.68 ? O4 N1L 8 G 1 HETATM 10 O O5 N1L . . . T 5 19.851 -34.777 31.788 1 64.52 ? O5 N1L 8 G 1 HETATM 11 O O6B N1L . . . T 5 19.183 -31.896 33.706 1 77.94 ? O6B N1L 8 G 1 HETATM 12 O O6A N1L . . . T 5 17.886 -32.898 32.204 1 68.11 ? O6A N1L 8 G 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 12 #