data_3E4P # _model_server_result.job_id jDa3chcdcwIrVZhrPvBqdQ _model_server_result.datetime_utc '2025-09-04 05:30:58' _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 3e4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":601}' # _entry.id 3E4P # _exptl.entry_id 3E4P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 104.061 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MALONIC 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 94.78 _cell.angle_gamma 90 _cell.entry_id 3E4P _cell.length_a 57.98 _cell.length_b 39.1 _cell.length_c 111.54 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3E4P _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? 3 D N N ? 3 G N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id E _struct_conn.ptnr1_label_atom_id SR _struct_conn.ptnr1_label_comp_id SR _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id SR _struct_conn.ptnr1_auth_seq_id 501 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id I _struct_conn.ptnr2_label_atom_id O _struct_conn.ptnr2_label_comp_id HOH _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id HOH _struct_conn.ptnr2_auth_seq_id 652 _struct_conn.ptnr2_symmetry 1_555 _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 2.778 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C3 H4 O4' _chem_comp.formula_weight 104.061 _chem_comp.id MLA _chem_comp.mon_nstd_flag . _chem_comp.name 'MALONIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'DICARBOXYLIC ACID C3;PROPANEDIOLIC ACID;METHANEDICARBOXYLIC 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 O1A MLA sing 224 n n C1 O1B MLA doub 225 n n C1 C2 MLA sing 226 n n O1A H1A MLA sing 227 n n C2 C3 MLA sing 228 n n C2 HC21 MLA sing 229 n n C2 HC22 MLA sing 230 n n C3 O3A MLA doub 231 n n C3 O3B MLA sing 232 n n O3B H3B MLA sing 233 n n # _atom_sites.entry_id 3E4P _atom_sites.fract_transf_matrix[1][1] 0.017247 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001441 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025575 _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] 0.008997 _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 2 SR A 1 502 502 SR SR . D 3 MLA A 1 701 701 MLA MLA . E 2 SR B 1 501 501 SR SR . F 2 SR B 1 503 503 SR SR . G 3 MLA B 1 601 601 MLA MLA . H 4 HOH A 1 702 7 HOH HOH . H 4 HOH A 2 703 9 HOH HOH . H 4 HOH A 3 704 10 HOH HOH . H 4 HOH A 4 705 11 HOH HOH . H 4 HOH A 5 706 20 HOH HOH . H 4 HOH A 6 707 21 HOH HOH . H 4 HOH A 7 708 32 HOH HOH . H 4 HOH A 8 709 43 HOH HOH . H 4 HOH A 9 710 44 HOH HOH . H 4 HOH A 10 711 48 HOH HOH . H 4 HOH A 11 712 66 HOH HOH . H 4 HOH A 12 713 77 HOH HOH . H 4 HOH A 13 714 81 HOH HOH . H 4 HOH A 14 715 84 HOH HOH . H 4 HOH A 15 716 87 HOH HOH . H 4 HOH A 16 717 90 HOH HOH . H 4 HOH A 17 718 98 HOH HOH . H 4 HOH A 18 719 115 HOH HOH . H 4 HOH A 19 720 116 HOH HOH . H 4 HOH A 20 721 117 HOH HOH . H 4 HOH A 21 722 119 HOH HOH . H 4 HOH A 22 723 121 HOH HOH . H 4 HOH A 23 724 122 HOH HOH . H 4 HOH A 24 725 123 HOH HOH . H 4 HOH A 25 726 124 HOH HOH . H 4 HOH A 26 727 131 HOH HOH . H 4 HOH A 27 728 134 HOH HOH . H 4 HOH A 28 729 135 HOH HOH . H 4 HOH A 29 730 137 HOH HOH . H 4 HOH A 30 731 138 HOH HOH . H 4 HOH A 31 732 139 HOH HOH . H 4 HOH A 32 733 141 HOH HOH . H 4 HOH A 33 734 233 HOH HOH . H 4 HOH A 34 735 236 HOH HOH . H 4 HOH A 35 736 241 HOH HOH . H 4 HOH A 36 737 303 HOH HOH . H 4 HOH A 37 738 306 HOH HOH . H 4 HOH A 38 739 307 HOH HOH . H 4 HOH A 39 740 308 HOH HOH . H 4 HOH A 40 741 310 HOH HOH . H 4 HOH A 41 742 311 HOH HOH . H 4 HOH A 42 743 314 HOH HOH . H 4 HOH A 43 744 316 HOH HOH . H 4 HOH A 44 745 321 HOH HOH . H 4 HOH A 45 746 324 HOH HOH . H 4 HOH A 46 747 325 HOH HOH . H 4 HOH A 47 748 326 HOH HOH . H 4 HOH A 48 749 333 HOH HOH . H 4 HOH A 49 750 334 HOH HOH . H 4 HOH A 50 751 336 HOH HOH . H 4 HOH A 51 752 338 HOH HOH . H 4 HOH A 52 753 343 HOH HOH . H 4 HOH A 53 754 344 HOH HOH . H 4 HOH A 54 755 345 HOH HOH . H 4 HOH A 55 756 348 HOH HOH . I 4 HOH B 1 602 8 HOH HOH . I 4 HOH B 2 603 13 HOH HOH . I 4 HOH B 3 604 15 HOH HOH . I 4 HOH B 4 605 26 HOH HOH . I 4 HOH B 5 606 29 HOH HOH . I 4 HOH B 6 607 31 HOH HOH . I 4 HOH B 7 608 36 HOH HOH . I 4 HOH B 8 609 42 HOH HOH . I 4 HOH B 9 610 45 HOH HOH . I 4 HOH B 10 611 51 HOH HOH . I 4 HOH B 11 612 54 HOH HOH . I 4 HOH B 12 613 57 HOH HOH . I 4 HOH B 13 614 82 HOH HOH . I 4 HOH B 14 615 88 HOH HOH . I 4 HOH B 15 616 97 HOH HOH . I 4 HOH B 16 617 100 HOH HOH . I 4 HOH B 17 618 101 HOH HOH . I 4 HOH B 18 619 104 HOH HOH . I 4 HOH B 19 620 110 HOH HOH . I 4 HOH B 20 621 111 HOH HOH . I 4 HOH B 21 622 112 HOH HOH . I 4 HOH B 22 623 113 HOH HOH . I 4 HOH B 23 624 114 HOH HOH . I 4 HOH B 24 625 120 HOH HOH . I 4 HOH B 25 626 127 HOH HOH . I 4 HOH B 26 627 128 HOH HOH . I 4 HOH B 27 628 140 HOH HOH . I 4 HOH B 28 629 143 HOH HOH . I 4 HOH B 29 630 144 HOH HOH . I 4 HOH B 30 631 145 HOH HOH . I 4 HOH B 31 632 202 HOH HOH . I 4 HOH B 32 633 203 HOH HOH . I 4 HOH B 33 634 206 HOH HOH . I 4 HOH B 34 635 211 HOH HOH . I 4 HOH B 35 636 217 HOH HOH . I 4 HOH B 36 637 219 HOH HOH . I 4 HOH B 37 638 220 HOH HOH . I 4 HOH B 38 639 229 HOH HOH . I 4 HOH B 39 640 235 HOH HOH . I 4 HOH B 40 641 248 HOH HOH . I 4 HOH B 41 642 302 HOH HOH . I 4 HOH B 42 643 304 HOH HOH . I 4 HOH B 43 644 305 HOH HOH . I 4 HOH B 44 645 309 HOH HOH . I 4 HOH B 45 646 317 HOH HOH . I 4 HOH B 46 647 318 HOH HOH . I 4 HOH B 47 648 319 HOH HOH . I 4 HOH B 48 649 320 HOH HOH . I 4 HOH B 49 650 327 HOH HOH . I 4 HOH B 50 651 328 HOH HOH . I 4 HOH B 51 652 329 HOH HOH . I 4 HOH B 52 653 330 HOH HOH . I 4 HOH B 53 654 331 HOH HOH . I 4 HOH B 54 655 337 HOH HOH . I 4 HOH B 55 656 339 HOH HOH . I 4 HOH B 56 657 341 HOH HOH . I 4 HOH B 57 658 342 HOH HOH . I 4 HOH B 58 659 349 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 MLA . . . G 3 16.381 -3.419 5.159 1 24.71 ? C1 MLA 601 B 1 HETATM 2 O O1A MLA . . . G 3 15.257 -3.118 4.717 1 25.3 ? O1A MLA 601 B 1 HETATM 3 O O1B MLA . . . G 3 17.433 -2.744 4.97 1 23.83 ? O1B MLA 601 B 1 HETATM 4 C C2 MLA . . . G 3 16.482 -4.722 6.033 1 22.28 ? C2 MLA 601 B 1 HETATM 5 C C3 MLA . . . G 3 15.113 -5.381 6.33 1 21.7 ? C3 MLA 601 B 1 HETATM 6 O O3A MLA . . . G 3 14.57 -5.148 7.458 1 24.17 ? O3A MLA 601 B 1 HETATM 7 O O3B MLA . . . G 3 14.644 -6.136 5.438 1 23.07 ? O3B MLA 601 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 7 #