data_5U8R # _model_server_result.job_id FF8Zf4fjbk5Sa1y21jxuqw _model_server_result.datetime_utc '2024-10-18 16:29:04' _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 5u8r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1003}' # _entry.id 5U8R # _exptl.entry_id 5U8R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 134.087 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-MALATE _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 5U8R _cell.length_a 95.03 _cell.length_b 201.73 _cell.length_c 117.75 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U8R _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 ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 G N N ? 6 H N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 4 n D NAG 1 B 1 NAG X 1051 NAG 4 n D NAG 2 B 2 NAG X 1052 NAG 4 n E NAG 1 C 1 NAG X 5772 NAG 4 n E NAG 2 C 2 NAG X 5773 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 152 A CYS 152 1_555 A SG CYS 175 A CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 A SG CYS 201 A CYS 201 1_555 A SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 A SG CYS 294 A CYS 294 1_555 A SG CYS 298 A CYS 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf16 A SG CYS 633 A CYS 633 1_555 A SG CYS 829 A CYS 849 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf17 A SG CYS 756 A CYS 776 1_555 A SG CYS 765 A CYS 785 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf18 B SG CYS 24 H CYS 22 1_555 B SG CYS 98 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf19 C SG CYS 24 L CYS 23 1_555 C SG CYS 89 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 21 A ASN 21 1_555 I C1 NAG . A NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 105 A ASN 105 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 A ND2 ASN 504 A ASN 504 1_555 J C1 NAG . A NAG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 A ND2 ASN 577 A ASN 577 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 A ND2 ASN 610 A ASN 610 1_555 K C1 NAG . A NAG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 A ND2 ASN 863 A ASN 883 1_555 L C1 NAG . A NAG 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 245 n n C1 O2 MLT sing 246 n n C1 C2 MLT sing 247 n n C2 O3 MLT sing 248 n n C2 C3 MLT sing 249 n n C2 H2 MLT sing 250 n n O3 HO3 MLT sing 251 n n C3 C4 MLT sing 252 n n C3 H31 MLT sing 253 n n C3 H32 MLT sing 254 n n C4 O4 MLT doub 255 n n C4 O5 MLT sing 256 n n O5 HO5 MLT sing 257 n n O2 H6 MLT sing 258 n n # _atom_sites.entry_id 5U8R _atom_sites.fract_transf_matrix[1][1] 0.010523 _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] 0.004957 _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] 0.008493 _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 F 5 SO4 A 1 1001 1 SO4 SO4 . G 6 MLT A 1 1002 401 MLT MLT . H 6 MLT A 1 1003 403 MLT MLT . I 7 NAG A 1 1004 211 NAG NAG . J 7 NAG A 1 1007 5044 NAG NAG . K 7 NAG A 1 1010 6101 NAG NAG . L 7 NAG A 1 1011 8831 NAG NAG . M 8 IMD H 1 201 297 IMD IMD . # 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 . . . H 6 8.07 -26.592 28.319 1 135.13 ? C1 MLT 1003 A 1 HETATM 2 O O1 MLT . . . H 6 7.943 -25.713 27.438 1 137.65 ? O1 MLT 1003 A 1 HETATM 3 O O2 MLT . . . H 6 8.841 -26.393 29.283 1 118.24 ? O2 MLT 1003 A 1 HETATM 4 C C2 MLT . . . H 6 7.295 -27.873 28.227 1 136.11 ? C2 MLT 1003 A 1 HETATM 5 O O3 MLT . . . H 6 6.555 -28.069 29.411 1 104.87 ? O3 MLT 1003 A 1 HETATM 6 C C3 MLT . . . H 6 8.253 -29.04 28.013 1 147.22 ? C3 MLT 1003 A 1 HETATM 7 C C4 MLT . . . H 6 8.147 -29.54 26.592 1 146.14 ? C4 MLT 1003 A 1 HETATM 8 O O4 MLT . . . H 6 9.072 -29.337 25.776 1 139.61 ? O4 MLT 1003 A 1 HETATM 9 O O5 MLT . . . H 6 7.135 -30.171 26.216 1 139.17 ? O5 MLT 1003 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 9 #