data_4L06 # _model_server_result.job_id RCgY5vGgCAJRXO8yRCTItg _model_server_result.datetime_utc '2024-11-30 16:42:58' _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 4l06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":503}' # _entry.id 4L06 # _exptl.entry_id 4L06 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-OXOGLUTARIC ACID' _entity.pdbx_number_of_molecules 6 _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 4L06 _cell.length_a 96.22 _cell.length_b 116.55 _cell.length_c 275.71 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L06 _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J,K,L,Y,Z 1 1 C,D,M,N,O,P,Q,R,AA,BA 2 1 E,F,S,T,U,V,W,X,CA,DA 3 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 I N N ? 4 L N N ? 4 O N N ? 4 R N N ? 4 U N N ? 4 X 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 metalc ? metalc1 A OD2 ASP 252 A ASP 252 1_555 J CA CA . B CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc2 A OD1 ASP 275 A ASP 275 1_555 G CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc3 A O ASP 275 A ASP 275 1_555 G CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.035 ? metalc ? metalc4 A OD1 ASP 279 A ASP 279 1_555 G CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc5 G CA CA . A CA 501 1_555 I O2 AKG . A AKG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc6 G CA CA . A CA 501 1_555 I O5 AKG . A AKG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc7 G CA CA . A CA 501 1_555 B OD1 ASP 252 B ASP 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc8 B OD1 ASP 275 B ASP 275 1_555 J CA CA . B CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc9 B O ASP 275 B ASP 275 1_555 J CA CA . B CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.132 ? metalc ? metalc10 B OD1 ASP 279 B ASP 279 1_555 J CA CA . B CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc11 J CA CA . B CA 501 1_555 L O2 AKG . B AKG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc12 J CA CA . B CA 501 1_555 L O5 AKG . B AKG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? metalc ? metalc13 C OD2 ASP 252 C ASP 252 1_555 P CA CA . D CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc14 C OD1 ASP 275 C ASP 275 1_555 M CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc15 C O ASP 275 C ASP 275 1_555 M CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.042 ? metalc ? metalc16 C OD2 ASP 279 C ASP 279 1_555 M CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc17 M CA CA . C CA 501 1_555 O O2 AKG . C AKG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc18 M CA CA . C CA 501 1_555 AA O HOH . C HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc19 M CA CA . C CA 501 1_555 D OD2 ASP 252 D ASP 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc20 D OD1 ASP 275 D ASP 275 1_555 P CA CA . D CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc21 D O ASP 275 D ASP 275 1_555 P CA CA . D CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc22 D OD2 ASP 279 D ASP 279 1_555 P CA CA . D CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc23 P CA CA . D CA 501 1_555 R O2 AKG . D AKG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc24 E OD1 ASP 252 E ASP 252 1_555 V CA CA . F CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc25 E OD1 ASP 275 E ASP 275 1_555 S CA CA . E CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc26 E O ASP 275 E ASP 275 1_555 S CA CA . E CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc27 E OD2 ASP 279 E ASP 279 1_555 S CA CA . E CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc28 S CA CA . E CA 501 1_555 U O2 AKG . E AKG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc29 S CA CA . E CA 501 1_555 U O5 AKG . E AKG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? metalc ? metalc30 S CA CA . E CA 501 1_555 CA O HOH . E HOH 624 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc31 S CA CA . E CA 501 1_555 F OD1 ASP 252 F ASP 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc32 F OD1 ASP 275 F ASP 275 1_555 V CA CA . F CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc33 F O ASP 275 F ASP 275 1_555 V CA CA . F CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc34 F OD2 ASP 279 F ASP 279 1_555 V CA CA . F CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc35 V CA CA . F CA 501 1_555 X O2 AKG . F AKG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? # _chem_comp.formula 'C5 H6 O5' _chem_comp.formula_weight 146.098 _chem_comp.id AKG _chem_comp.mon_nstd_flag . _chem_comp.name '2-OXOGLUTARIC ACID' _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 O1 AKG doub 1 n n C1 O2 AKG sing 2 n n C1 C2 AKG sing 3 n n O2 HO2 AKG sing 4 n n C2 O5 AKG doub 5 n n C2 C3 AKG sing 6 n n C3 C4 AKG sing 7 n n C3 H31 AKG sing 8 n n C3 H32 AKG sing 9 n n C4 C5 AKG sing 10 n n C4 H41 AKG sing 11 n n C4 H42 AKG sing 12 n n C5 O3 AKG doub 13 n n C5 O4 AKG sing 14 n n O4 HO4 AKG sing 15 n n # _atom_sites.entry_id 4L06 _atom_sites.fract_transf_matrix[1][1] 0.010393 _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] 0.00858 _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] 0.003627 _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 G 2 CA A 1 501 1 CA CA . H 3 NAP A 1 502 1 NAP NAP . I 4 AKG A 1 503 2 AKG AKG . J 2 CA B 1 501 2 CA CA . K 3 NAP B 1 502 2 NAP NAP . L 4 AKG B 1 503 1 AKG AKG . M 2 CA C 1 501 3 CA CA . N 3 NAP C 1 502 3 NAP NAP . O 4 AKG C 1 503 4 AKG AKG . P 2 CA D 1 501 4 CA CA . Q 3 NAP D 1 502 4 NAP NAP . R 4 AKG D 1 503 3 AKG AKG . S 2 CA E 1 501 5 CA CA . T 3 NAP E 1 502 5 NAP NAP . U 4 AKG E 1 503 6 AKG AKG . V 2 CA F 1 501 6 CA CA . W 3 NAP F 1 502 6 NAP NAP . X 4 AKG F 1 503 5 AKG AKG . Y 5 HOH A 1 601 7 HOH HOH . Y 5 HOH A 2 602 8 HOH HOH . Y 5 HOH A 3 603 9 HOH HOH . Y 5 HOH A 4 604 12 HOH HOH . Y 5 HOH A 5 605 21 HOH HOH . Y 5 HOH A 6 606 22 HOH HOH . Y 5 HOH A 7 607 23 HOH HOH . Y 5 HOH A 8 608 24 HOH HOH . Y 5 HOH A 9 609 25 HOH HOH . Y 5 HOH A 10 610 26 HOH HOH . Y 5 HOH A 11 611 27 HOH HOH . Y 5 HOH A 12 612 36 HOH HOH . Y 5 HOH A 13 613 37 HOH HOH . Y 5 HOH A 14 614 40 HOH HOH . Y 5 HOH A 15 615 41 HOH HOH . Y 5 HOH A 16 616 42 HOH HOH . Y 5 HOH A 17 617 43 HOH HOH . Y 5 HOH A 18 618 44 HOH HOH . Y 5 HOH A 19 619 45 HOH HOH . Y 5 HOH A 20 620 46 HOH HOH . Y 5 HOH A 21 621 47 HOH HOH . Y 5 HOH A 22 622 48 HOH HOH . Y 5 HOH A 23 623 50 HOH HOH . Y 5 HOH A 24 624 51 HOH HOH . Y 5 HOH A 25 625 52 HOH HOH . Y 5 HOH A 26 626 53 HOH HOH . Y 5 HOH A 27 627 57 HOH HOH . Y 5 HOH A 28 628 60 HOH HOH . Y 5 HOH A 29 629 61 HOH HOH . Y 5 HOH A 30 630 69 HOH HOH . Y 5 HOH A 31 631 72 HOH HOH . Y 5 HOH A 32 632 78 HOH HOH . Y 5 HOH A 33 633 94 HOH HOH . Y 5 HOH A 34 634 95 HOH HOH . Y 5 HOH A 35 635 100 HOH HOH . Y 5 HOH A 36 636 101 HOH HOH . Y 5 HOH A 37 637 102 HOH HOH . Y 5 HOH A 38 638 103 HOH HOH . Y 5 HOH A 39 639 104 HOH HOH . Y 5 HOH A 40 640 107 HOH HOH . Y 5 HOH A 41 641 108 HOH HOH . Y 5 HOH A 42 642 109 HOH HOH . Y 5 HOH A 43 643 113 HOH HOH . Y 5 HOH A 44 644 114 HOH HOH . Y 5 HOH A 45 645 115 HOH HOH . Y 5 HOH A 46 646 117 HOH HOH . Y 5 HOH A 47 647 118 HOH HOH . Z 5 HOH B 1 601 2 HOH HOH . Z 5 HOH B 2 602 3 HOH HOH . Z 5 HOH B 3 603 32 HOH HOH . Z 5 HOH B 4 604 38 HOH HOH . Z 5 HOH B 5 605 49 HOH HOH . Z 5 HOH B 6 606 59 HOH HOH . Z 5 HOH B 7 607 62 HOH HOH . Z 5 HOH B 8 608 63 HOH HOH . Z 5 HOH B 9 609 70 HOH HOH . Z 5 HOH B 10 610 71 HOH HOH . Z 5 HOH B 11 611 86 HOH HOH . Z 5 HOH B 12 612 88 HOH HOH . Z 5 HOH B 13 613 110 HOH HOH . Z 5 HOH B 14 614 111 HOH HOH . AA 5 HOH C 1 601 4 HOH HOH . AA 5 HOH C 2 602 5 HOH HOH . AA 5 HOH C 3 603 10 HOH HOH . AA 5 HOH C 4 604 15 HOH HOH . AA 5 HOH C 5 605 16 HOH HOH . AA 5 HOH C 6 606 17 HOH HOH . AA 5 HOH C 7 607 30 HOH HOH . AA 5 HOH C 8 608 39 HOH HOH . AA 5 HOH C 9 609 55 HOH HOH . AA 5 HOH C 10 610 56 HOH HOH . AA 5 HOH C 11 611 83 HOH HOH . AA 5 HOH C 12 612 84 HOH HOH . AA 5 HOH C 13 613 87 HOH HOH . AA 5 HOH C 14 614 112 HOH HOH . AA 5 HOH C 15 615 123 HOH HOH . AA 5 HOH C 16 616 124 HOH HOH . BA 5 HOH D 1 601 13 HOH HOH . BA 5 HOH D 2 602 54 HOH HOH . BA 5 HOH D 3 603 85 HOH HOH . BA 5 HOH D 4 604 120 HOH HOH . BA 5 HOH D 5 605 121 HOH HOH . BA 5 HOH D 6 606 129 HOH HOH . CA 5 HOH E 1 601 1 HOH HOH . CA 5 HOH E 2 602 6 HOH HOH . CA 5 HOH E 3 603 18 HOH HOH . CA 5 HOH E 4 604 19 HOH HOH . CA 5 HOH E 5 605 20 HOH HOH . CA 5 HOH E 6 606 31 HOH HOH . CA 5 HOH E 7 607 33 HOH HOH . CA 5 HOH E 8 608 34 HOH HOH . CA 5 HOH E 9 609 64 HOH HOH . CA 5 HOH E 10 610 73 HOH HOH . CA 5 HOH E 11 611 74 HOH HOH . CA 5 HOH E 12 612 77 HOH HOH . CA 5 HOH E 13 613 81 HOH HOH . CA 5 HOH E 14 614 82 HOH HOH . CA 5 HOH E 15 615 89 HOH HOH . CA 5 HOH E 16 616 90 HOH HOH . CA 5 HOH E 17 617 91 HOH HOH . CA 5 HOH E 18 618 92 HOH HOH . CA 5 HOH E 19 619 93 HOH HOH . CA 5 HOH E 20 620 97 HOH HOH . CA 5 HOH E 21 621 105 HOH HOH . CA 5 HOH E 22 622 106 HOH HOH . CA 5 HOH E 23 623 116 HOH HOH . CA 5 HOH E 24 624 122 HOH HOH . CA 5 HOH E 25 625 128 HOH HOH . DA 5 HOH F 1 601 11 HOH HOH . DA 5 HOH F 2 602 14 HOH HOH . DA 5 HOH F 3 603 28 HOH HOH . DA 5 HOH F 4 604 29 HOH HOH . DA 5 HOH F 5 605 35 HOH HOH . DA 5 HOH F 6 606 65 HOH HOH . DA 5 HOH F 7 607 66 HOH HOH . DA 5 HOH F 8 608 67 HOH HOH . DA 5 HOH F 9 609 68 HOH HOH . DA 5 HOH F 10 610 75 HOH HOH . DA 5 HOH F 11 611 76 HOH HOH . DA 5 HOH F 12 612 79 HOH HOH . DA 5 HOH F 13 613 80 HOH HOH . DA 5 HOH F 14 614 96 HOH HOH . DA 5 HOH F 15 615 98 HOH HOH . DA 5 HOH F 16 616 99 HOH HOH . DA 5 HOH F 17 617 119 HOH HOH . DA 5 HOH F 18 618 125 HOH HOH . DA 5 HOH F 19 619 126 HOH HOH . DA 5 HOH F 20 620 127 HOH HOH . DA 5 HOH F 21 621 130 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 AKG . . . L 4 25.173 -38.273 -31.695 1 80.1 ? C1 AKG 503 B 1 HETATM 2 O O1 AKG . . . L 4 24.521 -38.453 -32.743 1 80.26 ? O1 AKG 503 B 1 HETATM 3 O O2 AKG . . . L 4 24.609 -38.167 -30.583 1 81.12 ? O2 AKG 503 B 1 HETATM 4 C C2 AKG . . . L 4 26.626 -38.174 -31.807 1 80.36 ? C2 AKG 503 B 1 HETATM 5 O O5 AKG . . . L 4 27.285 -37.617 -30.939 1 82.89 ? O5 AKG 503 B 1 HETATM 6 C C3 AKG . . . L 4 27.3 -38.761 -33.027 1 76.5 ? C3 AKG 503 B 1 HETATM 7 C C4 AKG . . . L 4 28.7 -38.172 -33.166 1 75.23 ? C4 AKG 503 B 1 HETATM 8 C C5 AKG . . . L 4 29.421 -38.881 -34.29 1 74.64 ? C5 AKG 503 B 1 HETATM 9 O O3 AKG . . . L 4 28.812 -39.783 -34.91 1 77.5 ? O3 AKG 503 B 1 HETATM 10 O O4 AKG . . . L 4 30.596 -38.545 -34.561 1 70.74 ? O4 AKG 503 B 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 39 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 10 #