data_5FNV # _model_server_result.job_id pFPaHZXgf-tbi9J5CTV-EQ _model_server_result.datetime_utc '2024-12-01 12:15:49' _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 5fnv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":1443}' # _entry.id 5FNV # _exptl.entry_id 5FNV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 326.471 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description PIRONETIN _entity.pdbx_number_of_molecules 1 _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 5FNV _cell.length_a 106.16 _cell.length_b 157.2 _cell.length_c 181.68 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5FNV _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 PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z _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 # _struct_asym.details ? _struct_asym.entity_id 10 _struct_asym.id R _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 C SG CYS 316 C CYS 316 1_555 R C03 X3H . C X3H 1443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? metalc ? metalc1 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc2 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc3 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc4 A O THR 41 A THR 41 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc8 G O1G GTP . A GTP 1438 1_555 H MG MG . A MG 1439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc9 G O2B GTP . A GTP 1438 1_555 H MG MG . A MG 1439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc10 H MG MG . A MG 1439 1_555 V O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc11 H MG MG . A MG 1439 1_555 V O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc12 H MG MG . A MG 1439 1_555 V O HOH . A HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc13 H MG MG . A MG 1439 1_555 V O HOH . A HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 1430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc15 B OE1 GLU 111 B GLU 111 1_555 L CA CA . B CA 1431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc16 J O1A GDP . B GDP 1429 1_555 K MG MG . B MG 1430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc17 K MG MG . B MG 1430 1_555 W O HOH . B HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc18 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc19 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc20 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc21 C O THR 41 C THR 41 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc22 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc23 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? metalc ? metalc24 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc25 O O1B GTP . C GTP 1440 1_555 P MG MG . C MG 1441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc26 O O1G GTP . C GTP 1440 1_555 P MG MG . C MG 1441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc27 P MG MG . C MG 1441 1_555 X O HOH . C HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc28 P MG MG . C MG 1441 1_555 X O HOH . C HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc29 P MG MG . C MG 1441 1_555 X O HOH . C HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc30 P MG MG . C MG 1441 1_555 X O HOH . C HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc31 S O1B GTP . D GTP 1431 1_555 T MG MG . D MG 1432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.889 ? metalc ? metalc32 S O3G GTP . D GTP 1431 1_555 T MG MG . D MG 1432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? # _chem_comp.formula 'C19 H34 O4' _chem_comp.formula_weight 326.471 _chem_comp.id X3H _chem_comp.mon_nstd_flag . _chem_comp.name PIRONETIN _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 C14 C13 X3H sing 547 n n C13 C12 X3H doub 548 e n C18 C10 X3H sing 549 n n C12 C11 X3H sing 550 n n C11 C10 X3H sing 551 n n C10 C09 X3H sing 552 n n O09 C09 X3H sing 553 n n O09 C19 X3H sing 554 n n C09 C08 X3H sing 555 n n C08 C17 X3H sing 556 n n C08 C07 X3H sing 557 n n C07 C06 X3H sing 558 n n C07 O07 X3H sing 559 n n C06 C05 X3H sing 560 n n C15 C16 X3H sing 561 n n C15 C04 X3H sing 562 n n O06 C05 X3H sing 563 n n O06 C01 X3H sing 564 n n O01 C01 X3H doub 565 n n C05 C04 X3H sing 566 n n C01 C02 X3H sing 567 n n C04 C03 X3H sing 568 n n C02 C03 X3H sing 569 n n C16 H163 X3H sing 570 n n C16 H161 X3H sing 571 n n C16 H162 X3H sing 572 n n C15 H151 X3H sing 573 n n C15 H152 X3H sing 574 n n C04 H04 X3H sing 575 n n C03 H031 X3H sing 576 n n C03 H1 X3H sing 577 n n C02 H021 X3H sing 578 n n C02 H2 X3H sing 579 n n C05 H05 X3H sing 580 n n C06 H061 X3H sing 581 n n C06 H062 X3H sing 582 n n C07 H07 X3H sing 583 n n O07 H071 X3H sing 584 n n C08 H08 X3H sing 585 n n C17 H172 X3H sing 586 n n C17 H173 X3H sing 587 n n C17 H171 X3H sing 588 n n C09 H09 X3H sing 589 n n C19 H192 X3H sing 590 n n C19 H191 X3H sing 591 n n C19 H193 X3H sing 592 n n C10 H10 X3H sing 593 n n C18 H183 X3H sing 594 n n C18 H181 X3H sing 595 n n C18 H182 X3H sing 596 n n C11 H111 X3H sing 597 n n C11 H112 X3H sing 598 n n C12 H12 X3H sing 599 n n C13 H13 X3H sing 600 n n C14 H143 X3H sing 601 n n C14 H141 X3H sing 602 n n C14 H142 X3H sing 603 n n # _atom_sites.entry_id 5FNV _atom_sites.fract_transf_matrix[1][1] 0.00942 _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] 0.006361 _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] 0.005504 _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 1438 1438 GTP GTP . H 6 MG A 1 1439 1439 MG MG . I 7 CA A 1 1440 1440 CA CA . J 8 GDP B 1 1429 1429 GDP GDP . K 6 MG B 1 1430 1430 MG MG . L 7 CA B 1 1431 1431 CA CA . M 9 MES B 1 1432 1432 MES MES . N 9 MES B 1 1433 1433 MES MES . O 5 GTP C 1 1440 1440 GTP GTP . P 6 MG C 1 1441 1441 MG MG . Q 7 CA C 1 1442 1442 CA CA . R 10 X3H C 1 1443 1443 X3H X3H . S 5 GTP D 1 1431 1431 GTP GTP . T 6 MG D 1 1432 1432 MG MG . U 11 ACP F 1 1385 1385 ACP ACP . V 12 HOH A 1 2001 2001 HOH HOH . V 12 HOH A 2 2002 2002 HOH HOH . V 12 HOH A 3 2003 2003 HOH HOH . V 12 HOH A 4 2004 2004 HOH HOH . V 12 HOH A 5 2005 2005 HOH HOH . V 12 HOH A 6 2006 2006 HOH HOH . V 12 HOH A 7 2007 2007 HOH HOH . V 12 HOH A 8 2008 2008 HOH HOH . V 12 HOH A 9 2009 2009 HOH HOH . V 12 HOH A 10 2010 2010 HOH HOH . V 12 HOH A 11 2011 2011 HOH HOH . V 12 HOH A 12 2012 2012 HOH HOH . V 12 HOH A 13 2013 2013 HOH HOH . V 12 HOH A 14 2014 2014 HOH HOH . V 12 HOH A 15 2015 2015 HOH HOH . V 12 HOH A 16 2016 2016 HOH HOH . W 12 HOH B 1 2001 2001 HOH HOH . W 12 HOH B 2 2002 2002 HOH HOH . W 12 HOH B 3 2003 2003 HOH HOH . W 12 HOH B 4 2004 2004 HOH HOH . W 12 HOH B 5 2005 2005 HOH HOH . W 12 HOH B 6 2006 2006 HOH HOH . W 12 HOH B 7 2007 2007 HOH HOH . W 12 HOH B 8 2008 2008 HOH HOH . W 12 HOH B 9 2009 2009 HOH HOH . W 12 HOH B 10 2010 2010 HOH HOH . W 12 HOH B 11 2011 2011 HOH HOH . W 12 HOH B 12 2012 2012 HOH HOH . W 12 HOH B 13 2013 2013 HOH HOH . W 12 HOH B 14 2014 2014 HOH HOH . W 12 HOH B 15 2015 2015 HOH HOH . W 12 HOH B 16 2016 2016 HOH HOH . X 12 HOH C 1 2001 2001 HOH HOH . X 12 HOH C 2 2002 2002 HOH HOH . X 12 HOH C 3 2003 2003 HOH HOH . X 12 HOH C 4 2004 2004 HOH HOH . X 12 HOH C 5 2005 2005 HOH HOH . X 12 HOH C 6 2006 2006 HOH HOH . X 12 HOH C 7 2007 2007 HOH HOH . X 12 HOH C 8 2008 2008 HOH HOH . X 12 HOH C 9 2009 2009 HOH HOH . X 12 HOH C 10 2010 2010 HOH HOH . X 12 HOH C 11 2011 2011 HOH HOH . X 12 HOH C 12 2012 2012 HOH HOH . X 12 HOH C 13 2013 2013 HOH HOH . X 12 HOH C 14 2014 2014 HOH HOH . X 12 HOH C 15 2015 2015 HOH HOH . X 12 HOH C 16 2016 2016 HOH HOH . X 12 HOH C 17 2017 2017 HOH HOH . X 12 HOH C 18 2018 2018 HOH HOH . X 12 HOH C 19 2019 2019 HOH HOH . X 12 HOH C 20 2020 2020 HOH HOH . X 12 HOH C 21 2021 2021 HOH HOH . X 12 HOH C 22 2022 2022 HOH HOH . X 12 HOH C 23 2023 2023 HOH HOH . X 12 HOH C 24 2024 2024 HOH HOH . X 12 HOH C 25 2025 2025 HOH HOH . X 12 HOH C 26 2026 2026 HOH HOH . X 12 HOH C 27 2027 2027 HOH HOH . X 12 HOH C 28 2028 2028 HOH HOH . X 12 HOH C 29 2029 2029 HOH HOH . X 12 HOH C 30 2030 2030 HOH HOH . X 12 HOH C 31 2031 2031 HOH HOH . Y 12 HOH D 1 2001 2001 HOH HOH . Y 12 HOH D 2 2002 2002 HOH HOH . Y 12 HOH D 3 2003 2003 HOH HOH . Z 12 HOH F 1 2001 2001 HOH HOH . Z 12 HOH F 2 2002 2002 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 C14 X3H . . . R 10 19.819 38.128 -0.53 1 72.49 ? C14 X3H 1443 C 1 HETATM 2 C C16 X3H . . . R 10 7.401 35.173 4.785 1 65.82 ? C16 X3H 1443 C 1 HETATM 3 C C19 X3H . . . R 10 14.187 40.666 3.291 1 66.09 ? C19 X3H 1443 C 1 HETATM 4 C C18 X3H . . . R 10 15.207 37.655 0.501 1 67.67 ? C18 X3H 1443 C 1 HETATM 5 C C17 X3H . . . R 10 14.306 36.022 3.64 1 58.46 ? C17 X3H 1443 C 1 HETATM 6 O O01 X3H . . . R 10 8.355 40.348 5.031 1 60.08 ? O01 X3H 1443 C 1 HETATM 7 O O07 X3H . . . R 10 13.265 37.992 5.322 1 67.77 ? O07 X3H 1443 C 1 HETATM 8 C C13 X3H . . . R 10 18.52 38.666 0.025 1 72.77 ? C13 X3H 1443 C 1 HETATM 9 C C12 X3H . . . R 10 18.179 38.446 1.314 1 72.37 ? C12 X3H 1443 C 1 HETATM 10 C C15 X3H . . . R 10 8.336 36.322 4.473 1 64.06 ? C15 X3H 1443 C 1 HETATM 11 C C11 X3H . . . R 10 16.866 39.001 1.846 1 71.01 ? C11 X3H 1443 C 1 HETATM 12 C C02 X3H . . . R 10 8.017 38.662 6.614 1 62.79 ? C02 X3H 1443 C 1 HETATM 13 C C06 X3H . . . R 10 11.406 36.933 4.283 1 63.13 ? C06 X3H 1443 C 1 HETATM 14 O O09 X3H . . . R 10 14.141 39.567 2.4 1 62.77 ? O09 X3H 1443 C 1 HETATM 15 O O06 X3H . . . R 10 9.893 38.75 4.756 1 64.97 ? O06 X3H 1443 C 1 HETATM 16 C C01 X3H . . . R 10 8.777 39.286 5.445 1 62.34 ? C01 X3H 1443 C 1 HETATM 17 C C10 X3H . . . R 10 15.784 37.926 1.895 1 67.45 ? C10 X3H 1443 C 1 HETATM 18 C C08 X3H . . . R 10 13.66 37.3 3.128 1 60.93 ? C08 X3H 1443 C 1 HETATM 19 C C07 X3H . . . R 10 12.622 37.825 4.101 1 60.53 ? C07 X3H 1443 C 1 HETATM 20 C C03 X3H . . . R 10 8.66 37.296 6.799 1 59.59 ? C03 X3H 1443 C 1 HETATM 21 C C05 X3H . . . R 10 10.428 37.553 5.275 1 63.91 ? C05 X3H 1443 C 1 HETATM 22 C C04 X3H . . . R 10 9.31 36.6 5.633 1 62.01 ? C04 X3H 1443 C 1 HETATM 23 C C09 X3H . . . R 10 14.721 38.373 2.893 1 61.28 ? C09 X3H 1443 C 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #