data_5JPF # _model_server_result.job_id aaUAR44PWrgSlI6gYw8bVA _model_server_result.datetime_utc '2024-10-28 02:41:51' _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 5jpf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":504}' # _entry.id 5JPF # _exptl.entry_id 5JPF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 102.046 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MALONATE ION' _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 5JPF _cell.length_a 50.665 _cell.length_b 50.665 _cell.length_c 201.054 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JPF _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall 'P 32 2"' _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 4 E N N ? 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 covale ? covale1 A SG CYS 271 A CYS 438 1_555 B CB DAM 7 M DAM 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? covale ? covale2 B C DAL 1 M DAL 1 1_555 B N LEU 2 M LEU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale3 B N DAL 1 M DAL 1 1_555 B C DAM 7 M DAM 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale4 B C LEU 2 M LEU 2 1_555 B N ACB 3 M ACB 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale5 B CG ACB 3 M ACB 3 1_555 B N ARG 4 M ARG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale6 B C ARG 4 M ARG 4 1_555 B N 1ZN 5 M 1ZN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale7 B C 1ZN 5 M 1ZN 5 1_555 B N FGA 6 M FGA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale8 B CD FGA 6 M FGA 6 1_555 B N DAM 7 M DAM 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A OD2 ASP 62 A ASP 229 1_555 D MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 A NE2 HIS 64 A HIS 231 1_555 D MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc3 A OD2 ASP 90 A ASP 257 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc4 A OD2 ASP 90 A ASP 257 1_555 D MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc5 A OD1 ASN 122 A ASN 289 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc6 A NE2 HIS 171 A HIS 338 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc7 A ND1 HIS 246 A HIS 413 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc8 C MN MN . A MN 501 1_555 H O HOH . A HOH 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc9 D MN MN . A MN 502 1_555 H O HOH . A HOH 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc10 D MN MN . A MN 502 1_555 I O HOH . M HOH 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? # _chem_comp.formula 'C3 H2 O4 -2' _chem_comp.formula_weight 102.046 _chem_comp.id MLI _chem_comp.mon_nstd_flag . _chem_comp.name 'MALONATE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 MLI sing 351 n n C1 C3 MLI sing 352 n n C1 H11 MLI sing 353 n n C1 H12 MLI sing 354 n n C2 O6 MLI doub 355 n n C2 O7 MLI sing 356 n n C3 O8 MLI doub 357 n n C3 O9 MLI sing 358 n n # _atom_sites.entry_id 5JPF _atom_sites.fract_transf_matrix[1][1] 0.019737 _atom_sites.fract_transf_matrix[1][2] 0.011395 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022791 _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] 0.004974 _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 C 3 MN A 1 501 1 MN MN . D 3 MN A 1 502 2 MN MN . E 4 MLI A 1 503 1 MLI MLI . F 4 MLI A 1 504 3 MLI MLI . G 4 MLI A 1 505 4 MLI MLI . H 5 HOH A 1 601 35 HOH HOH . H 5 HOH A 2 602 26 HOH HOH . H 5 HOH A 3 603 27 HOH HOH . H 5 HOH A 4 604 2 HOH HOH . H 5 HOH A 5 605 45 HOH HOH . H 5 HOH A 6 606 22 HOH HOH . H 5 HOH A 7 607 14 HOH HOH . H 5 HOH A 8 608 10 HOH HOH . H 5 HOH A 9 609 19 HOH HOH . H 5 HOH A 10 610 15 HOH HOH . H 5 HOH A 11 611 6 HOH HOH . H 5 HOH A 12 612 1 HOH HOH . H 5 HOH A 13 613 33 HOH HOH . H 5 HOH A 14 614 29 HOH HOH . H 5 HOH A 15 615 12 HOH HOH . H 5 HOH A 16 616 49 HOH HOH . H 5 HOH A 17 617 16 HOH HOH . H 5 HOH A 18 618 34 HOH HOH . H 5 HOH A 19 619 8 HOH HOH . H 5 HOH A 20 620 13 HOH HOH . H 5 HOH A 21 621 3 HOH HOH . H 5 HOH A 22 622 42 HOH HOH . H 5 HOH A 23 623 9 HOH HOH . H 5 HOH A 24 624 44 HOH HOH . H 5 HOH A 25 625 7 HOH HOH . H 5 HOH A 26 626 20 HOH HOH . H 5 HOH A 27 627 48 HOH HOH . H 5 HOH A 28 628 17 HOH HOH . H 5 HOH A 29 629 46 HOH HOH . H 5 HOH A 30 630 43 HOH HOH . H 5 HOH A 31 631 11 HOH HOH . H 5 HOH A 32 632 39 HOH HOH . H 5 HOH A 33 633 4 HOH HOH . H 5 HOH A 34 634 5 HOH HOH . H 5 HOH A 35 635 18 HOH HOH . H 5 HOH A 36 636 38 HOH HOH . H 5 HOH A 37 637 24 HOH HOH . H 5 HOH A 38 638 21 HOH HOH . H 5 HOH A 39 639 28 HOH HOH . H 5 HOH A 40 640 37 HOH HOH . H 5 HOH A 41 641 41 HOH HOH . H 5 HOH A 42 642 36 HOH HOH . H 5 HOH A 43 643 25 HOH HOH . H 5 HOH A 44 644 23 HOH HOH . H 5 HOH A 45 645 47 HOH HOH . H 5 HOH A 46 646 40 HOH HOH . I 5 HOH M 1 101 31 HOH HOH . I 5 HOH M 2 102 32 HOH HOH . I 5 HOH M 3 103 50 HOH HOH . I 5 HOH M 4 104 30 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 MLI . . . F 4 152.152 -7.663 5.159 1 37.65 ? C1 MLI 504 A 1 HETATM 2 C C2 MLI . . . F 4 151.944 -9.021 5.834 1 40.13 ? C2 MLI 504 A 1 HETATM 3 C C3 MLI . . . F 4 153.577 -7.142 5.359 1 41.66 ? C3 MLI 504 A 1 HETATM 4 O O6 MLI . . . F 4 150.784 -9.505 5.912 1 41.95 ? O6 MLI 504 A 1 HETATM 5 O O7 MLI . . . F 4 152.914 -9.663 6.316 1 44.76 ? O7 MLI 504 A 1 HETATM 6 O O8 MLI . . . F 4 154.154 -6.533 4.42 1 44.6 ? O8 MLI 504 A 1 HETATM 7 O O9 MLI . . . F 4 154.177 -7.306 6.455 1 47.59 ? O9 MLI 504 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 7 #