data_5MJQ # _model_server_result.job_id 6B5HgmSnN_3iAFBpJpm93A _model_server_result.datetime_utc '2024-11-15 03:13:56' _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 5mjq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5MJQ # _exptl.entry_id 5MJQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 588.694 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description PHYCOCYANOBILIN _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation N73X _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 5MJQ _cell.length_a 187.8 _cell.length_b 187.8 _cell.length_c 60.7 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MJQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 60.7 5 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 60.7 6 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 60.7 # 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 D N N ? 3 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 covale ? covale1 A SG CYS 84 A CYS 84 1_555 C CAC CYC . A CYC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? covale ? covale2 B C GLY 71 B GLY 71 1_555 B N MEN 72 B MEN 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale3 B C MEN 72 B MEN 72 1_555 B N ALA 73 B ALA 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 B SG CYS 82 B CYS 82 1_555 D CAC CYC . B CYC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.762 ? covale ? covale5 B SG CYS 153 B CYS 153 1_555 E CAC CYC . B CYC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.713 ? # _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 5MJQ _atom_sites.fract_transf_matrix[1][1] 0.005325 _atom_sites.fract_transf_matrix[1][2] 0.003074 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006149 _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] 0.016474 _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 1 501 501 CYC CYC . D 3 CYC B 1 201 502 CYC CYC . E 3 CYC B 1 202 503 CYC CYC . # 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 . . . C 3 21.76 -32.696 17.219 1 14.23 ? CHA CYC 501 A 1 HETATM 2 N NA CYC . . . C 3 23.211 -30.676 17.82 1 13.75 ? NA CYC 501 A 1 HETATM 3 C C1A CYC . . . C 3 21.971 -31.412 17.376 1 14.32 ? C1A CYC 501 A 1 HETATM 4 C C2A CYC . . . C 3 20.923 -30.333 17.128 1 17.55 ? C2A CYC 501 A 1 HETATM 5 C C3A CYC . . . C 3 21.491 -29.016 17.408 1 15.24 ? C3A CYC 501 A 1 HETATM 6 C C4A CYC . . . C 3 22.904 -29.222 17.834 1 13.15 ? C4A CYC 501 A 1 HETATM 7 C CMA CYC . . . C 3 20.71 -27.712 17.267 1 16.52 ? CMA CYC 501 A 1 HETATM 8 C CAA CYC . . . C 3 19.491 -30.571 16.663 1 21.35 ? CAA CYC 501 A 1 HETATM 9 C CBA CYC . . . C 3 19.385 -30.363 15.152 1 22.73 ? CBA CYC 501 A 1 HETATM 10 C CGA CYC . . . C 3 20.498 -31.112 14.425 1 23.83 ? CGA CYC 501 A 1 HETATM 11 O O1A CYC . . . C 3 21.585 -30.526 14.188 1 23.89 ? O1A CYC 501 A 1 HETATM 12 O O2A CYC . . . C 3 20.334 -32.305 14.056 1 23.64 ? O2A CYC 501 A 1 HETATM 13 C CHB CYC . . . C 3 23.907 -28.144 18.233 1 12.36 ? CHB CYC 501 A 1 HETATM 14 N NB CYC . . . C 3 23.153 -26.476 16.446 1 12.22 ? NB CYC 501 A 1 HETATM 15 C C1B CYC . . . C 3 23.84 -26.927 17.74 1 11.78 ? C1B CYC 501 A 1 HETATM 16 C C2B CYC . . . C 3 24.421 -25.694 18.344 1 12.04 ? C2B CYC 501 A 1 HETATM 17 C C3B CYC . . . C 3 24.142 -24.564 17.534 1 12.33 ? C3B CYC 501 A 1 HETATM 18 C C4B CYC . . . C 3 23.356 -24.96 16.334 1 13.95 ? C4B CYC 501 A 1 HETATM 19 C CMB CYC . . . C 3 25.205 -25.657 19.65 1 11.27 ? CMB CYC 501 A 1 HETATM 20 C CAB CYC . . . C 3 24.58 -23.137 17.836 1 10.88 ? CAB CYC 501 A 1 HETATM 21 C CBB CYC . . . C 3 25.584 -22.697 16.776 1 10.13 ? CBB CYC 501 A 1 HETATM 22 O OB CYC . . . C 3 22.969 -24.249 15.471 1 16.27 ? OB CYC 501 A 1 HETATM 23 N NC CYC . . . C 3 25.176 -36.574 20.893 1 15.6 ? NC CYC 501 A 1 HETATM 24 C C1C CYC . . . C 3 26.122 -37.467 21.628 1 14.73 ? C1C CYC 501 A 1 HETATM 25 C C2C CYC . . . C 3 27.405 -36.744 21.752 1 15.59 ? C2C CYC 501 A 1 HETATM 26 C C3C CYC . . . C 3 27.04 -35.292 21.595 1 15.31 ? C3C CYC 501 A 1 HETATM 27 C C4C CYC . . . C 3 25.924 -35.297 20.571 1 15.51 ? C4C CYC 501 A 1 HETATM 28 C CMC CYC . . . C 3 28.028 -37.008 23.143 1 16.73 ? CMC CYC 501 A 1 HETATM 29 C CAC CYC . . . C 3 28.27 -34.487 21.16 1 14.8 ? CAC CYC 501 A 1 HETATM 30 C CBC CYC . . . C 3 29.055 -34.064 22.398 1 12.16 ? CBC CYC 501 A 1 HETATM 31 O OC CYC . . . C 3 25.894 -38.549 22.039 1 14.25 ? OC CYC 501 A 1 HETATM 32 C CHD CYC . . . C 3 25.815 -34.567 19.473 1 14.7 ? CHD CYC 501 A 1 HETATM 33 N ND CYC . . . C 3 23.778 -33.443 18.405 1 15.15 ? ND CYC 501 A 1 HETATM 34 C C1D CYC . . . C 3 24.552 -34.54 18.606 1 15.23 ? C1D CYC 501 A 1 HETATM 35 C C2D CYC . . . C 3 24.011 -35.58 17.879 1 12.54 ? C2D CYC 501 A 1 HETATM 36 C C3D CYC . . . C 3 22.914 -35.107 17.252 1 14.6 ? C3D CYC 501 A 1 HETATM 37 C C4D CYC . . . C 3 22.769 -33.788 17.571 1 13.97 ? C4D CYC 501 A 1 HETATM 38 C CMD CYC . . . C 3 24.542 -37.012 17.784 1 11.23 ? CMD CYC 501 A 1 HETATM 39 C CAD CYC . . . C 3 21.952 -35.857 16.336 1 15.87 ? CAD CYC 501 A 1 HETATM 40 C CBD CYC . . . C 3 20.561 -35.876 16.976 1 17.13 ? CBD CYC 501 A 1 HETATM 41 C CGD CYC . . . C 3 19.506 -36.22 15.93 1 20.63 ? CGD CYC 501 A 1 HETATM 42 O O1D CYC . . . C 3 18.699 -37.157 16.157 1 22.04 ? O1D CYC 501 A 1 HETATM 43 O O2D CYC . . . C 3 19.44 -35.576 14.849 1 21.51 ? O2D CYC 501 A 1 HETATM 44 H HHA CYC . . . C 3 20.94 -32.961 16.869 1 17.17 ? HHA CYC 501 A 1 HETATM 45 H HMA1 CYC . . . C 3 19.808 -27.838 17.6 1 19.92 ? HMA1 CYC 501 A 1 HETATM 46 H HMA2 CYC . . . C 3 21.15 -27.015 17.778 1 19.92 ? HMA2 CYC 501 A 1 HETATM 47 H HMA3 CYC . . . C 3 20.677 -27.455 16.332 1 19.92 ? HMA3 CYC 501 A 1 HETATM 48 H HAA1 CYC . . . C 3 19.229 -31.479 16.881 1 25.71 ? HAA1 CYC 501 A 1 HETATM 49 H HAA2 CYC . . . C 3 18.899 -29.948 17.114 1 25.71 ? HAA2 CYC 501 A 1 HETATM 50 H HBA1 CYC . . . C 3 18.525 -30.69 14.843 1 27.37 ? HBA1 CYC 501 A 1 HETATM 51 H HBA2 CYC . . . C 3 19.456 -29.416 14.954 1 27.37 ? HBA2 CYC 501 A 1 HETATM 52 H HHB CYC . . . C 3 24.582 -28.353 18.838 1 14.93 ? HHB CYC 501 A 1 HETATM 53 H HB CYC . . . C 3 22.728 -26.978 15.891 1 14.77 ? HB CYC 501 A 1 HETATM 54 H HMB1 CYC . . . C 3 25.042 -24.813 20.101 1 13.63 ? HMB1 CYC 501 A 1 HETATM 55 H HMB2 CYC . . . C 3 24.919 -26.388 20.22 1 13.63 ? HMB2 CYC 501 A 1 HETATM 56 H HMB3 CYC . . . C 3 26.152 -25.745 19.461 1 13.63 ? HMB3 CYC 501 A 1 HETATM 57 H HAB1 CYC . . . C 3 23.808 -22.549 17.816 1 13.15 ? HAB1 CYC 501 A 1 HETATM 58 H HAB2 CYC . . . C 3 24.994 -23.102 18.712 1 13.15 ? HAB2 CYC 501 A 1 HETATM 59 H HBB1 CYC . . . C 3 26.266 -23.38 16.674 1 12.26 ? HBB1 CYC 501 A 1 HETATM 60 H HBB2 CYC . . . C 3 26 -21.865 17.051 1 12.26 ? HBB2 CYC 501 A 1 HETATM 61 H HBB3 CYC . . . C 3 25.127 -22.567 15.931 1 12.26 ? HBB3 CYC 501 A 1 HETATM 62 H HC CYC . . . C 3 24.361 -36.755 20.686 1 18.82 ? HC CYC 501 A 1 HETATM 63 H H2C CYC . . . C 3 28.013 -37.015 21.047 1 18.81 ? H2C CYC 501 A 1 HETATM 64 H H3C CYC . . . C 3 26.703 -34.949 22.438 1 18.47 ? H3C CYC 501 A 1 HETATM 65 H HMC1 CYC . . . C 3 27.678 -37.838 23.502 1 20.18 ? HMC1 CYC 501 A 1 HETATM 66 H HMC2 CYC . . . C 3 27.805 -36.277 23.741 1 20.18 ? HMC2 CYC 501 A 1 HETATM 67 H HMC3 CYC . . . C 3 28.992 -37.073 23.058 1 20.18 ? HMC3 CYC 501 A 1 HETATM 68 H HAC1 CYC . . . C 3 27.985 -33.699 20.672 1 17.86 ? HAC1 CYC 501 A 1 HETATM 69 H HBC1 CYC . . . C 3 28.437 -33.811 23.102 1 14.69 ? HBC1 CYC 501 A 1 HETATM 70 H HBC2 CYC . . . C 3 29.623 -33.308 22.179 1 14.69 ? HBC2 CYC 501 A 1 HETATM 71 H HBC3 CYC . . . C 3 29.605 -34.803 22.702 1 14.69 ? HBC3 CYC 501 A 1 HETATM 72 H HHD CYC . . . C 3 26.54 -34.045 19.216 1 17.74 ? HHD CYC 501 A 1 HETATM 73 H HD CYC . . . C 3 23.908 -32.665 18.746 1 18.27 ? HD CYC 501 A 1 HETATM 74 H HMD1 CYC . . . C 3 24.916 -37.275 18.64 1 13.58 ? HMD1 CYC 501 A 1 HETATM 75 H HMD2 CYC . . . C 3 23.816 -37.611 17.55 1 13.58 ? HMD2 CYC 501 A 1 HETATM 76 H HMD3 CYC . . . C 3 25.231 -37.057 17.103 1 13.58 ? HMD3 CYC 501 A 1 HETATM 77 H HAD1 CYC . . . C 3 22.264 -36.767 16.213 1 19.15 ? HAD1 CYC 501 A 1 HETATM 78 H HAD2 CYC . . . C 3 21.907 -35.41 15.477 1 19.15 ? HAD2 CYC 501 A 1 HETATM 79 H HBD1 CYC . . . C 3 20.369 -35.002 17.351 1 20.65 ? HBD1 CYC 501 A 1 HETATM 80 H HBD2 CYC . . . C 3 20.542 -36.54 17.682 1 20.65 ? HBD2 CYC 501 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 80 #