data_4GY3 # _model_server_result.job_id pQXKHMMuqlFQHYDclla-6A _model_server_result.datetime_utc '2025-08-03 21:21:18' _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 4gy3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":202}' # _entry.id 4GY3 # _exptl.entry_id 4GY3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 588.694 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description PHYCOCYANOBILIN _entity.pdbx_number_of_molecules 3 _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 4GY3 _cell.length_a 153.82 _cell.length_b 153.82 _cell.length_c 39.54 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GY3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _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 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 76.91 133.212028 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -76.91 133.212028 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 M N N ? 3 N 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 A SG CYS 84 A CYS 84 1_555 C CAC CYC . A CYC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? covale ? covale2 B C GLY 71 B GLY 71 1_555 B N MEN 72 B MEN 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.291 ? covale ? covale3 B C MEN 72 B MEN 72 1_555 B N ALA 73 B ALA 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale4 B SG CYS 82 B CYS 84 1_555 M CAC CYC . B CYC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? covale ? covale5 B SG CYS 153 B CYS 155 1_555 N CAC CYC . B CYC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.813 ? # _chem_comp.formula 'C33 H40 N4 O6' _chem_comp.formula_weight 588.694 _chem_comp.id CYC _chem_comp.mon_nstd_flag . _chem_comp.name PHYCOCYANOBILIN _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 CHA C1A CYC doub 70 z n CHA C4D CYC sing 71 n n CHA HHA CYC sing 72 n n NA C1A CYC sing 73 n n NA C4A CYC doub 74 n n C1A C2A CYC sing 75 n n C2A C3A CYC doub 76 n n C2A CAA CYC sing 77 n n C3A C4A CYC sing 78 n n C3A CMA CYC sing 79 n n C4A CHB CYC sing 80 n n CMA HMA1 CYC sing 81 n n CMA HMA2 CYC sing 82 n n CMA HMA3 CYC sing 83 n n CAA CBA CYC sing 84 n n CAA HAA1 CYC sing 85 n n CAA HAA2 CYC sing 86 n n CBA CGA CYC sing 87 n n CBA HBA1 CYC sing 88 n n CBA HBA2 CYC sing 89 n n CGA O1A CYC doub 90 n n CGA O2A CYC sing 91 n n O2A H2A CYC sing 92 n n CHB C1B CYC doub 93 z n CHB HHB CYC sing 94 n n NB C1B CYC sing 95 n n NB C4B CYC sing 96 n n NB HB CYC sing 97 n n C1B C2B CYC sing 98 n n C2B C3B CYC doub 99 n n C2B CMB CYC sing 100 n n C3B C4B CYC sing 101 n n C3B CAB CYC sing 102 n n C4B OB CYC doub 103 n n CMB HMB1 CYC sing 104 n n CMB HMB2 CYC sing 105 n n CMB HMB3 CYC sing 106 n n CAB CBB CYC sing 107 n n CAB HAB1 CYC sing 108 n n CAB HAB2 CYC sing 109 n n CBB HBB1 CYC sing 110 n n CBB HBB2 CYC sing 111 n n CBB HBB3 CYC sing 112 n n NC C1C CYC sing 113 n n NC C4C CYC sing 114 n n NC HC CYC sing 115 n n C1C C2C CYC sing 116 n n C1C OC CYC doub 117 n n C2C C3C CYC sing 118 n n C2C CMC CYC sing 119 n n C2C H2C CYC sing 120 n n C3C C4C CYC sing 121 n n C3C CAC CYC sing 122 n n C3C H3C CYC sing 123 n n C4C CHD CYC doub 124 z n CMC HMC1 CYC sing 125 n n CMC HMC2 CYC sing 126 n n CMC HMC3 CYC sing 127 n n CAC CBC CYC sing 128 n n CAC HAC1 CYC sing 129 n n CAC HAC2 CYC sing 130 n n CBC HBC1 CYC sing 131 n n CBC HBC2 CYC sing 132 n n CBC HBC3 CYC sing 133 n n CHD C1D CYC sing 134 n n CHD HHD CYC sing 135 n n ND C1D CYC sing 136 n y ND C4D CYC sing 137 n y ND HD CYC sing 138 n n C1D C2D CYC doub 139 n y C2D C3D CYC sing 140 n y C2D CMD CYC sing 141 n n C3D C4D CYC doub 142 n y C3D CAD CYC sing 143 n n CMD HMD1 CYC sing 144 n n CMD HMD2 CYC sing 145 n n CMD HMD3 CYC sing 146 n n CAD CBD CYC sing 147 n n CAD HAD1 CYC sing 148 n n CAD HAD2 CYC sing 149 n n CBD CGD CYC sing 150 n n CBD HBD1 CYC sing 151 n n CBD HBD2 CYC sing 152 n n CGD O1D CYC doub 153 n n CGD O2D CYC sing 154 n n O2D H2D CYC sing 155 n n # _atom_sites.entry_id 4GY3 _atom_sites.fract_transf_matrix[1][1] 0.006501 _atom_sites.fract_transf_matrix[1][2] 0.003753 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007507 _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] 0.025291 _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 3 CYC A 1 201 484 CYC CYC . D 4 URE A 1 202 1 URE URE . E 4 URE A 1 203 2 URE URE . F 4 URE A 1 204 5 URE URE . G 4 URE A 1 205 6 URE URE . H 4 URE A 1 206 7 URE URE . I 4 URE A 1 207 8 URE URE . J 4 URE A 1 208 11 URE URE . K 4 URE A 1 209 13 URE URE . L 4 URE A 1 210 16 URE URE . M 3 CYC B 1 201 584 CYC CYC . N 3 CYC B 1 202 555 CYC CYC . O 4 URE B 1 203 3 URE URE . P 4 URE B 1 204 4 URE URE . Q 4 URE B 1 205 9 URE URE . R 4 URE B 1 206 10 URE URE . S 4 URE B 1 207 12 URE URE . T 4 URE B 1 208 14 URE URE . U 4 URE B 1 209 15 URE URE . V 4 URE B 1 210 17 URE URE . W 4 URE B 1 211 18 URE URE . X 4 URE B 1 212 19 URE URE . Y 5 HOH A 1 301 6 HOH HOH . Y 5 HOH A 2 302 9 HOH HOH . Y 5 HOH A 3 303 12 HOH HOH . Y 5 HOH A 4 304 16 HOH HOH . Y 5 HOH A 5 305 17 HOH HOH . Y 5 HOH A 6 306 27 HOH HOH . Y 5 HOH A 7 307 30 HOH HOH . Y 5 HOH A 8 308 32 HOH HOH . Y 5 HOH A 9 309 33 HOH HOH . Y 5 HOH A 10 310 34 HOH HOH . Y 5 HOH A 11 311 37 HOH HOH . Y 5 HOH A 12 312 38 HOH HOH . Y 5 HOH A 13 313 43 HOH HOH . Y 5 HOH A 14 314 46 HOH HOH . Y 5 HOH A 15 315 48 HOH HOH . Y 5 HOH A 16 316 52 HOH HOH . Y 5 HOH A 17 317 53 HOH HOH . Y 5 HOH A 18 318 61 HOH HOH . Y 5 HOH A 19 319 62 HOH HOH . Y 5 HOH A 20 320 63 HOH HOH . Y 5 HOH A 21 321 64 HOH HOH . Y 5 HOH A 22 322 67 HOH HOH . Y 5 HOH A 23 323 70 HOH HOH . Y 5 HOH A 24 324 72 HOH HOH . Y 5 HOH A 25 325 74 HOH HOH . Y 5 HOH A 26 326 75 HOH HOH . Z 5 HOH B 1 301 1 HOH HOH . Z 5 HOH B 2 302 2 HOH HOH . Z 5 HOH B 3 303 3 HOH HOH . Z 5 HOH B 4 304 4 HOH HOH . Z 5 HOH B 5 305 5 HOH HOH . Z 5 HOH B 6 306 7 HOH HOH . Z 5 HOH B 7 307 8 HOH HOH . Z 5 HOH B 8 308 10 HOH HOH . Z 5 HOH B 9 309 11 HOH HOH . Z 5 HOH B 10 310 13 HOH HOH . Z 5 HOH B 11 311 14 HOH HOH . Z 5 HOH B 12 312 15 HOH HOH . Z 5 HOH B 13 313 18 HOH HOH . Z 5 HOH B 14 314 19 HOH HOH . Z 5 HOH B 15 315 20 HOH HOH . Z 5 HOH B 16 316 21 HOH HOH . Z 5 HOH B 17 317 22 HOH HOH . Z 5 HOH B 18 318 23 HOH HOH . Z 5 HOH B 19 319 24 HOH HOH . Z 5 HOH B 20 320 25 HOH HOH . Z 5 HOH B 21 321 26 HOH HOH . Z 5 HOH B 22 322 28 HOH HOH . Z 5 HOH B 23 323 29 HOH HOH . Z 5 HOH B 24 324 31 HOH HOH . Z 5 HOH B 25 325 35 HOH HOH . Z 5 HOH B 26 326 36 HOH HOH . Z 5 HOH B 27 327 39 HOH HOH . Z 5 HOH B 28 328 40 HOH HOH . Z 5 HOH B 29 329 41 HOH HOH . Z 5 HOH B 30 330 42 HOH HOH . Z 5 HOH B 31 331 44 HOH HOH . Z 5 HOH B 32 332 45 HOH HOH . Z 5 HOH B 33 333 47 HOH HOH . Z 5 HOH B 34 334 49 HOH HOH . Z 5 HOH B 35 335 50 HOH HOH . Z 5 HOH B 36 336 51 HOH HOH . Z 5 HOH B 37 337 54 HOH HOH . Z 5 HOH B 38 338 55 HOH HOH . Z 5 HOH B 39 339 56 HOH HOH . Z 5 HOH B 40 340 57 HOH HOH . Z 5 HOH B 41 341 58 HOH HOH . Z 5 HOH B 42 342 59 HOH HOH . Z 5 HOH B 43 343 60 HOH HOH . Z 5 HOH B 44 344 65 HOH HOH . Z 5 HOH B 45 345 66 HOH HOH . Z 5 HOH B 46 346 68 HOH HOH . Z 5 HOH B 47 347 69 HOH HOH . Z 5 HOH B 48 348 71 HOH HOH . Z 5 HOH B 49 349 73 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 CHA CYC . . . N 3 -38.953 62.172 -5.557 1 26.5 ? CHA CYC 202 B 1 HETATM 2 N NA CYC . . . N 3 -37.668 63.902 -6.724 1 25.24 ? NA CYC 202 B 1 HETATM 3 C C1A CYC . . . N 3 -38.363 62.742 -6.644 1 25.17 ? C1A CYC 202 B 1 HETATM 4 C C2A CYC . . . N 3 -38.333 62.053 -7.935 1 24.25 ? C2A CYC 202 B 1 HETATM 5 C C3A CYC . . . N 3 -37.571 62.942 -8.763 1 25.77 ? C3A CYC 202 B 1 HETATM 6 C C4A CYC . . . N 3 -37.162 64.1 -7.963 1 26.22 ? C4A CYC 202 B 1 HETATM 7 C CMA CYC . . . N 3 -37.265 62.66 -10.213 1 22.35 ? CMA CYC 202 B 1 HETATM 8 C CAA CYC . . . N 3 -38.982 60.727 -8.28 1 23.78 ? CAA CYC 202 B 1 HETATM 9 C CBA CYC . . . N 3 -40.173 60.793 -9.141 1 20.18 ? CBA CYC 202 B 1 HETATM 10 C CGA CYC . . . N 3 -41.242 61.617 -8.443 1 23.97 ? CGA CYC 202 B 1 HETATM 11 O O1A CYC . . . N 3 -41.931 61.003 -7.618 1 22.79 ? O1A CYC 202 B 1 HETATM 12 O O2A CYC . . . N 3 -41.391 62.828 -8.708 1 21.51 ? O2A CYC 202 B 1 HETATM 13 C CHB CYC . . . N 3 -36.36 65.298 -8.284 1 25.72 ? CHB CYC 202 B 1 HETATM 14 N NB CYC . . . N 3 -34.686 64.26 -9.604 1 27.06 ? NB CYC 202 B 1 HETATM 15 C C1B CYC . . . N 3 -35.203 65.342 -9.05 1 28.27 ? C1B CYC 202 B 1 HETATM 16 C C2B CYC . . . N 3 -34.404 66.499 -9.363 1 28.2 ? C2B CYC 202 B 1 HETATM 17 C C3B CYC . . . N 3 -33.331 66.074 -10.179 1 30.29 ? C3B CYC 202 B 1 HETATM 18 C C4B CYC . . . N 3 -33.616 64.687 -10.254 1 29.05 ? C4B CYC 202 B 1 HETATM 19 C CMB CYC . . . N 3 -34.67 67.856 -8.915 1 24.69 ? CMB CYC 202 B 1 HETATM 20 C CAB CYC . . . N 3 -32.19 66.838 -10.816 1 30.99 ? CAB CYC 202 B 1 HETATM 21 C CBB CYC . . . N 3 -32.624 67.469 -12.168 1 29.89 ? CBB CYC 202 B 1 HETATM 22 O OB CYC . . . N 3 -32.788 63.871 -10.973 1 30.26 ? OB CYC 202 B 1 HETATM 23 N NC CYC . . . N 3 -41.597 64.889 -0.344 1 27.67 ? NC CYC 202 B 1 HETATM 24 C C1C CYC . . . N 3 -42.144 65.579 0.593 1 28.39 ? C1C CYC 202 B 1 HETATM 25 C C2C CYC . . . N 3 -41.282 66.722 1.175 1 29.66 ? C2C CYC 202 B 1 HETATM 26 C C3C CYC . . . N 3 -40.128 66.689 0.226 1 29.78 ? C3C CYC 202 B 1 HETATM 27 C C4C CYC . . . N 3 -40.387 65.439 -0.572 1 29.33 ? C4C CYC 202 B 1 HETATM 28 C CMC CYC . . . N 3 -42.069 68.026 1.33 1 26.33 ? CMC CYC 202 B 1 HETATM 29 C CAC CYC . . . N 3 -38.852 66.423 0.954 1 31.08 ? CAC CYC 202 B 1 HETATM 30 C CBC CYC . . . N 3 -37.834 67.344 0.719 1 33.05 ? CBC CYC 202 B 1 HETATM 31 O OC CYC . . . N 3 -43.353 65.397 1.067 1 31.16 ? OC CYC 202 B 1 HETATM 32 C CHD CYC . . . N 3 -39.527 64.915 -1.466 1 27.13 ? CHD CYC 202 B 1 HETATM 33 N ND CYC . . . N 3 -39.138 63.852 -3.62 1 28.26 ? ND CYC 202 B 1 HETATM 34 C C1D CYC . . . N 3 -39.591 63.744 -2.309 1 28.49 ? C1D CYC 202 B 1 HETATM 35 C C2D CYC . . . N 3 -40.038 62.423 -2.036 1 28.18 ? C2D CYC 202 B 1 HETATM 36 C C3D CYC . . . N 3 -39.829 61.672 -3.252 1 27.74 ? C3D CYC 202 B 1 HETATM 37 C C4D CYC . . . N 3 -39.294 62.623 -4.21 1 26.63 ? C4D CYC 202 B 1 HETATM 38 C CMD CYC . . . N 3 -40.582 61.874 -0.727 1 23.64 ? CMD CYC 202 B 1 HETATM 39 C CAD CYC . . . N 3 -40.06 60.245 -3.542 1 30.53 ? CAD CYC 202 B 1 HETATM 40 C CBD CYC . . . N 3 -38.739 59.678 -3.343 1 35.71 ? CBD CYC 202 B 1 HETATM 41 C CGD CYC . . . N 3 -38.546 58.272 -3.64 1 39.67 ? CGD CYC 202 B 1 HETATM 42 O O1D CYC . . . N 3 -39.012 57.389 -2.972 1 48.32 ? O1D CYC 202 B 1 HETATM 43 O O2D CYC . . . N 3 -37.808 57.943 -4.682 1 42.73 ? O2D CYC 202 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #