data_5U8Q # _model_server_result.job_id FKG8o-I3VLU4EDTkp_qqYw _model_server_result.datetime_utc '2025-01-03 03:21:57' _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 5u8q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1003}' # _entry.id 5U8Q # _exptl.entry_id 5U8Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 134.087 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-MALATE _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 90 _cell.entry_id 5U8Q _cell.length_a 88.69 _cell.length_b 197.66 _cell.length_c 117.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U8Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 MAN NAG C1 O1 . O4 HO4 . sing 4 ? 6 4 3 MAN MAN C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 5 n E NAG 1 C 1 NAG X 1051 NAG 5 n E NAG 2 C 2 NAG X 1052 NAG 6 n F NAG 1 D 1 NAG X 5771 NAG 6 n F NAG 2 D 2 NAG X 5772 NAG 6 n F MAN 3 D 3 MAN X 5773 MAN 6 n F MAN 4 D 4 MAN X 5774 MAN 5 n G NAG 1 E 1 NAG X 8831 NAG 5 n G NAG 2 E 2 NAG X 8832 NAG # 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 3 A CYS 3 1_555 A SG CYS 22 A CYS 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 120 A CYS 120 1_555 A SG CYS 148 A CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 152 A CYS 152 1_555 A SG CYS 175 A CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 162 A CYS 162 1_555 A SG CYS 181 A CYS 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 185 A CYS 185 1_555 A SG CYS 194 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 A SG CYS 189 A CYS 189 1_555 A SG CYS 200 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 201 A CYS 201 1_555 A SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 A SG CYS 205 A CYS 205 1_555 A SG CYS 218 A CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 A SG CYS 221 A CYS 221 1_555 A SG CYS 230 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 A SG CYS 234 A CYS 234 1_555 A SG CYS 246 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 A SG CYS 252 A CYS 252 1_555 A SG CYS 273 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 A SG CYS 277 A CYS 277 1_555 A SG CYS 291 A CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 A SG CYS 294 A CYS 294 1_555 A SG CYS 298 A CYS 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf14 A SG CYS 302 A CYS 302 1_555 A SG CYS 323 A CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf15 A SG CYS 425 A CYS 425 1_555 A SG CYS 458 A CYS 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 A SG CYS 514 A CYS 514 1_555 A SG CYS 514 A CYS 514 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf17 A SG CYS 633 A CYS 633 1_555 A SG CYS 829 A CYS 849 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf18 A SG CYS 756 A CYS 776 1_555 A SG CYS 765 A CYS 785 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf19 B SG CYS 6 B CYS 6 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf20 B SG CYS 18 B CYS 18 1_555 B SG CYS 61 B CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf21 B SG CYS 47 B CYS 47 1_555 B SG CYS 52 B CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf22 C SG CYS 24 H CYS 22 1_555 C SG CYS 98 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf23 D SG CYS 24 L CYS 23 1_555 D SG CYS 89 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 21 A ASN 21 1_555 K C1 NAG . A NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 105 A ASN 105 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 504 A ASN 504 1_555 L C1 NAG . A NAG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 A ND2 ASN 577 A ASN 577 1_555 F C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 A ND2 ASN 850 A ASN 870 1_555 M C1 NAG . A NAG 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 A ND2 ASN 863 A ASN 883 1_555 G C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 F O4 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale9 F O4 NAG . D NAG 2 1_555 F C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 F O4 MAN . D MAN 3 1_555 F C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale11 G O4 NAG . E NAG 1 1_555 G C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _chem_comp.formula 'C4 H6 O5' _chem_comp.formula_weight 134.087 _chem_comp.id MLT _chem_comp.mon_nstd_flag . _chem_comp.name D-MALATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(2R)-2-HYDROXYBUTANEDIOIC ACID;2-HYDROXY-SUCCINIC 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 O1 MLT doub 259 n n C1 O2 MLT sing 260 n n C1 C2 MLT sing 261 n n C2 O3 MLT sing 262 n n C2 C3 MLT sing 263 n n C2 H2 MLT sing 264 n n O3 HO3 MLT sing 265 n n C3 C4 MLT sing 266 n n C3 H31 MLT sing 267 n n C3 H32 MLT sing 268 n n C4 O4 MLT doub 269 n n C4 O5 MLT sing 270 n n O5 HO5 MLT sing 271 n n O2 H6 MLT sing 272 n n # _atom_sites.entry_id 5U8Q _atom_sites.fract_transf_matrix[1][1] 0.011275 _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] 0.005059 _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] 0.0085 _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 H 7 SO4 A 1 1001 1 SO4 SO4 . I 7 SO4 A 1 1002 2 SO4 SO4 . J 8 MLT A 1 1003 401 MLT MLT . K 9 NAG A 1 1004 211 NAG NAG . L 9 NAG A 1 1007 5041 NAG NAG . M 9 NAG A 1 1012 8701 NAG NAG . # 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 MLT . . . J 8 37.997 40.939 -32.025 1 153.23 ? C1 MLT 1003 A 1 HETATM 2 O O1 MLT . . . J 8 38.306 40.74 -33.22 1 144.93 ? O1 MLT 1003 A 1 HETATM 3 O O2 MLT . . . J 8 38.895 41.159 -31.183 1 137.31 ? O2 MLT 1003 A 1 HETATM 4 C C2 MLT . . . J 8 36.558 40.91 -31.603 1 159.49 ? C2 MLT 1003 A 1 HETATM 5 O O3 MLT . . . J 8 36.449 40.345 -30.316 1 151.99 ? O3 MLT 1003 A 1 HETATM 6 C C3 MLT . . . J 8 35.752 40.083 -32.598 1 160.8 ? C3 MLT 1003 A 1 HETATM 7 C C4 MLT . . . J 8 34.824 40.988 -33.373 1 161.68 ? C4 MLT 1003 A 1 HETATM 8 O O4 MLT . . . J 8 35.081 41.299 -34.556 1 156.83 ? O4 MLT 1003 A 1 HETATM 9 O O5 MLT . . . J 8 33.785 41.434 -32.84 1 160.73 ? O5 MLT 1003 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 9 #