data_5XR3 # _model_server_result.job_id W-8yJnbeGqFYMOtNyxtZpg _model_server_result.datetime_utc '2024-11-05 00:34:47' _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 5xr3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 5XR3 # _exptl.entry_id 5XR3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 74.035 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GLYOXYLIC ACID' _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 5XR3 _cell.length_a 97.199 _cell.length_b 130.125 _cell.length_c 187.954 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XR3 _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,K 1 1 C,D 2 1 E,F,J,L 3 1 G,H,M,N 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 ? 2 I N N ? 2 J 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 LEU 189 A LEU 189 1_555 A N CGV 190 A CGV 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale2 A C CGV 190 A CGV 190 1_555 A N HIS 191 A HIS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale3 B C LEU 189 B LEU 189 1_555 B N CGV 190 B CGV 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale4 B C CGV 190 B CGV 190 1_555 B N HIS 191 B HIS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 C C LEU 189 C LEU 189 1_555 C N CGV 190 C CGV 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale6 C C CGV 190 C CGV 190 1_555 C N HIS 191 C HIS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale7 D C LEU 189 D LEU 189 1_555 D N CGV 190 D CGV 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale8 D C CGV 190 D CGV 190 1_555 D N HIS 191 D HIS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale9 E C LEU 189 E LEU 189 1_555 E N CGV 190 E CGV 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale10 E C CGV 190 E CGV 190 1_555 E N HIS 191 E HIS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale11 F C LEU 189 F LEU 189 1_555 F N CGV 190 F CGV 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale12 F C CGV 190 F CGV 190 1_555 F N HIS 191 F HIS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 G C LEU 189 G LEU 189 1_555 G N CGV 190 G CGV 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale14 G C CGV 190 G CGV 190 1_555 G N HIS 191 G HIS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale15 H C LEU 189 H LEU 189 1_555 H N CGV 190 H CGV 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale16 H C CGV 190 H CGV 190 1_555 H N HIS 191 H HIS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _chem_comp.formula 'C2 H2 O3' _chem_comp.formula_weight 74.035 _chem_comp.id GLV _chem_comp.mon_nstd_flag . _chem_comp.name 'GLYOXYLIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYOXALATE;GLYOXYLATE # 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 O1 GLV doub 140 n n C1 C2 GLV sing 141 n n C1 H1 GLV sing 142 n n C2 O2 GLV doub 143 n n C2 O3 GLV sing 144 n n O3 HO3 GLV sing 145 n n # _atom_sites.entry_id 5XR3 _atom_sites.fract_transf_matrix[1][1] 0.010288 _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] 0.007685 _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] 0.00532 _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 2 GLV A 1 401 401 GLV GLV . J 2 GLV E 1 401 401 GLV GLV . K 3 HOH A 1 501 501 HOH HOH . K 3 HOH A 2 502 502 HOH HOH . K 3 HOH A 3 503 503 HOH HOH . L 3 HOH F 1 401 401 HOH HOH . L 3 HOH F 2 402 402 HOH HOH . M 3 HOH G 1 401 401 HOH HOH . N 3 HOH H 1 401 401 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 GLV . . . I 2 -13.265 -21.271 -13.368 1 50.56 ? C1 GLV 401 A 1 HETATM 2 O O1 GLV . . . I 2 -13.758 -22.376 -13.244 1 47.74 ? O1 GLV 401 A 1 HETATM 3 C C2 GLV . . . I 2 -12.038 -20.953 -12.62 1 52.92 ? C2 GLV 401 A 1 HETATM 4 O O2 GLV . . . I 2 -11.508 -19.836 -12.849 1 57.36 ? O2 GLV 401 A 1 HETATM 5 O O3 GLV . . . I 2 -11.554 -21.8 -11.821 1 48.33 ? O3 GLV 401 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 5 #