data_5XAG # _model_server_result.job_id FqjVtFOQmvV8hCwfLWK0ng _model_server_result.datetime_utc '2024-11-17 02:35:13' _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 5xag # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"GA","auth_seq_id":504}' # _entry.id 5XAG # _exptl.entry_id 5XAG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 12 _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 5XAG _cell.length_a 104.27 _cell.length_b 156.117 _cell.length_c 182.107 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XAG _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA _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 ? 7 I N N ? 7 J N N ? 7 L N N ? 7 O N N ? 7 P N N ? 7 Q N N ? 7 U N N ? 7 X N N ? 7 Y N N ? 7 Z N N ? 7 FA N N ? 7 GA 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 GA O3 GOL . D GOL 504 1_555 IA N3 IMD . E IMD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc8 A OE2 GLU 71 A GLU 71 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc9 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc10 H MG MG . A MG 502 1_555 LA O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.864 ? metalc ? metalc11 H MG MG . A MG 502 1_555 LA O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc12 B OE1 GLN 11 B GLN 11 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc13 B OE1 GLU 111 B GLU 113 1_555 R CA CA . B CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc14 B OE1 GLU 111 B GLU 113 1_555 AA CA CA . C CA 507 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc15 B OE2 GLU 111 B GLU 113 1_555 AA CA CA . C CA 507 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? metalc ? metalc16 B OD2 ASP 177 B ASP 179 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? metalc ? metalc17 M O2A GDP . B GDP 501 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc18 C OE2 GLU 71 C GLU 71 1_555 W MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? metalc ? metalc19 V O3G GTP . C GTP 502 1_555 W MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc20 V O2B GTP . C GTP 502 1_555 W MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc21 W MG MG . C MG 503 1_555 NA O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc22 W MG MG . C MG 503 1_555 NA O HOH . C HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc23 D OE1 GLN 11 D GLN 11 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc24 F OD2 ASP 318 F ASP 318 1_555 JA MG MG . F MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 GOL sing 278 n n C1 C2 GOL sing 279 n n C1 H11 GOL sing 280 n n C1 H12 GOL sing 281 n n O1 HO1 GOL sing 282 n n C2 O2 GOL sing 283 n n C2 C3 GOL sing 284 n n C2 H2 GOL sing 285 n n O2 HO2 GOL sing 286 n n C3 O3 GOL sing 287 n n C3 H31 GOL sing 288 n n C3 H32 GOL sing 289 n n O3 HO3 GOL sing 290 n n # _atom_sites.entry_id 5XAG _atom_sites.fract_transf_matrix[1][1] 0.00959 _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] 0.006405 _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] 0.005491 _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 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 GOL A 1 503 503 GOL GOL . J 7 GOL A 1 504 504 GOL GOL . K 8 CA A 1 505 505 CA CA . L 7 GOL A 1 506 506 GOL GOL . M 9 GDP B 1 501 501 GDP GDP . N 6 MG B 1 502 502 MG MG . O 7 GOL B 1 503 503 GOL GOL . P 7 GOL B 1 504 504 GOL GOL . Q 7 GOL B 1 505 505 GOL GOL . R 8 CA B 1 506 506 CA CA . S 10 MES B 1 507 507 MES MES . T 11 93X B 1 508 508 93X 93X . U 7 GOL C 1 501 501 GOL GOL . V 5 GTP C 1 502 502 GTP GTP . W 6 MG C 1 503 503 MG MG . X 7 GOL C 1 504 504 GOL GOL . Y 7 GOL C 1 505 505 GOL GOL . Z 7 GOL C 1 506 506 GOL GOL . AA 8 CA C 1 507 507 CA CA . BA 12 IMD C 1 508 508 IMD IMD . CA 12 IMD C 1 509 509 IMD IMD . DA 9 GDP D 1 501 501 GDP GDP . EA 6 MG D 1 502 502 MG MG . FA 7 GOL D 1 503 503 GOL GOL . GA 7 GOL D 1 504 504 GOL GOL . HA 11 93X D 1 505 505 93X 93X . IA 12 IMD E 1 201 201 IMD IMD . JA 6 MG F 1 401 401 MG MG . KA 13 ACP F 1 402 402 ACP ACP . LA 14 HOH A 1 601 601 HOH HOH . LA 14 HOH A 2 602 602 HOH HOH . LA 14 HOH A 3 603 603 HOH HOH . LA 14 HOH A 4 604 604 HOH HOH . LA 14 HOH A 5 605 605 HOH HOH . LA 14 HOH A 6 606 606 HOH HOH . LA 14 HOH A 7 607 607 HOH HOH . LA 14 HOH A 8 608 608 HOH HOH . LA 14 HOH A 9 609 609 HOH HOH . LA 14 HOH A 10 610 610 HOH HOH . LA 14 HOH A 11 611 611 HOH HOH . LA 14 HOH A 12 612 612 HOH HOH . LA 14 HOH A 13 613 613 HOH HOH . LA 14 HOH A 14 614 614 HOH HOH . LA 14 HOH A 15 615 615 HOH HOH . LA 14 HOH A 16 616 616 HOH HOH . LA 14 HOH A 17 617 617 HOH HOH . LA 14 HOH A 18 618 618 HOH HOH . LA 14 HOH A 19 619 619 HOH HOH . LA 14 HOH A 20 620 620 HOH HOH . MA 14 HOH B 1 601 601 HOH HOH . MA 14 HOH B 2 602 602 HOH HOH . MA 14 HOH B 3 603 603 HOH HOH . MA 14 HOH B 4 604 604 HOH HOH . MA 14 HOH B 5 605 605 HOH HOH . MA 14 HOH B 6 606 606 HOH HOH . MA 14 HOH B 7 607 607 HOH HOH . MA 14 HOH B 8 608 608 HOH HOH . MA 14 HOH B 9 609 609 HOH HOH . MA 14 HOH B 10 610 610 HOH HOH . MA 14 HOH B 11 611 611 HOH HOH . MA 14 HOH B 12 612 612 HOH HOH . MA 14 HOH B 13 613 613 HOH HOH . MA 14 HOH B 14 614 614 HOH HOH . MA 14 HOH B 15 615 615 HOH HOH . MA 14 HOH B 16 616 616 HOH HOH . MA 14 HOH B 17 617 617 HOH HOH . MA 14 HOH B 18 618 618 HOH HOH . MA 14 HOH B 19 619 619 HOH HOH . MA 14 HOH B 20 620 620 HOH HOH . NA 14 HOH C 1 601 601 HOH HOH . NA 14 HOH C 2 602 602 HOH HOH . NA 14 HOH C 3 603 603 HOH HOH . NA 14 HOH C 4 604 604 HOH HOH . NA 14 HOH C 5 605 605 HOH HOH . NA 14 HOH C 6 606 606 HOH HOH . NA 14 HOH C 7 607 607 HOH HOH . NA 14 HOH C 8 608 608 HOH HOH . NA 14 HOH C 9 609 609 HOH HOH . NA 14 HOH C 10 610 610 HOH HOH . NA 14 HOH C 11 611 611 HOH HOH . NA 14 HOH C 12 612 612 HOH HOH . NA 14 HOH C 13 613 613 HOH HOH . NA 14 HOH C 14 614 614 HOH HOH . NA 14 HOH C 15 615 615 HOH HOH . NA 14 HOH C 16 616 616 HOH HOH . NA 14 HOH C 17 617 617 HOH HOH . NA 14 HOH C 18 618 618 HOH HOH . NA 14 HOH C 19 619 619 HOH HOH . NA 14 HOH C 20 620 620 HOH HOH . NA 14 HOH C 21 621 621 HOH HOH . NA 14 HOH C 22 622 622 HOH HOH . NA 14 HOH C 23 623 623 HOH HOH . NA 14 HOH C 24 624 624 HOH HOH . NA 14 HOH C 25 625 625 HOH HOH . NA 14 HOH C 26 626 626 HOH HOH . NA 14 HOH C 27 627 627 HOH HOH . NA 14 HOH C 28 628 628 HOH HOH . NA 14 HOH C 29 629 629 HOH HOH . NA 14 HOH C 30 630 630 HOH HOH . NA 14 HOH C 31 631 631 HOH HOH . NA 14 HOH C 32 632 632 HOH HOH . NA 14 HOH C 33 633 633 HOH HOH . NA 14 HOH C 34 634 634 HOH HOH . NA 14 HOH C 35 635 635 HOH HOH . NA 14 HOH C 36 636 636 HOH HOH . NA 14 HOH C 37 637 637 HOH HOH . NA 14 HOH C 38 638 638 HOH HOH . NA 14 HOH C 39 639 639 HOH HOH . NA 14 HOH C 40 640 640 HOH HOH . NA 14 HOH C 41 641 641 HOH HOH . NA 14 HOH C 42 642 642 HOH HOH . NA 14 HOH C 43 643 643 HOH HOH . NA 14 HOH C 44 644 644 HOH HOH . NA 14 HOH C 45 645 645 HOH HOH . NA 14 HOH C 46 646 646 HOH HOH . NA 14 HOH C 47 647 647 HOH HOH . NA 14 HOH C 48 648 648 HOH HOH . OA 14 HOH D 1 601 601 HOH HOH . OA 14 HOH D 2 602 602 HOH HOH . OA 14 HOH D 3 603 603 HOH HOH . OA 14 HOH D 4 604 604 HOH HOH . OA 14 HOH D 5 605 605 HOH HOH . OA 14 HOH D 6 606 606 HOH HOH . OA 14 HOH D 7 607 607 HOH HOH . OA 14 HOH D 8 608 608 HOH HOH . OA 14 HOH D 9 609 609 HOH HOH . PA 14 HOH E 1 301 301 HOH HOH . PA 14 HOH E 2 302 302 HOH HOH . PA 14 HOH E 3 303 303 HOH HOH . PA 14 HOH E 4 304 304 HOH HOH . PA 14 HOH E 5 305 305 HOH HOH . PA 14 HOH E 6 306 306 HOH HOH . PA 14 HOH E 7 307 307 HOH HOH . PA 14 HOH E 8 308 308 HOH HOH . PA 14 HOH E 9 309 309 HOH HOH . PA 14 HOH E 10 310 310 HOH HOH . PA 14 HOH E 11 311 311 HOH HOH . PA 14 HOH E 12 312 312 HOH HOH . PA 14 HOH E 13 313 313 HOH HOH . PA 14 HOH E 14 314 314 HOH HOH . PA 14 HOH E 15 315 315 HOH HOH . QA 14 HOH F 1 501 501 HOH HOH . QA 14 HOH F 2 502 502 HOH HOH . QA 14 HOH F 3 503 503 HOH HOH . QA 14 HOH F 4 504 504 HOH HOH . QA 14 HOH F 5 505 505 HOH HOH . QA 14 HOH F 6 506 506 HOH HOH . QA 14 HOH F 7 507 507 HOH HOH . QA 14 HOH F 8 508 508 HOH HOH . QA 14 HOH F 9 509 509 HOH HOH . QA 14 HOH F 10 510 510 HOH HOH . QA 14 HOH F 11 511 511 HOH HOH . QA 14 HOH F 12 512 512 HOH HOH . QA 14 HOH F 13 513 513 HOH HOH . QA 14 HOH F 14 514 514 HOH HOH . QA 14 HOH F 15 515 515 HOH HOH . QA 14 HOH F 16 516 516 HOH HOH . QA 14 HOH F 17 517 517 HOH HOH . QA 14 HOH F 18 518 518 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 GOL . . . GA 7 30.002 -5.485 21.186 1 111.03 ? C1 GOL 504 D 1 HETATM 2 O O1 GOL . . . GA 7 31.142 -5.297 20.375 1 113.26 ? O1 GOL 504 D 1 HETATM 3 C C2 GOL . . . GA 7 30.392 -6.087 22.534 1 107.37 ? C2 GOL 504 D 1 HETATM 4 O O2 GOL . . . GA 7 29.904 -5.292 23.593 1 101.97 ? O2 GOL 504 D 1 HETATM 5 C C3 GOL . . . GA 7 29.857 -7.511 22.647 1 109.93 ? C3 GOL 504 D 1 HETATM 6 O O3 GOL . . . GA 7 30.659 -8.364 21.856 1 118.15 ? O3 GOL 504 D 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 359 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 6 #