data_4YJJ # _model_server_result.job_id tp7m1HYC823EPCljzOB-Pg _model_server_result.datetime_utc '2024-11-15 00:39:25' _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":"H","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 . . . H 3 12.816 27.517 -25.607 1 22.54 ? CHA CYC 201 C 1 HETATM 2 N NA CYC . . . H 3 14.172 25.628 -24.767 1 22.87 ? NA CYC 201 C 1 HETATM 3 C C1A CYC . . . H 3 14.077 26.799 -25.423 1 22.55 ? C1A CYC 201 C 1 HETATM 4 C C2A CYC . . . H 3 15.327 27.345 -25.964 1 21.82 ? C2A CYC 201 C 1 HETATM 5 C C3A CYC . . . H 3 16.324 26.338 -25.529 1 22.36 ? C3A CYC 201 C 1 HETATM 6 C C4A CYC . . . H 3 15.497 25.318 -24.814 1 21.87 ? C4A CYC 201 C 1 HETATM 7 C CMA CYC . . . H 3 17.805 26.394 -25.794 1 22.59 ? CMA CYC 201 C 1 HETATM 8 C CAA CYC . . . H 3 15.486 28.658 -26.692 1 21.91 ? CAA CYC 201 C 1 HETATM 9 C CBA CYC . . . H 3 16.063 28.575 -28.096 1 22.34 ? CBA CYC 201 C 1 HETATM 10 C CGA CYC . . . H 3 15.137 27.736 -28.913 1 21.64 ? CGA CYC 201 C 1 HETATM 11 O O1A CYC . . . H 3 15.464 26.569 -29.216 1 22.27 ? O1A CYC 201 C 1 HETATM 12 O O2A CYC . . . H 3 14.069 28.259 -29.211 1 20.72 ? O2A CYC 201 C 1 HETATM 13 C CHB CYC . . . H 3 15.893 24.01 -24.237 1 20.45 ? CHB CYC 201 C 1 HETATM 14 N NB CYC . . . H 3 17.764 23.464 -25.756 1 19.17 ? NB CYC 201 C 1 HETATM 15 C C1B CYC . . . H 3 16.921 23.122 -24.798 1 19.32 ? C1B CYC 201 C 1 HETATM 16 C C2B CYC . . . H 3 17.232 21.8 -24.238 1 20.04 ? C2B CYC 201 C 1 HETATM 17 C C3B CYC . . . H 3 18.396 21.29 -25.024 1 19.71 ? C3B CYC 201 C 1 HETATM 18 C C4B CYC . . . H 3 18.606 22.446 -25.921 1 18.82 ? C4B CYC 201 C 1 HETATM 19 C CMB CYC . . . H 3 16.482 21.134 -23.121 1 21.3 ? CMB CYC 201 C 1 HETATM 20 C CAB CYC . . . H 3 19.145 19.96 -24.899 1 19.34 ? CAB CYC 201 C 1 HETATM 21 C CBB CYC . . . H 3 19.647 19.397 -26.214 1 19.29 ? CBB CYC 201 C 1 HETATM 22 O OB CYC . . . H 3 19.534 22.495 -26.799 1 18.13 ? OB CYC 201 C 1 HETATM 23 N NC CYC . . . H 3 7.406 26.658 -22.18 1 23.58 ? NC CYC 201 C 1 HETATM 24 C C1C CYC . . . H 3 6.378 26.533 -21.361 1 24.11 ? C1C CYC 201 C 1 HETATM 25 C C2C CYC . . . H 3 6.251 25.066 -21 1 23.86 ? C2C CYC 201 C 1 HETATM 26 C C3C CYC . . . H 3 7.687 24.584 -21.185 1 24.14 ? C3C CYC 201 C 1 HETATM 27 C C4C CYC . . . H 3 8.209 25.577 -22.212 1 23.62 ? C4C CYC 201 C 1 HETATM 28 C CMC CYC . . . H 3 5.607 24.697 -19.669 1 22.85 ? CMC CYC 201 C 1 HETATM 29 C CAC CYC . . . H 3 7.755 23.085 -21.502 1 24.29 ? CAC CYC 201 C 1 HETATM 30 C CBC CYC . . . H 3 8.225 22.305 -20.298 1 23.99 ? CBC CYC 201 C 1 HETATM 31 O OC CYC . . . H 3 5.679 27.444 -20.942 1 24.24 ? OC CYC 201 C 1 HETATM 32 C CHD CYC . . . H 3 9.239 25.302 -23.065 1 22.63 ? CHD CYC 201 C 1 HETATM 33 N ND CYC . . . H 3 11.189 26.196 -24.258 1 21.99 ? ND CYC 201 C 1 HETATM 34 C C1D CYC . . . H 3 9.851 26.282 -24.035 1 22.33 ? C1D CYC 201 C 1 HETATM 35 C C2D CYC . . . H 3 9.241 27.453 -24.753 1 21.7 ? C2D CYC 201 C 1 HETATM 36 C C3D CYC . . . H 3 10.366 28.061 -25.458 1 21.39 ? C3D CYC 201 C 1 HETATM 37 C C4D CYC . . . H 3 11.478 27.174 -25.125 1 21.76 ? C4D CYC 201 C 1 HETATM 38 C CMD CYC . . . H 3 7.845 27.986 -24.868 1 22.88 ? CMD CYC 201 C 1 HETATM 39 C CAD CYC . . . H 3 10.402 29.262 -26.364 1 21.24 ? CAD CYC 201 C 1 HETATM 40 C CBD CYC . . . H 3 11.134 30.445 -25.728 1 21.63 ? CBD CYC 201 C 1 HETATM 41 C CGD CYC . . . H 3 11.235 31.596 -26.693 1 21.99 ? CGD CYC 201 C 1 HETATM 42 O O1D CYC . . . H 3 11.525 32.672 -26.15 1 20.87 ? O1D CYC 201 C 1 HETATM 43 O O2D CYC . . . H 3 11.03 31.454 -27.942 1 23.05 ? O2D CYC 201 C 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #