data_3AGA # _model_server_result.job_id ncTvtHK-4SmeI08XrtpNjw _model_server_result.datetime_utc '2024-12-28 23:18:28' _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 3aga # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1000}' # _entry.id 3AGA # _exptl.entry_id 3AGA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 626.699 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-{(2Z,3S,4S)-5-[(Z)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-2-[(5R)-2-[(3-ethyl-5-formyl-4-methyl-1H-pyrrol-2-yl)methyl]-5-(methoxycarbonyl)-3-methyl-4-oxo-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene]-4-methyl-3,4-dihydro-2H-pyrrol-3-yl}propanoic 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 90 _cell.angle_gamma 90 _cell.entry_id 3AGA _cell.length_a 45.5 _cell.length_b 85.64 _cell.length_c 133.3 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AGA _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 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 _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 ? 2 C N N ? 2 E 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 D NA NA . A NA 1 1_555 A O LEU 156 A LEU 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc2 D NA NA . A NA 1 1_555 A O LEU 158 A LEU 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc3 D NA NA . A NA 1 1_555 A O VAL 161 A VAL 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc4 F NA NA . B NA 2 1_555 H O HOH . B HOH 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc5 F NA NA . B NA 2 1_555 B O LEU 156 B LEU 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc6 F NA NA . B NA 2 1_555 B O LEU 158 B LEU 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc7 F NA NA . B NA 2 1_555 B O VAL 161 B VAL 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.937 ? # _chem_comp.formula 'C35 H38 N4 O7' _chem_comp.formula_weight 626.699 _chem_comp.id RCC _chem_comp.mon_nstd_flag . _chem_comp.name '3-{(2Z,3S,4S)-5-[(Z)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-2-[(5R)-2-[(3-ethyl-5-formyl-4-methyl-1H-pyrrol-2-yl)methyl]-5-(methoxycarbonyl)-3-methyl-4-oxo-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene]-4-methyl-3,4-dihydro-2H-pyrrol-3-yl}propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Red chlorophyll catabolite' # 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 NA C1A RCC sing 277 n n NA C4A RCC doub 278 n n NB C1B RCC sing 279 n n NB C4B RCC sing 280 n n OB C4B RCC doub 281 n n NC C1C RCC sing 282 n y NC C4C RCC sing 283 n y OC CHC RCC doub 284 n n ND C1D RCC sing 285 n y ND C4D RCC sing 286 n y C1A C2A RCC sing 287 n n C1A CHA RCC doub 288 n n O1A CGA RCC doub 289 n n C1B C2B RCC sing 290 n n C1B CHB RCC doub 291 z n C1C C2C RCC doub 292 n y C1C CHC RCC sing 293 n n C1D C2D RCC doub 294 z y C1D CHD RCC sing 295 n n O1D CGD RCC doub 296 n n C2A C3A RCC sing 297 n n C2A CAA RCC sing 298 n n O2A CGA RCC sing 299 n n C2B C3B RCC doub 300 n n C2B CMB RCC sing 301 n n C2C C3C RCC sing 302 n y C2C CMC RCC sing 303 n n C2D C3D RCC sing 304 n y C2D CMD RCC sing 305 n n O2D CED RCC sing 306 n n O2D CGD RCC sing 307 n n C3A C4A RCC sing 308 n n C3A CMA RCC sing 309 n n C3B C4B RCC sing 310 n n C3B CAB RCC sing 311 n n C3C C4C RCC doub 312 n y C3C CAC RCC sing 313 n n C3D C4D RCC doub 314 n y C3D CAD RCC sing 315 n n C4A CHB RCC sing 316 n n C4C CHD RCC sing 317 n n C4D CHA RCC sing 318 n n CAA CBA RCC sing 319 n n CAB CBB RCC doub 320 n n CAC CBC RCC sing 321 n n CAD CBD RCC sing 322 n n CAD OBD RCC doub 323 n n CBA CGA RCC sing 324 n n CBD CGD RCC sing 325 n n CBD CHA RCC sing 326 n n NB HNB RCC sing 327 n n NC HNC RCC sing 328 n n ND HND RCC sing 329 n n C2A H2A RCC sing 330 n n C3A H3A RCC sing 331 n n CAA HAA RCC sing 332 n n CAA HAAA RCC sing 333 n n CAB HAB RCC sing 334 n n CAC HAC RCC sing 335 n n CAC HACA RCC sing 336 n n CBA HBA RCC sing 337 n n CBA HBAA RCC sing 338 n n CBB HBB RCC sing 339 n n CBB HBBA RCC sing 340 n n CBC HBC RCC sing 341 n n CBC HBCA RCC sing 342 n n CBC HBCB RCC sing 343 n n CBD HBD RCC sing 344 n n CED HED RCC sing 345 n n CED HEDA RCC sing 346 n n CED HEDB RCC sing 347 n n CHB HHB RCC sing 348 n n CHC HHC RCC sing 349 n n CHD HHD RCC sing 350 n n CHD HHDA RCC sing 351 n n CMA HMA RCC sing 352 n n CMA HMAA RCC sing 353 n n CMA HMAB RCC sing 354 n n CMB HMB RCC sing 355 n n CMB HMBA RCC sing 356 n n CMB HMBB RCC sing 357 n n CMC HMC RCC sing 358 n n CMC HMCA RCC sing 359 n n CMC HMCB RCC sing 360 n n CMD HMD RCC sing 361 n n CMD HMDA RCC sing 362 n n CMD HMDB RCC sing 363 n n O2A HO2A RCC sing 364 n n # _atom_sites.entry_id 3AGA _atom_sites.fract_transf_matrix[1][1] 0.021978 _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] 0.011677 _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] 0.007502 _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 RCC A 1 1000 1000 RCC RCC . D 3 NA A 1 1 1 NA NA . E 2 RCC B 1 1000 1000 RCC RCC . F 3 NA B 1 2 2 NA NA . G 4 HOH A 1 3 3 HOH HOH . G 4 HOH A 2 4 4 HOH HOH . G 4 HOH A 3 7 7 HOH HOH . G 4 HOH A 4 8 8 HOH HOH . G 4 HOH A 5 9 9 HOH HOH . G 4 HOH A 6 10 10 HOH HOH . G 4 HOH A 7 11 11 HOH HOH . G 4 HOH A 8 12 12 HOH HOH . G 4 HOH A 9 15 15 HOH HOH . G 4 HOH A 10 16 16 HOH HOH . G 4 HOH A 11 17 17 HOH HOH . G 4 HOH A 12 18 18 HOH HOH . G 4 HOH A 13 20 20 HOH HOH . G 4 HOH A 14 23 23 HOH HOH . G 4 HOH A 15 24 24 HOH HOH . G 4 HOH A 16 25 25 HOH HOH . G 4 HOH A 17 26 26 HOH HOH . G 4 HOH A 18 29 29 HOH HOH . H 4 HOH B 1 5 5 HOH HOH . H 4 HOH B 2 13 13 HOH HOH . H 4 HOH B 3 14 14 HOH HOH . H 4 HOH B 4 19 19 HOH HOH . H 4 HOH B 5 21 21 HOH HOH . H 4 HOH B 6 22 22 HOH HOH . H 4 HOH B 7 27 27 HOH HOH . H 4 HOH B 8 28 28 HOH HOH . H 4 HOH B 9 30 30 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 NA RCC . . . C 2 -12.021 8.406 -14.768 1 145.1 ? NA RCC 1000 A 1 HETATM 2 N NB RCC . . . C 2 -9.183 8.877 -14.828 1 146.94 ? NB RCC 1000 A 1 HETATM 3 O OB RCC . . . C 2 -7.623 10.581 -14.794 1 148.34 ? OB RCC 1000 A 1 HETATM 4 N NC RCC . . . C 2 -9.754 12.19 -16.567 1 135 ? NC RCC 1000 A 1 HETATM 5 O OC RCC . . . C 2 -7.455 10.977 -19.103 1 131.68 ? OC RCC 1000 A 1 HETATM 6 N ND RCC . . . C 2 -11.957 11.429 -14.685 1 142.06 ? ND RCC 1000 A 1 HETATM 7 C C1A RCC . . . C 2 -13.439 8.53 -14.713 1 144.28 ? C1A RCC 1000 A 1 HETATM 8 O O1A RCC . . . C 2 -17.625 6.248 -14.108 1 140.57 ? O1A RCC 1000 A 1 HETATM 9 C C1B RCC . . . C 2 -9.196 7.478 -14.911 1 146.58 ? C1B RCC 1000 A 1 HETATM 10 C C1C RCC . . . C 2 -8.602 12.109 -17.352 1 133.9 ? C1C RCC 1000 A 1 HETATM 11 C C1D RCC . . . C 2 -11.929 12.83 -14.663 1 140.82 ? C1D RCC 1000 A 1 HETATM 12 O O1D RCC . . . C 2 -15.764 8.978 -12.462 1 147.24 ? O1D RCC 1000 A 1 HETATM 13 C C2A RCC . . . C 2 -14.082 7.138 -14.728 1 144.14 ? C2A RCC 1000 A 1 HETATM 14 O O2A RCC . . . C 2 -16.221 4.597 -13.679 1 139.87 ? O2A RCC 1000 A 1 HETATM 15 C C2B RCC . . . C 2 -7.752 7.041 -15.01 1 147.22 ? C2B RCC 1000 A 1 HETATM 16 C C2C RCC . . . C 2 -7.712 13.149 -16.942 1 134.42 ? C2C RCC 1000 A 1 HETATM 17 C C2D RCC . . . C 2 -13.261 13.329 -14.624 1 141.87 ? C2D RCC 1000 A 1 HETATM 18 O O2D RCC . . . C 2 -17.619 9.917 -13.386 1 147.65 ? O2D RCC 1000 A 1 HETATM 19 C C3A RCC . . . C 2 -12.862 6.177 -14.8 1 144.74 ? C3A RCC 1000 A 1 HETATM 20 C C3B RCC . . . C 2 -6.938 8.18 -14.977 1 147.58 ? C3B RCC 1000 A 1 HETATM 21 C C3C RCC . . . C 2 -8.365 13.868 -15.876 1 134.51 ? C3C RCC 1000 A 1 HETATM 22 C C3D RCC . . . C 2 -14.117 12.189 -14.619 1 143.22 ? C3D RCC 1000 A 1 HETATM 23 C C4A RCC . . . C 2 -11.671 7.147 -14.821 1 145.16 ? C4A RCC 1000 A 1 HETATM 24 C C4B RCC . . . C 2 -7.868 9.371 -14.858 1 147.52 ? C4B RCC 1000 A 1 HETATM 25 C C4C RCC . . . C 2 -9.631 13.246 -15.67 1 135.79 ? C4C RCC 1000 A 1 HETATM 26 C C4D RCC . . . C 2 -13.272 11.033 -14.658 1 143.33 ? C4D RCC 1000 A 1 HETATM 27 C CAA RCC . . . C 2 -15.035 6.911 -15.906 1 143.56 ? CAA RCC 1000 A 1 HETATM 28 C CAB RCC . . . C 2 -5.479 8.327 -15.037 1 147.35 ? CAB RCC 1000 A 1 HETATM 29 C CAC RCC . . . C 2 -7.818 15.037 -15.14 1 133.51 ? CAC RCC 1000 A 1 HETATM 30 C CAD RCC . . . C 2 -15.512 11.778 -14.588 1 144.45 ? CAD RCC 1000 A 1 HETATM 31 C CBA RCC . . . C 2 -15.923 5.666 -15.816 1 142.09 ? CBA RCC 1000 A 1 HETATM 32 C CBB RCC . . . C 2 -4.545 7.362 -15.141 1 147.72 ? CBB RCC 1000 A 1 HETATM 33 C CBC RCC . . . C 2 -7.112 14.661 -13.856 1 133.24 ? CBC RCC 1000 A 1 HETATM 34 C CBD RCC . . . C 2 -15.51 10.209 -14.612 1 145.44 ? CBD RCC 1000 A 1 HETATM 35 O OBD RCC . . . C 2 -16.535 12.465 -14.553 1 144.34 ? OBD RCC 1000 A 1 HETATM 36 C CED RCC . . . C 2 -18.431 9.433 -12.289 1 147.45 ? CED RCC 1000 A 1 HETATM 37 C CGA RCC . . . C 2 -16.676 5.574 -14.515 1 140.96 ? CGA RCC 1000 A 1 HETATM 38 C CGD RCC . . . C 2 -16.256 9.638 -13.392 1 146.85 ? CGD RCC 1000 A 1 HETATM 39 C CHA RCC . . . C 2 -14.023 9.783 -14.663 1 144.34 ? CHA RCC 1000 A 1 HETATM 40 C CHB RCC . . . C 2 -10.298 6.667 -14.902 1 145.71 ? CHB RCC 1000 A 1 HETATM 41 C CHC RCC . . . C 2 -8.449 11.089 -18.386 1 132.41 ? CHC RCC 1000 A 1 HETATM 42 C CHD RCC . . . C 2 -10.675 13.634 -14.676 1 138.37 ? CHD RCC 1000 A 1 HETATM 43 C CMA RCC . . . C 2 -12.834 5.273 -13.59 1 145.06 ? CMA RCC 1000 A 1 HETATM 44 C CMB RCC . . . C 2 -7.404 5.619 -15.12 1 147.32 ? CMB RCC 1000 A 1 HETATM 45 C CMC RCC . . . C 2 -6.384 13.441 -17.493 1 135.13 ? CMC RCC 1000 A 1 HETATM 46 C CMD RCC . . . C 2 -13.664 14.741 -14.595 1 141.98 ? CMD RCC 1000 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #