data_4YJJ # _model_server_result.job_id eDXkrRCJetR7B1m3E8fQ3g _model_server_result.datetime_utc '2024-11-15 00:23:17' _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 4yjj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 4YJJ # _exptl.entry_id 4YJJ _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 6 _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 4YJJ _cell.length_a 102.354 _cell.length_b 102.354 _cell.length_c 109.021 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YJJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,K,L 1 1,2,3 C,D,H,I,J,M,N 2 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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.354 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.177 88.641164 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J 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 E CAC CYC . A CYC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.727 ? covale ? covale2 B C GLY 71 B GLY 71 1_555 B N MEN 72 B MEN 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C MEN 72 B MEN 72 1_555 B N ALA 73 B ALA 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale4 B SG CYS 82 B CYS 82 1_555 F CAC CYC . B CYC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? covale ? covale5 C SG CYS 84 C CYS 84 1_555 H CAC CYC . C CYC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 ? covale ? covale6 D C GLY 71 D GLY 71 1_555 D N MEN 72 D MEN 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale7 D C MEN 72 D MEN 72 1_555 D N ALA 73 D ALA 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 D SG CYS 82 D CYS 82 1_555 I CAC CYC . D CYC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? covale ? covale9 D SG CYS 153 D CYS 153 1_555 J CAC CYC . D CYC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.747 ? # _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 ? # _atom_sites.entry_id 4YJJ _atom_sites.fract_transf_matrix[1][1] 0.00977 _atom_sites.fract_transf_matrix[1][2] 0.005641 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011281 _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] 0.009173 _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 E 3 CYC A 1 201 201 CYC CYC . F 3 CYC B 1 201 201 CYC CYC . G 3 CYC B 1 202 202 CYC CYC . H 3 CYC C 1 201 201 CYC CYC . I 3 CYC D 1 201 201 CYC CYC . J 3 CYC D 1 202 202 CYC CYC . K 4 HOH A 1 301 94 HOH HOH . K 4 HOH A 2 302 90 HOH HOH . K 4 HOH A 3 303 17 HOH HOH . K 4 HOH A 4 304 4 HOH HOH . K 4 HOH A 5 305 81 HOH HOH . K 4 HOH A 6 306 25 HOH HOH . K 4 HOH A 7 307 6 HOH HOH . K 4 HOH A 8 308 57 HOH HOH . K 4 HOH A 9 309 22 HOH HOH . K 4 HOH A 10 310 24 HOH HOH . K 4 HOH A 11 311 40 HOH HOH . K 4 HOH A 12 312 41 HOH HOH . K 4 HOH A 13 313 43 HOH HOH . K 4 HOH A 14 314 18 HOH HOH . K 4 HOH A 15 315 49 HOH HOH . K 4 HOH A 16 316 50 HOH HOH . K 4 HOH A 17 317 47 HOH HOH . K 4 HOH A 18 318 21 HOH HOH . K 4 HOH A 19 319 97 HOH HOH . K 4 HOH A 20 320 73 HOH HOH . K 4 HOH A 21 321 83 HOH HOH . K 4 HOH A 22 322 84 HOH HOH . K 4 HOH A 23 323 30 HOH HOH . K 4 HOH A 24 324 12 HOH HOH . K 4 HOH A 25 325 55 HOH HOH . K 4 HOH A 26 326 74 HOH HOH . K 4 HOH A 27 327 45 HOH HOH . K 4 HOH A 28 328 63 HOH HOH . L 4 HOH B 1 301 82 HOH HOH . L 4 HOH B 2 302 9 HOH HOH . L 4 HOH B 3 303 51 HOH HOH . L 4 HOH B 4 304 92 HOH HOH . L 4 HOH B 5 305 38 HOH HOH . L 4 HOH B 6 306 59 HOH HOH . L 4 HOH B 7 307 70 HOH HOH . L 4 HOH B 8 308 72 HOH HOH . L 4 HOH B 9 309 60 HOH HOH . L 4 HOH B 10 310 16 HOH HOH . L 4 HOH B 11 311 27 HOH HOH . L 4 HOH B 12 312 46 HOH HOH . L 4 HOH B 13 313 95 HOH HOH . L 4 HOH B 14 314 61 HOH HOH . L 4 HOH B 15 315 58 HOH HOH . L 4 HOH B 16 316 42 HOH HOH . L 4 HOH B 17 317 86 HOH HOH . L 4 HOH B 18 318 39 HOH HOH . L 4 HOH B 19 319 75 HOH HOH . L 4 HOH B 20 320 87 HOH HOH . L 4 HOH B 21 321 85 HOH HOH . L 4 HOH B 22 322 3 HOH HOH . L 4 HOH B 23 323 11 HOH HOH . M 4 HOH C 1 301 8 HOH HOH . M 4 HOH C 2 302 23 HOH HOH . M 4 HOH C 3 303 32 HOH HOH . M 4 HOH C 4 304 44 HOH HOH . M 4 HOH C 5 305 88 HOH HOH . M 4 HOH C 6 306 35 HOH HOH . M 4 HOH C 7 307 69 HOH HOH . M 4 HOH C 8 308 19 HOH HOH . M 4 HOH C 9 309 54 HOH HOH . M 4 HOH C 10 310 31 HOH HOH . M 4 HOH C 11 311 2 HOH HOH . M 4 HOH C 12 312 93 HOH HOH . M 4 HOH C 13 313 80 HOH HOH . M 4 HOH C 14 314 52 HOH HOH . M 4 HOH C 15 315 78 HOH HOH . M 4 HOH C 16 316 66 HOH HOH . M 4 HOH C 17 317 96 HOH HOH . M 4 HOH C 18 318 28 HOH HOH . M 4 HOH C 19 319 33 HOH HOH . M 4 HOH C 20 320 48 HOH HOH . M 4 HOH C 21 321 13 HOH HOH . M 4 HOH C 22 322 67 HOH HOH . M 4 HOH C 23 323 26 HOH HOH . M 4 HOH C 24 324 1 HOH HOH . M 4 HOH C 25 325 15 HOH HOH . M 4 HOH C 26 326 79 HOH HOH . M 4 HOH C 27 327 29 HOH HOH . M 4 HOH C 28 328 98 HOH HOH . M 4 HOH C 29 329 77 HOH HOH . M 4 HOH C 30 330 56 HOH HOH . M 4 HOH C 31 331 34 HOH HOH . N 4 HOH D 1 301 10 HOH HOH . N 4 HOH D 2 302 20 HOH HOH . N 4 HOH D 3 303 5 HOH HOH . N 4 HOH D 4 304 37 HOH HOH . N 4 HOH D 5 305 71 HOH HOH . N 4 HOH D 6 306 53 HOH HOH . N 4 HOH D 7 307 76 HOH HOH . N 4 HOH D 8 308 7 HOH HOH . N 4 HOH D 9 309 36 HOH HOH . N 4 HOH D 10 310 14 HOH HOH . N 4 HOH D 11 311 89 HOH HOH . N 4 HOH D 12 312 65 HOH HOH . N 4 HOH D 13 313 64 HOH HOH . N 4 HOH D 14 314 62 HOH HOH . N 4 HOH D 15 315 91 HOH HOH . N 4 HOH D 16 316 68 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 68.558 -4.899 1.283 1 18.12 ? CHA CYC 201 A 1 HETATM 2 N NA CYC . . . E 3 66.287 -4.631 0.34 1 17.65 ? NA CYC 201 A 1 HETATM 3 C C1A CYC . . . E 3 67.333 -4.153 1.053 1 17.93 ? C1A CYC 201 A 1 HETATM 4 C C2A CYC . . . E 3 67.167 -2.813 1.624 1 17.68 ? C2A CYC 201 A 1 HETATM 5 C C3A CYC . . . E 3 65.829 -2.427 1.143 1 17.84 ? C3A CYC 201 A 1 HETATM 6 C C4A CYC . . . E 3 65.367 -3.638 0.391 1 17.48 ? C4A CYC 201 A 1 HETATM 7 C CMA CYC . . . E 3 65.179 -1.107 1.428 1 18.08 ? CMA CYC 201 A 1 HETATM 8 C CAA CYC . . . E 3 68.157 -2.015 2.401 1 18.04 ? CAA CYC 201 A 1 HETATM 9 C CBA CYC . . . E 3 67.671 -1.698 3.785 1 18.72 ? CBA CYC 201 A 1 HETATM 10 C CGA CYC . . . E 3 67.748 -2.932 4.6 1 19.04 ? CGA CYC 201 A 1 HETATM 11 O O1A CYC . . . E 3 66.664 -3.413 4.932 1 19.28 ? O1A CYC 201 A 1 HETATM 12 O O2A CYC . . . E 3 68.866 -3.384 4.91 1 19.21 ? O2A CYC 201 A 1 HETATM 13 C CHB CYC . . . E 3 64.054 -3.9 -0.244 1 17.5 ? CHB CYC 201 A 1 HETATM 14 N NB CYC . . . E 3 62.681 -2.574 1.35 1 17.24 ? NB CYC 201 A 1 HETATM 15 C C1B CYC . . . E 3 62.767 -3.417 0.313 1 17.67 ? C1B CYC 201 A 1 HETATM 16 C C2B CYC . . . E 3 61.451 -3.742 -0.304 1 17.9 ? C2B CYC 201 A 1 HETATM 17 C C3B CYC . . . E 3 60.484 -2.974 0.508 1 17.86 ? C3B CYC 201 A 1 HETATM 18 C C4B CYC . . . E 3 61.393 -2.299 1.477 1 17.66 ? C4B CYC 201 A 1 HETATM 19 C CMB CYC . . . E 3 61.144 -4.671 -1.461 1 18.09 ? CMB CYC 201 A 1 HETATM 20 C CAB CYC . . . E 3 58.98 -2.94 0.314 1 18.01 ? CAB CYC 201 A 1 HETATM 21 C CBB CYC . . . E 3 58.197 -2.973 1.595 1 18.16 ? CBB CYC 201 A 1 HETATM 22 O OB CYC . . . E 3 61.001 -1.507 2.404 1 18.23 ? OB CYC 201 A 1 HETATM 23 N NC CYC . . . E 3 70.496 -9.988 -2.328 1 21.27 ? NC CYC 201 A 1 HETATM 24 C C1C CYC . . . E 3 70.797 -10.992 -3.163 1 22.12 ? C1C CYC 201 A 1 HETATM 25 C C2C CYC . . . E 3 69.585 -11.789 -3.476 1 21.52 ? C2C CYC 201 A 1 HETATM 26 C C3C CYC . . . E 3 68.525 -10.715 -3.274 1 21.77 ? C3C CYC 201 A 1 HETATM 27 C C4C CYC . . . E 3 69.168 -9.802 -2.228 1 21.21 ? C4C CYC 201 A 1 HETATM 28 C CMC CYC . . . E 3 69.592 -12.554 -4.799 1 20.93 ? CMC CYC 201 A 1 HETATM 29 C CAC CYC . . . E 3 67.167 -11.357 -2.969 1 22.44 ? CAC CYC 201 A 1 HETATM 30 C CBC CYC . . . E 3 66.23 -11.37 -4.163 1 22.18 ? CBC CYC 201 A 1 HETATM 31 O OC CYC . . . E 3 71.861 -11.266 -3.676 1 24.19 ? OC CYC 201 A 1 HETATM 32 C CHD CYC . . . E 3 68.453 -9.08 -1.3 1 19.76 ? CHD CYC 201 A 1 HETATM 33 N ND CYC . . . E 3 68.256 -6.987 -0.081 1 18.79 ? ND CYC 201 A 1 HETATM 34 C C1D CYC . . . E 3 69.011 -8.084 -0.321 1 19.19 ? C1D CYC 201 A 1 HETATM 35 C C2D CYC . . . E 3 70.344 -7.995 0.384 1 18.92 ? C2D CYC 201 A 1 HETATM 36 C C3D CYC . . . E 3 70.28 -6.708 1.098 1 18.75 ? C3D CYC 201 A 1 HETATM 37 C C4D CYC . . . E 3 68.946 -6.22 0.776 1 18.42 ? C4D CYC 201 A 1 HETATM 38 C CMD CYC . . . E 3 71.517 -8.924 0.455 1 18.96 ? CMD CYC 201 A 1 HETATM 39 C CAD CYC . . . E 3 71.268 -5.984 1.981 1 19.37 ? CAD CYC 201 A 1 HETATM 40 C CBD CYC . . . E 3 71.779 -4.775 1.19 1 19.74 ? CBD CYC 201 A 1 HETATM 41 C CGD CYC . . . E 3 72.943 -4.063 1.812 1 20.15 ? CGD CYC 201 A 1 HETATM 42 O O1D CYC . . . E 3 73.684 -3.469 0.993 1 21.18 ? O1D CYC 201 A 1 HETATM 43 O O2D CYC . . . E 3 73.113 -4.063 3.069 1 20.83 ? O2D CYC 201 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 43 #