data_6Y4M # _model_server_result.job_id G3P1tESoTsD98yEsTLoguw _model_server_result.datetime_utc '2024-11-24 23:21:22' _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 6y4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1005}' # _entry.id 6Y4M # _exptl.entry_id 6Y4M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 421.573 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(1~{R},3~{R})-1-acetyloxy-1-[4-methanoyl-5-(2-phenylmethoxyethyl)-2,3-dihydro-1,3-thiazol-2-yl]-4-methyl-pentan-3-yl]-methyl-azanium' _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 6Y4M _cell.length_a 103.961 _cell.length_b 152.59 _cell.length_c 185.989 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y4M _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,AA,BA _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 11 _struct_asym.id N _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 M C31 O9B . B O9B 1004 1_555 T N VAL . C VAL 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale2 N C5 O9H . B O9H 1005 1_555 O NBI OH5 . B OH5 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 N N3 O9H . B O9H 1005 1_555 T C VAL . C VAL 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc7 G O1G GTP . A GTP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc8 G O1B GTP . A GTP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc9 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc10 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc11 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc12 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc13 K MG MG . B MG 1002 1_555 Y O HOH . B HOH 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc14 K MG MG . B MG 1002 1_555 Z O HOH . C HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc15 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc16 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc17 C O THR 41 C THR 41 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc18 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc19 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc20 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc22 P O1G GTP . C GTP 1001 1_555 Q MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc23 P O1B GTP . C GTP 1001 1_555 Q MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc24 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc25 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc26 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc27 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc28 U O1G GTP . D GTP 1001 1_555 V MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc29 U O1B GTP . D GTP 1001 1_555 V MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc30 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc31 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc32 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc33 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? # _chem_comp.formula 'C22 H33 N2 O4 S 1' _chem_comp.formula_weight 421.573 _chem_comp.id O9H _chem_comp.mon_nstd_flag . _chem_comp.name '[(1~{R},3~{R})-1-acetyloxy-1-[4-methanoyl-5-(2-phenylmethoxyethyl)-2,3-dihydro-1,3-thiazol-2-yl]-4-methyl-pentan-3-yl]-methyl-azanium' _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 C26 C25 O9H doub 431 n y C26 C21 O9H sing 432 n y C20 C21 O9H sing 433 n n C20 O4 O9H sing 434 n n C25 C24 O9H sing 435 n y C21 C22 O9H doub 436 n y C19 O4 O9H sing 437 n n C19 C18 O9H sing 438 n n C24 C23 O9H doub 439 n y C22 C23 O9H sing 440 n y C18 C3 O9H sing 441 n n C3 S1 O9H sing 442 n n C3 C4 O9H doub 443 n n S1 C2 O9H sing 444 n n O8 C45 O9H doub 445 n n C4 C5 O9H sing 446 n n C4 N1 O9H sing 447 n n C45 C46 O9H sing 448 n n C45 O7 O9H sing 449 n n C5 O1 O9H doub 450 n n C2 N1 O9H sing 451 n n C2 C1 O9H sing 452 n n C1 O7 O9H sing 453 n n C1 C27 O9H sing 454 n n C41 N3 O9H sing 455 n n N3 C28 O9H sing 456 n n C27 C28 O9H sing 457 n n C28 C42 O9H sing 458 n n C42 C43 O9H sing 459 n n C42 C44 O9H sing 460 n n N1 H1 O9H sing 461 n n C5 H2 O9H sing 462 n n C1 H3 O9H sing 463 n n C2 H4 O9H sing 464 n n C18 H5 O9H sing 465 n n C18 H6 O9H sing 466 n n C19 H7 O9H sing 467 n n C19 H8 O9H sing 468 n n C20 H9 O9H sing 469 n n C20 H10 O9H sing 470 n n C22 H11 O9H sing 471 n n C23 H12 O9H sing 472 n n C24 H13 O9H sing 473 n n C25 H14 O9H sing 474 n n C26 H15 O9H sing 475 n n C27 H16 O9H sing 476 n n C27 H17 O9H sing 477 n n C28 H18 O9H sing 478 n n N3 H19 O9H sing 479 n n N3 H20 O9H sing 480 n n C41 H21 O9H sing 481 n n C41 H22 O9H sing 482 n n C41 H23 O9H sing 483 n n C42 H24 O9H sing 484 n n C43 H25 O9H sing 485 n n C43 H26 O9H sing 486 n n C43 H27 O9H sing 487 n n C44 H28 O9H sing 488 n n C44 H29 O9H sing 489 n n C44 H30 O9H sing 490 n n C46 H31 O9H sing 491 n n C46 H32 O9H sing 492 n n C46 H33 O9H sing 493 n n # _atom_sites.entry_id 6Y4M _atom_sites.fract_transf_matrix[1][1] 0.009619 _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] 0.006554 _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] 0.005377 _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 1001 1001 GTP GTP . H 6 MG A 1 1002 1002 MG MO6 . I 7 CA A 1 1003 1003 CA CA . J 8 GDP B 1 1001 1001 GDP GDP . K 6 MG B 1 1002 1002 MG MG . L 9 MES B 1 1003 1004 MES MES . M 10 O9B B 1 1004 2001 O9B ABB . N 11 O9H B 1 1005 2001 O9H ABB . O 12 OH5 B 1 1006 2001 OH5 ABB . P 5 GTP C 1 1001 1001 GTP GTP . Q 6 MG C 1 1002 1002 MG MO6 . R 7 CA C 1 1003 1003 CA CA . S 13 PGE C 1 1004 1004 PGE PGE . T 14 VAL C 1 1005 2001 VAL ABB . U 5 GTP D 1 1001 1001 GTP GTP . V 6 MG D 1 1002 1002 MG MO6 . W 15 ACP F 1 401 401 ACP ACP . X 16 HOH A 1 1101 1002 HOH MO6 . X 16 HOH A 2 1102 1002 HOH MO6 . X 16 HOH A 3 1103 1002 HOH MO6 . X 16 HOH A 4 1104 11 HOH HOH . X 16 HOH A 5 1105 1002 HOH MO6 . X 16 HOH A 6 1106 8 HOH HOH . X 16 HOH A 7 1107 10 HOH HOH . X 16 HOH A 8 1108 13 HOH HOH . X 16 HOH A 9 1109 7 HOH HOH . Y 16 HOH B 1 1101 20 HOH HOH . Y 16 HOH B 2 1102 18 HOH HOH . Y 16 HOH B 3 1103 5 HOH HOH . Y 16 HOH B 4 1104 16 HOH HOH . Y 16 HOH B 5 1105 4 HOH HOH . Y 16 HOH B 6 1106 14 HOH HOH . Y 16 HOH B 7 1107 6 HOH HOH . Y 16 HOH B 8 1108 21 HOH HOH . Y 16 HOH B 9 1109 1 HOH HOH . Y 16 HOH B 10 1110 9 HOH HOH . Y 16 HOH B 11 1111 19 HOH HOH . Z 16 HOH C 1 1101 1002 HOH MO6 . Z 16 HOH C 2 1102 1002 HOH MO6 . Z 16 HOH C 3 1103 1002 HOH MO6 . Z 16 HOH C 4 1104 15 HOH HOH . Z 16 HOH C 5 1105 1002 HOH MO6 . Z 16 HOH C 6 1106 2 HOH HOH . Z 16 HOH C 7 1107 3 HOH HOH . AA 16 HOH D 1 1101 1002 HOH MO6 . AA 16 HOH D 2 1102 17 HOH HOH . AA 16 HOH D 3 1103 1002 HOH MO6 . AA 16 HOH D 4 1104 1002 HOH MO6 . AA 16 HOH D 5 1105 1002 HOH MO6 . BA 16 HOH E 1 201 12 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 N N1 O9H . . . N 11 -3.593 26.024 14.891 1 60.05 ? N1 O9H 1005 B 1 HETATM 2 C C5 O9H . . . N 11 -3.993 23.705 14.165 1 62.09 ? C5 O9H 1005 B 1 HETATM 3 O O1 O9H . . . N 11 -3.982 23.282 15.318 1 61.96 ? O1 O9H 1005 B 1 HETATM 4 C C1 O9H . . . N 11 -2.721 28.304 15.129 1 61.93 ? C1 O9H 1005 B 1 HETATM 5 C C2 O9H . . . N 11 -3.494 27.235 14.43 1 61.81 ? C2 O9H 1005 B 1 HETATM 6 S S1 O9H . . . N 11 -4.337 27.535 12.955 1 63.42 ? S1 O9H 1005 B 1 HETATM 7 C C3 O9H . . . N 11 -4.633 25.842 12.858 1 62.87 ? C3 O9H 1005 B 1 HETATM 8 C C4 O9H . . . N 11 -4.085 25.164 13.921 1 60.75 ? C4 O9H 1005 B 1 HETATM 9 C C18 O9H . . . N 11 -5.419 25.329 11.689 1 65.8 ? C18 O9H 1005 B 1 HETATM 10 C C19 O9H . . . N 11 -4.556 25.021 10.488 1 68.68 ? C19 O9H 1005 B 1 HETATM 11 O O4 O9H . . . N 11 -3.897 23.768 10.678 1 71.86 ? O4 O9H 1005 B 1 HETATM 12 C C20 O9H . . . N 11 -2.841 23.543 9.752 1 71.4 ? C20 O9H 1005 B 1 HETATM 13 C C21 O9H . . . N 11 -1.595 24.297 10.159 1 72.37 ? C21 O9H 1005 B 1 HETATM 14 C C22 O9H . . . N 11 -0.911 23.953 11.312 1 73.39 ? C22 O9H 1005 B 1 HETATM 15 C C23 O9H . . . N 11 0.233 24.642 11.688 1 73.18 ? C23 O9H 1005 B 1 HETATM 16 C C24 O9H . . . N 11 0.699 25.68 10.914 1 72.33 ? C24 O9H 1005 B 1 HETATM 17 C C25 O9H . . . N 11 0.028 26.032 9.767 1 71.76 ? C25 O9H 1005 B 1 HETATM 18 C C26 O9H . . . N 11 -1.116 25.344 9.389 1 72.07 ? C26 O9H 1005 B 1 HETATM 19 C C27 O9H . . . N 11 -3.211 28.453 16.568 1 58.32 ? C27 O9H 1005 B 1 HETATM 20 C C28 O9H . . . N 11 -2.879 29.811 17.192 1 55.39 ? C28 O9H 1005 B 1 HETATM 21 N N3 O9H . . . N 11 -3.165 30.909 16.231 1 53.37 ? N3 O9H 1005 B 1 HETATM 22 C C41 O9H . . . N 11 -4.553 31.056 15.776 1 54.21 ? C41 O9H 1005 B 1 HETATM 23 C C42 O9H . . . N 11 -3.553 30.073 18.547 1 55.34 ? C42 O9H 1005 B 1 HETATM 24 C C43 O9H . . . N 11 -2.787 31.11 19.355 1 56.06 ? C43 O9H 1005 B 1 HETATM 25 C C44 O9H . . . N 11 -3.736 28.798 19.362 1 55.61 ? C44 O9H 1005 B 1 HETATM 26 O O7 O9H . . . N 11 -1.308 27.944 15.162 1 68.69 ? O7 O9H 1005 B 1 HETATM 27 C C45 O9H . . . N 11 -0.563 28.118 14.062 1 68.68 ? C45 O9H 1005 B 1 HETATM 28 O O8 O9H . . . N 11 -1.015 28.418 12.993 1 70.21 ? O8 O9H 1005 B 1 HETATM 29 C C46 O9H . . . N 11 0.875 27.882 14.358 1 67.72 ? C46 O9H 1005 B 1 # _model_server_stats.io_time_ms 160 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #