data_5KKH # _model_server_result.job_id N9GkUmT5GLfFL-QTPSRSXw _model_server_result.datetime_utc '2024-11-23 21:05:38' _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 5kkh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":304}' # _entry.id 5KKH # _exptl.entry_id 5KKH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _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 116.26 _cell.angle_gamma 90 _cell.entry_id 5KKH _cell.length_a 106.11 _cell.length_b 61.27 _cell.length_c 119.03 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KKH _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 K N N ? 4 O 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 NZ LYS 224 A LYS 224 1_555 G C15 RET . A RET 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale2 B NZ LYS 224 B LYS 224 1_555 K C15 RET . B RET 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.306 ? covale ? covale3 C NZ LYS 224 C LYS 224 1_555 O C15 RET . C RET 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.289 ? # _chem_comp.formula 'C20 H28 O' _chem_comp.formula_weight 284.436 _chem_comp.id RET _chem_comp.mon_nstd_flag . _chem_comp.name RETINAL _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 C1 C2 RET sing 392 n n C1 C6 RET sing 393 n n C1 C16 RET sing 394 n n C1 C17 RET sing 395 n n C2 C3 RET sing 396 n n C2 H21 RET sing 397 n n C2 H22 RET sing 398 n n C3 C4 RET sing 399 n n C3 H31 RET sing 400 n n C3 H32 RET sing 401 n n C4 C5 RET sing 402 n n C4 H41 RET sing 403 n n C4 H42 RET sing 404 n n C5 C6 RET doub 405 n n C5 C18 RET sing 406 n n C6 C7 RET sing 407 n n C7 C8 RET doub 408 e n C7 H7 RET sing 409 n n C8 C9 RET sing 410 n n C8 H8 RET sing 411 n n C9 C10 RET doub 412 e n C9 C19 RET sing 413 n n C10 C11 RET sing 414 n n C10 H10 RET sing 415 n n C11 C12 RET doub 416 e n C11 H11 RET sing 417 n n C12 C13 RET sing 418 n n C12 H12 RET sing 419 n n C13 C14 RET doub 420 e n C13 C20 RET sing 421 n n C14 C15 RET sing 422 n n C14 H14 RET sing 423 n n C15 O1 RET doub 424 n n C15 H15 RET sing 425 n n C16 H161 RET sing 426 n n C16 H162 RET sing 427 n n C16 H163 RET sing 428 n n C17 H171 RET sing 429 n n C17 H172 RET sing 430 n n C17 H173 RET sing 431 n n C18 H181 RET sing 432 n n C18 H182 RET sing 433 n n C18 H183 RET sing 434 n n C19 H191 RET sing 435 n n C19 H192 RET sing 436 n n C19 H193 RET sing 437 n n C20 H201 RET sing 438 n n C20 H202 RET sing 439 n n C20 H203 RET sing 440 n n # _atom_sites.entry_id 5KKH _atom_sites.fract_transf_matrix[1][1] 0.009424 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00465 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016321 _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] 0.009368 _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 D 2 OLC A 1 301 3 OLC OLC . E 3 OLB A 1 302 5 OLB OLB . F 2 OLC A 1 303 7 OLC OLC . G 4 RET A 1 304 301 RET RET . H 2 OLC B 1 301 4 OLC OLC . I 2 OLC B 1 302 6 OLC OLC . J 3 OLB B 1 303 9 OLB OLB . K 4 RET B 1 304 303 RET RET . L 2 OLC C 1 301 1 OLC OLC . M 2 OLC C 1 302 2 OLC OLC . N 3 OLB C 1 303 8 OLB OLB . O 4 RET C 1 304 302 RET RET . P 5 HOH A 1 401 19 HOH HOH . P 5 HOH A 2 402 69 HOH HOH . P 5 HOH A 3 403 67 HOH HOH . P 5 HOH A 4 404 43 HOH HOH . P 5 HOH A 5 405 4 HOH HOH . P 5 HOH A 6 406 75 HOH HOH . P 5 HOH A 7 407 50 HOH HOH . P 5 HOH A 8 408 18 HOH HOH . P 5 HOH A 9 409 1 HOH HOH . P 5 HOH A 10 410 47 HOH HOH . P 5 HOH A 11 411 87 HOH HOH . P 5 HOH A 12 412 49 HOH HOH . P 5 HOH A 13 413 36 HOH HOH . P 5 HOH A 14 414 22 HOH HOH . P 5 HOH A 15 415 5 HOH HOH . P 5 HOH A 16 416 59 HOH HOH . P 5 HOH A 17 417 14 HOH HOH . P 5 HOH A 18 418 70 HOH HOH . P 5 HOH A 19 419 21 HOH HOH . P 5 HOH A 20 420 76 HOH HOH . P 5 HOH A 21 421 63 HOH HOH . P 5 HOH A 22 422 80 HOH HOH . P 5 HOH A 23 423 20 HOH HOH . P 5 HOH A 24 424 2 HOH HOH . P 5 HOH A 25 425 51 HOH HOH . P 5 HOH A 26 426 45 HOH HOH . P 5 HOH A 27 427 42 HOH HOH . P 5 HOH A 28 428 7 HOH HOH . P 5 HOH A 29 429 79 HOH HOH . P 5 HOH A 30 430 33 HOH HOH . P 5 HOH A 31 431 60 HOH HOH . P 5 HOH A 32 432 77 HOH HOH . Q 5 HOH B 1 401 12 HOH HOH . Q 5 HOH B 2 402 37 HOH HOH . Q 5 HOH B 3 403 83 HOH HOH . Q 5 HOH B 4 404 16 HOH HOH . Q 5 HOH B 5 405 81 HOH HOH . Q 5 HOH B 6 406 15 HOH HOH . Q 5 HOH B 7 407 6 HOH HOH . Q 5 HOH B 8 408 8 HOH HOH . Q 5 HOH B 9 409 10 HOH HOH . Q 5 HOH B 10 410 11 HOH HOH . Q 5 HOH B 11 411 71 HOH HOH . Q 5 HOH B 12 412 55 HOH HOH . Q 5 HOH B 13 413 9 HOH HOH . Q 5 HOH B 14 414 24 HOH HOH . Q 5 HOH B 15 415 54 HOH HOH . Q 5 HOH B 16 416 74 HOH HOH . Q 5 HOH B 17 417 53 HOH HOH . Q 5 HOH B 18 418 85 HOH HOH . Q 5 HOH B 19 419 38 HOH HOH . Q 5 HOH B 20 420 13 HOH HOH . Q 5 HOH B 21 421 82 HOH HOH . Q 5 HOH B 22 422 62 HOH HOH . R 5 HOH C 1 401 39 HOH HOH . R 5 HOH C 2 402 66 HOH HOH . R 5 HOH C 3 403 28 HOH HOH . R 5 HOH C 4 404 32 HOH HOH . R 5 HOH C 5 405 61 HOH HOH . R 5 HOH C 6 406 68 HOH HOH . R 5 HOH C 7 407 65 HOH HOH . R 5 HOH C 8 408 23 HOH HOH . R 5 HOH C 9 409 25 HOH HOH . R 5 HOH C 10 410 73 HOH HOH . R 5 HOH C 11 411 26 HOH HOH . R 5 HOH C 12 412 86 HOH HOH . R 5 HOH C 13 413 44 HOH HOH . R 5 HOH C 14 414 58 HOH HOH . R 5 HOH C 15 415 34 HOH HOH . R 5 HOH C 16 416 29 HOH HOH . R 5 HOH C 17 417 72 HOH HOH . R 5 HOH C 18 418 48 HOH HOH . R 5 HOH C 19 419 41 HOH HOH . R 5 HOH C 20 420 17 HOH HOH . R 5 HOH C 21 421 57 HOH HOH . R 5 HOH C 22 422 27 HOH HOH . R 5 HOH C 23 423 56 HOH HOH . R 5 HOH C 24 424 31 HOH HOH . R 5 HOH C 25 425 30 HOH HOH . R 5 HOH C 26 426 64 HOH HOH . R 5 HOH C 27 427 40 HOH HOH . R 5 HOH C 28 428 46 HOH HOH . R 5 HOH C 29 429 84 HOH HOH . R 5 HOH C 30 430 78 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 C1 RET . . . K 4 -17.123 20.394 141.05 1 7.23 ? C1 RET 304 B 1 HETATM 2 C C2 RET . . . K 4 -16.698 19.465 142.183 1 5.93 ? C2 RET 304 B 1 HETATM 3 C C3 RET . . . K 4 -16.697 18.025 141.679 1 7.15 ? C3 RET 304 B 1 HETATM 4 C C4 RET . . . K 4 -15.503 17.903 140.735 1 9.11 ? C4 RET 304 B 1 HETATM 5 C C5 RET . . . K 4 -15.711 18.87 139.596 1 13.45 ? C5 RET 304 B 1 HETATM 6 C C6 RET . . . K 4 -16.516 19.95 139.713 1 4.63 ? C6 RET 304 B 1 HETATM 7 C C7 RET . . . K 4 -16.668 20.714 138.49 1 9.9 ? C7 RET 304 B 1 HETATM 8 C C8 RET . . . K 4 -17.119 21.985 138.402 1 6.16 ? C8 RET 304 B 1 HETATM 9 C C9 RET . . . K 4 -17.197 22.671 137.128 1 8.19 ? C9 RET 304 B 1 HETATM 10 C C10 RET . . . K 4 -17.899 23.827 137.124 1 11.77 ? C10 RET 304 B 1 HETATM 11 C C11 RET . . . K 4 -18.081 24.664 136.08 1 10.24 ? C11 RET 304 B 1 HETATM 12 C C12 RET . . . K 4 -18.524 25.865 136.506 1 5.74 ? C12 RET 304 B 1 HETATM 13 C C13 RET . . . K 4 -18.815 26.986 135.641 1 11.09 ? C13 RET 304 B 1 HETATM 14 C C14 RET . . . K 4 -19.698 27.906 136.085 1 19.68 ? C14 RET 304 B 1 HETATM 15 C C15 RET . . . K 4 -20.07 29.061 135.292 1 20.96 ? C15 RET 304 B 1 HETATM 16 C C16 RET . . . K 4 -18.652 20.37 140.973 1 5.51 ? C16 RET 304 B 1 HETATM 17 C C17 RET . . . K 4 -16.615 21.772 141.481 1 7.25 ? C17 RET 304 B 1 HETATM 18 C C18 RET . . . K 4 -15.19 18.462 138.236 1 9.34 ? C18 RET 304 B 1 HETATM 19 C C19 RET . . . K 4 -16.501 22.109 135.911 1 12.11 ? C19 RET 304 B 1 HETATM 20 C C20 RET . . . K 4 -18.128 27.099 134.301 1 10.99 ? C20 RET 304 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #