data_8J98 # _model_server_result.job_id IvoX1iY93eJpOPmJPu-8ww _model_server_result.datetime_utc '2025-06-18 16:42:03' _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 8j98 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":307}' # _entry.id 8J98 # _exptl.entry_id 8J98 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 586.678 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[5-[[(3~{R},4~{R})-3-ethenyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid' _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 120 _cell.entry_id 8J98 _cell.length_a 105.987 _cell.length_b 105.987 _cell.length_c 41.691 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8J98 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall 'P 65' _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 5 _struct_asym.id H _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 A SG CYS 127 A CYS 127 1_555 H CMB 9UY . A 9UY 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? metalc ? metalc1 A O GLY 116 A GLY 116 1_555 C NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.075 ? metalc ? metalc2 A OD2 ASP 123 A ASP 123 1_555 C NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.101 ? # _chem_comp.formula 'C33 H38 N4 O6' _chem_comp.formula_weight 586.678 _chem_comp.id 9UY _chem_comp.mon_nstd_flag . _chem_comp.name '3-[5-[[(3~{R},4~{R})-3-ethenyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Billeverdin IXa, bound form' # 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 O1D CGD 9UY doub 1 n n O2A CGA 9UY doub 2 n n CGD O2D 9UY sing 3 n n CGD CBD 9UY sing 4 n n CAD CBD 9UY sing 5 n n CAD C3D 9UY sing 6 n n CGA O1A 9UY sing 7 n n CGA CBA 9UY sing 8 n n CAA CBA 9UY sing 9 n n CAA C2A 9UY sing 10 n n C3D C2D 9UY sing 11 n y C3D C4D 9UY doub 12 n y CMD C2D 9UY sing 13 n n CHA C4D 9UY sing 14 n n CHA C1A 9UY sing 15 n n C2D C1D 9UY doub 16 n y C2A C1A 9UY doub 17 n y C2A C3A 9UY sing 18 n y C4D ND 9UY sing 19 n y C1A NA 9UY sing 20 n y CMA C3A 9UY sing 21 n n C3A C4A 9UY doub 22 n y C1D ND 9UY sing 23 n y C1D CHD 9UY sing 24 n n NA C4A 9UY sing 25 n y CHD C4C 9UY sing 26 n n C4A CHB 9UY sing 27 n n CHB C1B 9UY sing 28 n n C4C C3C 9UY sing 29 n n C4C NC 9UY doub 30 n n C3C CAC 9UY sing 31 n n C3C C2C 9UY sing 32 n n NC C1C 9UY sing 33 n n C1B NB 9UY doub 34 n n C1B C2B 9UY sing 35 n n NB C4B 9UY sing 36 n n CAC CBC 9UY doub 37 n n CMC C2C 9UY sing 38 n n C2C C1C 9UY sing 39 n n C2B CMB 9UY sing 40 n n C2B C3B 9UY doub 41 n n C4B OB 9UY doub 42 n n C4B C3B 9UY sing 43 n n C1C OC 9UY doub 44 n n C3B CAB 9UY sing 45 n n CAB CBB 9UY doub 46 n n O2D H1 9UY sing 47 n n CBD H2 9UY sing 48 n n CBD H3 9UY sing 49 n n CAD H4 9UY sing 50 n n CAD H5 9UY sing 51 n n CMD H6 9UY sing 52 n n CMD H7 9UY sing 53 n n CMD H8 9UY sing 54 n n CHD H9 9UY sing 55 n n CHD H10 9UY sing 56 n n C3C H11 9UY sing 57 n n CAC H12 9UY sing 58 n n CBC H13 9UY sing 59 n n CBC H14 9UY sing 60 n n C2C H15 9UY sing 61 n n CMC H16 9UY sing 62 n n CMC H17 9UY sing 63 n n CMC H18 9UY sing 64 n n ND H19 9UY sing 65 n n CHA H20 9UY sing 66 n n CHA H21 9UY sing 67 n n CAA H22 9UY sing 68 n n CAA H23 9UY sing 69 n n CBA H24 9UY sing 70 n n CBA H25 9UY sing 71 n n O1A H26 9UY sing 72 n n CMA H27 9UY sing 73 n n CMA H28 9UY sing 74 n n CMA H29 9UY sing 75 n n NA H30 9UY sing 76 n n CHB H31 9UY sing 77 n n CHB H32 9UY sing 78 n n CMB H33 9UY sing 79 n n CMB H34 9UY sing 80 n n CMB H35 9UY sing 81 n n CAB H36 9UY sing 82 n n CBB H37 9UY sing 83 n n CBB H38 9UY sing 84 n n # _atom_sites.entry_id 8J98 _atom_sites.fract_transf_matrix[1][1] 0.009435 _atom_sites.fract_transf_matrix[1][2] 0.005447 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010895 _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] 0.023986 _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 B 2 NA A 1 301 1 NA NA . C 2 NA A 1 302 2 NA NA . D 3 FMT A 1 303 3 FMT FMT . E 4 GOL A 1 304 4 GOL GOL . F 3 FMT A 1 305 5 FMT FMT . G 3 FMT A 1 306 6 FMT FMT . H 5 9UY A 1 307 1 9UY 9UY . # 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 O O2D 9UY . . . H 5 -5.798 46.463 10.234 1 19.96 ? O2D 9UY 307 A 1 HETATM 2 C CGD 9UY . . . H 5 -5.857 45.397 9.56 1 22.73 ? CGD 9UY 307 A 1 HETATM 3 O O1D 9UY . . . H 5 -5.974 45.457 8.304 1 31.3 ? O1D 9UY 307 A 1 HETATM 4 C CBD 9UY . . . H 5 -5.776 44.022 10.257 1 18.37 ? CBD 9UY 307 A 1 HETATM 5 C CAD 9UY . . . H 5 -7.15 43.599 10.843 1 22.08 ? CAD 9UY 307 A 1 HETATM 6 C C3D 9UY . . . H 5 -7.895 44.802 11.496 1 22.95 ? C3D 9UY 307 A 1 HETATM 7 C C2D 9UY . . . H 5 -9.167 45.182 11.231 1 23.49 ? C2D 9UY 307 A 1 HETATM 8 C CMD 9UY . . . H 5 -10.119 44.496 10.224 1 17.28 ? CMD 9UY 307 A 1 HETATM 9 C C1D 9UY . . . H 5 -9.454 46.286 12.015 1 24.6 ? C1D 9UY 307 A 1 HETATM 10 C CHD 9UY . . . H 5 -10.81 47.059 12.043 1 21.93 ? CHD 9UY 307 A 1 HETATM 11 C C4C 9UY . . . H 5 -11.036 47.856 10.726 1 21.11 ? C4C 9UY 307 A 1 HETATM 12 C C3C 9UY . . . H 5 -12.23 48.724 10.567 1 22.07 ? C3C 9UY 307 A 1 HETATM 13 C CAC 9UY . . . H 5 -13.286 48.377 11.608 1 17.15 ? CAC 9UY 307 A 1 HETATM 14 C CBC 9UY . . . H 5 -14.501 48.326 11.066 1 19.8 ? CBC 9UY 307 A 1 HETATM 15 C C2C 9UY . . . H 5 -12.741 48.41 9.139 1 18.05 ? C2C 9UY 307 A 1 HETATM 16 C CMC 9UY . . . H 5 -13.143 49.649 8.437 1 15.92 ? CMC 9UY 307 A 1 HETATM 17 C C1C 9UY . . . H 5 -11.517 47.767 8.443 1 16.8 ? C1C 9UY 307 A 1 HETATM 18 O OC 9UY . . . H 5 -11.337 47.654 7.273 1 16.9 ? OC 9UY 307 A 1 HETATM 19 N NC 9UY . . . H 5 -10.641 47.328 9.501 1 17.84 ? NC 9UY 307 A 1 HETATM 20 C C4D 9UY . . . H 5 -7.38 45.656 12.458 1 20.24 ? C4D 9UY 307 A 1 HETATM 21 N ND 9UY . . . H 5 -8.345 46.571 12.765 1 19.24 ? ND 9UY 307 A 1 HETATM 22 C CHA 9UY . . . H 5 -5.925 45.552 13.028 1 27.81 ? CHA 9UY 307 A 1 HETATM 23 C C1A 9UY . . . H 5 -5.651 46.294 14.377 1 27.56 ? C1A 9UY 307 A 1 HETATM 24 C C2A 9UY . . . H 5 -4.719 45.875 15.31 1 34.21 ? C2A 9UY 307 A 1 HETATM 25 C CAA 9UY . . . H 5 -3.813 44.616 15.195 1 36.92 ? CAA 9UY 307 A 1 HETATM 26 C CBA 9UY . . . H 5 -2.359 45.066 14.901 1 38.25 ? CBA 9UY 307 A 1 HETATM 27 C CGA 9UY . . . H 5 -1.553 43.878 14.338 1 54.93 ? CGA 9UY 307 A 1 HETATM 28 O O2A 9UY . . . H 5 -1.092 43.926 13.164 1 67 ? O2A 9UY 307 A 1 HETATM 29 O O1A 9UY . . . H 5 -1.355 42.856 15.055 1 54.71 ? O1A 9UY 307 A 1 HETATM 30 C C3A 9UY . . . H 5 -4.731 46.75 16.342 1 28.99 ? C3A 9UY 307 A 1 HETATM 31 C CMA 9UY . . . H 5 -3.849 46.676 17.615 1 36.86 ? CMA 9UY 307 A 1 HETATM 32 C C4A 9UY . . . H 5 -5.672 47.722 16.067 1 25.22 ? C4A 9UY 307 A 1 HETATM 33 N NA 9UY . . . H 5 -6.227 47.442 14.847 1 26.06 ? NA 9UY 307 A 1 HETATM 34 C CHB 9UY . . . H 5 -5.98 48.927 17.001 1 31.45 ? CHB 9UY 307 A 1 HETATM 35 C C1B 9UY . . . H 5 -7.425 48.991 17.552 1 24.17 ? C1B 9UY 307 A 1 HETATM 36 C C2B 9UY . . . H 5 -7.781 49.101 19.001 1 23.3 ? C2B 9UY 307 A 1 HETATM 37 C CMB 9UY . . . H 5 -6.79 49.131 20.183 1 26.67 ? CMB 9UY 307 A 1 HETATM 38 C C3B 9UY . . . H 5 -9.246 49.158 19.101 1 23.98 ? C3B 9UY 307 A 1 HETATM 39 C CAB 9UY . . . H 5 -10.048 49.267 20.406 1 29.39 ? CAB 9UY 307 A 1 HETATM 40 C CBB 9UY . . . H 5 -10.147 50.429 21.036 1 24.2 ? CBB 9UY 307 A 1 HETATM 41 C C4B 9UY . . . H 5 -9.848 49.101 17.693 1 23.46 ? C4B 9UY 307 A 1 HETATM 42 O OB 9UY . . . H 5 -11 49.127 17.408 1 18.32 ? OB 9UY 307 A 1 HETATM 43 N NB 9UY . . . H 5 -8.671 49.003 16.742 1 23.8 ? NB 9UY 307 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #