data_2VJR # _model_server_result.job_id Hj-2Hq-37VcJiyrU8GTAUw _model_server_result.datetime_utc '2025-03-06 09:42:58' _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 2vjr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1153}' # _entry.id 2VJR # _exptl.entry_id 2VJR _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 2VJR _cell.length_a 117.538 _cell.length_b 117.538 _cell.length_c 116.163 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VJR _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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' 10_444 -y-1,-x-1,-z-1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -58.769 -101.790894 -58.0815 3 'crystal symmetry operation' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -58.0815 4 'crystal symmetry operation' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -58.769 -101.790894 0 5 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 58.769 -101.790894 0 6 'crystal symmetry operation' 12_544 x,x-y-1,-z-1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 58.769 -101.790894 -58.0815 # 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 82 A CYS 82 1_555 C CAC CYC . A CYC 1082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? covale ? covale2 B SG CYS 82 B CYS 82 1_555 D CAC CYC . B CYC 1082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? covale ? covale3 B SG CYS 153 B CYS 153 1_555 E CAC CYC . B CYC 1153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? # _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 2VJR _atom_sites.fract_transf_matrix[1][1] 0.008508 _atom_sites.fract_transf_matrix[1][2] 0.004912 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009824 _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] 0.008609 _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 1082 1082 CYC CYC . D 3 CYC B 1 1082 1082 CYC CYC . E 3 CYC B 1 1153 1153 CYC CYC . F 4 HOH A 1 2001 2001 HOH HOH . F 4 HOH A 2 2002 2002 HOH HOH . F 4 HOH A 3 2003 2003 HOH HOH . F 4 HOH A 4 2004 2004 HOH HOH . F 4 HOH A 5 2005 2005 HOH HOH . F 4 HOH A 6 2006 2006 HOH HOH . F 4 HOH A 7 2007 2007 HOH HOH . F 4 HOH A 8 2008 2008 HOH HOH . F 4 HOH A 9 2009 2009 HOH HOH . F 4 HOH A 10 2010 2010 HOH HOH . F 4 HOH A 11 2011 2011 HOH HOH . F 4 HOH A 12 2012 2012 HOH HOH . F 4 HOH A 13 2013 2013 HOH HOH . F 4 HOH A 14 2014 2014 HOH HOH . F 4 HOH A 15 2015 2015 HOH HOH . F 4 HOH A 16 2016 2016 HOH HOH . F 4 HOH A 17 2017 2017 HOH HOH . F 4 HOH A 18 2018 2018 HOH HOH . F 4 HOH A 19 2019 2019 HOH HOH . F 4 HOH A 20 2020 2020 HOH HOH . F 4 HOH A 21 2021 2021 HOH HOH . F 4 HOH A 22 2022 2022 HOH HOH . F 4 HOH A 23 2023 2023 HOH HOH . F 4 HOH A 24 2024 2024 HOH HOH . F 4 HOH A 25 2025 2025 HOH HOH . F 4 HOH A 26 2026 2026 HOH HOH . F 4 HOH A 27 2027 2027 HOH HOH . F 4 HOH A 28 2028 2028 HOH HOH . F 4 HOH A 29 2029 2029 HOH HOH . F 4 HOH A 30 2030 2030 HOH HOH . F 4 HOH A 31 2031 2031 HOH HOH . F 4 HOH A 32 2032 2032 HOH HOH . F 4 HOH A 33 2033 2033 HOH HOH . F 4 HOH A 34 2034 2034 HOH HOH . F 4 HOH A 35 2035 2035 HOH HOH . F 4 HOH A 36 2036 2036 HOH HOH . F 4 HOH A 37 2037 2037 HOH HOH . F 4 HOH A 38 2038 2038 HOH HOH . F 4 HOH A 39 2039 2039 HOH HOH . G 4 HOH B 1 2001 2001 HOH HOH . G 4 HOH B 2 2002 2002 HOH HOH . G 4 HOH B 3 2003 2003 HOH HOH . G 4 HOH B 4 2004 2004 HOH HOH . G 4 HOH B 5 2005 2005 HOH HOH . G 4 HOH B 6 2006 2006 HOH HOH . G 4 HOH B 7 2007 2007 HOH HOH . G 4 HOH B 8 2008 2008 HOH HOH . G 4 HOH B 9 2009 2009 HOH HOH . G 4 HOH B 10 2010 2010 HOH HOH . G 4 HOH B 11 2011 2011 HOH HOH . G 4 HOH B 12 2012 2012 HOH HOH . G 4 HOH B 13 2013 2013 HOH HOH . G 4 HOH B 14 2014 2014 HOH HOH . G 4 HOH B 15 2015 2015 HOH HOH . G 4 HOH B 16 2016 2016 HOH HOH . G 4 HOH B 17 2017 2017 HOH HOH . G 4 HOH B 18 2018 2018 HOH HOH . G 4 HOH B 19 2019 2019 HOH HOH . G 4 HOH B 20 2020 2020 HOH HOH . G 4 HOH B 21 2021 2021 HOH HOH . G 4 HOH B 22 2022 2022 HOH HOH . G 4 HOH B 23 2023 2023 HOH HOH . G 4 HOH B 24 2024 2024 HOH HOH . G 4 HOH B 25 2025 2025 HOH HOH . G 4 HOH B 26 2026 2026 HOH HOH . G 4 HOH B 27 2027 2027 HOH HOH . G 4 HOH B 28 2028 2028 HOH HOH . G 4 HOH B 29 2029 2029 HOH HOH . G 4 HOH B 30 2030 2030 HOH HOH . G 4 HOH B 31 2031 2031 HOH HOH . G 4 HOH B 32 2032 2032 HOH HOH . G 4 HOH B 33 2033 2033 HOH HOH . G 4 HOH B 34 2034 2034 HOH HOH . G 4 HOH B 35 2035 2035 HOH HOH . G 4 HOH B 36 2036 2036 HOH HOH . G 4 HOH B 37 2037 2037 HOH HOH . G 4 HOH B 38 2038 2038 HOH HOH . G 4 HOH B 39 2039 2039 HOH HOH . G 4 HOH B 40 2040 2040 HOH HOH . G 4 HOH B 41 2041 2041 HOH HOH . G 4 HOH B 42 2042 2042 HOH HOH . G 4 HOH B 43 2043 2043 HOH HOH . G 4 HOH B 44 2044 2044 HOH HOH . G 4 HOH B 45 2045 2045 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 . . . E 3 9.811 -20.963 -20.46 1 31.48 ? CHA CYC 1153 B 1 HETATM 2 N NA CYC . . . E 3 9.906 -23.106 -21.699 1 31.81 ? NA CYC 1153 B 1 HETATM 3 C C1A CYC . . . E 3 9.474 -21.839 -21.59 1 31.49 ? C1A CYC 1153 B 1 HETATM 4 C C2A CYC . . . E 3 8.606 -21.388 -22.697 1 32.07 ? C2A CYC 1153 B 1 HETATM 5 C C3A CYC . . . E 3 8.528 -22.564 -23.579 1 31.75 ? C3A CYC 1153 B 1 HETATM 6 C C4A CYC . . . E 3 9.362 -23.567 -22.863 1 32.06 ? C4A CYC 1153 B 1 HETATM 7 C CMA CYC . . . E 3 7.767 -22.644 -24.872 1 31.72 ? CMA CYC 1153 B 1 HETATM 8 C CAA CYC . . . E 3 7.957 -20.043 -22.901 1 32.8 ? CAA CYC 1153 B 1 HETATM 9 C CBA CYC . . . E 3 8.815 -19.232 -23.875 1 35.27 ? CBA CYC 1153 B 1 HETATM 10 C CGA CYC . . . E 3 10.101 -18.76 -23.213 1 37.04 ? CGA CYC 1153 B 1 HETATM 11 O O1A CYC . . . E 3 11.187 -19.208 -23.655 1 37.93 ? O1A CYC 1153 B 1 HETATM 12 O O2A CYC . . . E 3 10.038 -17.938 -22.262 1 37.23 ? O2A CYC 1153 B 1 HETATM 13 C CHB CYC . . . E 3 9.652 -24.982 -23.195 1 31.9 ? CHB CYC 1153 B 1 HETATM 14 N NB CYC . . . E 3 7.793 -25.56 -24.796 1 32.16 ? NB CYC 1153 B 1 HETATM 15 C C1B CYC . . . E 3 8.866 -25.897 -24.053 1 31.92 ? C1B CYC 1153 B 1 HETATM 16 C C2B CYC . . . E 3 9.297 -27.307 -24.223 1 31.17 ? C2B CYC 1153 B 1 HETATM 17 C C3B CYC . . . E 3 8.32 -27.86 -25.172 1 32.13 ? C3B CYC 1153 B 1 HETATM 18 C C4B CYC . . . E 3 7.46 -26.694 -25.446 1 32.54 ? C4B CYC 1153 B 1 HETATM 19 C CMB CYC . . . E 3 10.445 -27.976 -23.545 1 32.04 ? CMB CYC 1153 B 1 HETATM 20 C CAB CYC . . . E 3 8.202 -29.236 -25.755 1 32.41 ? CAB CYC 1153 B 1 HETATM 21 C CBB CYC . . . E 3 8.967 -29.279 -27.051 1 33.75 ? CBB CYC 1153 B 1 HETATM 22 O OB CYC . . . E 3 6.482 -26.807 -26.279 1 33.12 ? OB CYC 1153 B 1 HETATM 23 N NC CYC . . . E 3 14.11 -21.949 -15.8 1 28.98 ? NC CYC 1153 B 1 HETATM 24 C C1C CYC . . . E 3 15.203 -22.062 -15.047 1 30.9 ? C1C CYC 1153 B 1 HETATM 25 C C2C CYC . . . E 3 15.512 -23.513 -14.819 1 30.12 ? C2C CYC 1153 B 1 HETATM 26 C C3C CYC . . . E 3 14.486 -24.226 -15.719 1 29.07 ? C3C CYC 1153 B 1 HETATM 27 C C4C CYC . . . E 3 13.678 -23.099 -16.3 1 28.67 ? C4C CYC 1153 B 1 HETATM 28 C CMC CYC . . . E 3 16.975 -23.844 -15.068 1 30.06 ? CMC CYC 1153 B 1 HETATM 29 C CAC CYC . . . E 3 13.608 -25.086 -14.795 1 28.11 ? CAC CYC 1153 B 1 HETATM 30 C CBC CYC . . . E 3 12.892 -26.264 -15.391 1 25.56 ? CBC CYC 1153 B 1 HETATM 31 O OC CYC . . . E 3 15.876 -21.143 -14.583 1 31.87 ? OC CYC 1153 B 1 HETATM 32 C CHD CYC . . . E 3 12.615 -23.296 -17.115 1 30.34 ? CHD CYC 1153 B 1 HETATM 33 N ND CYC . . . E 3 11.193 -22.397 -18.914 1 30.32 ? ND CYC 1153 B 1 HETATM 34 C C1D CYC . . . E 3 11.795 -22.201 -17.733 1 30.45 ? C1D CYC 1153 B 1 HETATM 35 C C2D CYC . . . E 3 11.564 -20.816 -17.212 1 31.58 ? C2D CYC 1153 B 1 HETATM 36 C C3D CYC . . . E 3 10.755 -20.172 -18.249 1 30.81 ? C3D CYC 1153 B 1 HETATM 37 C C4D CYC . . . E 3 10.622 -21.229 -19.253 1 31.22 ? C4D CYC 1153 B 1 HETATM 38 C CMD CYC . . . E 3 12.03 -20.154 -15.951 1 31.03 ? CMD CYC 1153 B 1 HETATM 39 C CAD CYC . . . E 3 10.206 -18.766 -18.296 1 31.27 ? CAD CYC 1153 B 1 HETATM 40 C CBD CYC . . . E 3 8.892 -18.676 -17.496 1 32.33 ? CBD CYC 1153 B 1 HETATM 41 C CGD CYC . . . E 3 7.688 -19.406 -18.083 1 33.58 ? CGD CYC 1153 B 1 HETATM 42 O O1D CYC . . . E 3 7.005 -20.11 -17.306 1 34.73 ? O1D CYC 1153 B 1 HETATM 43 O O2D CYC . . . E 3 7.377 -19.295 -19.291 1 33.26 ? O2D CYC 1153 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #