data_2Z55 # _model_server_result.job_id vgH5xrvizP1jTe4rucc67A _model_server_result.datetime_utc '2024-11-02 07:30:27' _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 2z55 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":260}' # _entry.id 2Z55 # _exptl.entry_id 2Z55 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 4 _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 2Z55 _cell.length_a 108.83 _cell.length_b 108.83 _cell.length_c 220.71 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Z55 _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,PQS trimeric 3 author_and_software_defined_assembly 1 PISA,PQS trimeric 3 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 PQS trimeric 3 software_defined_assembly 5 PQS trimeric 3 software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I,J,K,U 1 1,2,3 B,F,L,M,N,V 2 1,2,3 C,G,H,O,P,Q,W 3 1 D,R,S,T,X 4 1 C,G,H,O,P,Q,W 5 1,4,5 D,R,S,T,X 6 1,4,5 # 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' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -54.415 -94.249545 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 54.415 -94.249545 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 L N N ? 3 O N N ? 3 R N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 MAN GLC C1 O1 . O2 HO2 . sing 2 ? 2 3 2 GAL MAN C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n E GLC 1 C 1 GLC ? 281 GLC 2 n E MAN 2 C 2 MAN ? 282 MAN 2 n E GAL 3 C 3 GAL ? 283 GAL 2 n F GLC 1 F 1 GLC ? 281 GLC 2 n F MAN 2 F 2 MAN ? 282 MAN 2 n F GAL 3 F 3 GAL ? 283 GAL 2 n G GLC 1 G 1 GLC ? 281 GLC 2 n G MAN 2 G 2 MAN ? 282 MAN 2 n G GAL 3 G 3 GAL ? 283 GAL 2 n H GLC 1 H 1 GLC ? 281 GLC 2 n H MAN 2 H 2 MAN ? 282 MAN 2 n H GAL 3 H 3 GAL ? 283 GAL # 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 221 A LYS 221 1_555 I C15 RET . A RET 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? covale ? covale2 K O3 L2P . A L2P 280 1_555 E C1 GLC . C GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 B NZ LYS 221 B LYS 221 1_555 L C15 RET . B RET 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale4 N O3 L2P . B L2P 280 1_555 F C1 GLC . F GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 C NZ LYS 221 D LYS 221 1_555 O C15 RET . D RET 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale6 Q O3 L2P . D L2P 280 1_555 G C1 GLC . G GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale7 D NZ LYS 221 E LYS 221 1_555 R C15 RET . E RET 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale8 T O3 L2P . E L2P 280 1_555 H C1 GLC . H GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale9 E O2 GLC . C GLC 1 1_555 E C1 MAN . C MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale10 E O6 MAN . C MAN 2 1_555 E C1 GAL . C GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale11 F O2 GLC . F GLC 1 1_555 F C1 MAN . F MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale12 F O6 MAN . F MAN 2 1_555 F C1 GAL . F GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale13 G O2 GLC . G GLC 1 1_555 G C1 MAN . G MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale14 G O6 MAN . G MAN 2 1_555 G C1 GAL . G GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale15 H O2 GLC . H GLC 1 1_555 H C1 MAN . H MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale16 H O6 MAN . H MAN 2 1_555 H C1 GAL . H GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? # _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 577 n n C1 C6 RET sing 578 n n C1 C16 RET sing 579 n n C1 C17 RET sing 580 n n C2 C3 RET sing 581 n n C2 H21 RET sing 582 n n C2 H22 RET sing 583 n n C3 C4 RET sing 584 n n C3 H31 RET sing 585 n n C3 H32 RET sing 586 n n C4 C5 RET sing 587 n n C4 H41 RET sing 588 n n C4 H42 RET sing 589 n n C5 C6 RET doub 590 n n C5 C18 RET sing 591 n n C6 C7 RET sing 592 n n C7 C8 RET doub 593 e n C7 H7 RET sing 594 n n C8 C9 RET sing 595 n n C8 H8 RET sing 596 n n C9 C10 RET doub 597 e n C9 C19 RET sing 598 n n C10 C11 RET sing 599 n n C10 H10 RET sing 600 n n C11 C12 RET doub 601 e n C11 H11 RET sing 602 n n C12 C13 RET sing 603 n n C12 H12 RET sing 604 n n C13 C14 RET doub 605 e n C13 C20 RET sing 606 n n C14 C15 RET sing 607 n n C14 H14 RET sing 608 n n C15 O1 RET doub 609 n n C15 H15 RET sing 610 n n C16 H161 RET sing 611 n n C16 H162 RET sing 612 n n C16 H163 RET sing 613 n n C17 H171 RET sing 614 n n C17 H172 RET sing 615 n n C17 H173 RET sing 616 n n C18 H181 RET sing 617 n n C18 H182 RET sing 618 n n C18 H183 RET sing 619 n n C19 H191 RET sing 620 n n C19 H192 RET sing 621 n n C19 H193 RET sing 622 n n C20 H201 RET sing 623 n n C20 H202 RET sing 624 n n C20 H203 RET sing 625 n n # _atom_sites.entry_id 2Z55 _atom_sites.fract_transf_matrix[1][1] 0.009189 _atom_sites.fract_transf_matrix[1][2] 0.005305 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01061 _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] 0.004531 _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 I 3 RET A 1 260 260 RET RET . J 4 22B A 1 270 270 22B 22B . K 5 L2P A 1 280 280 L2P L2P . L 3 RET B 1 260 260 RET RET . M 4 22B B 1 270 270 22B 22B . N 5 L2P B 1 280 280 L2P L2P . O 3 RET D 1 260 260 RET RET . P 4 22B D 1 270 270 22B 22B . Q 5 L2P D 1 280 280 L2P L2P . R 3 RET E 1 260 260 RET RET . S 4 22B E 1 270 270 22B 22B . T 5 L2P E 1 280 280 L2P L2P . U 6 HOH A 1 284 271 HOH HOH . U 6 HOH A 2 285 272 HOH HOH . U 6 HOH A 3 286 273 HOH HOH . U 6 HOH A 4 287 274 HOH HOH . U 6 HOH A 5 288 275 HOH HOH . U 6 HOH A 6 289 276 HOH HOH . U 6 HOH A 7 290 277 HOH HOH . U 6 HOH A 8 291 278 HOH HOH . U 6 HOH A 9 292 279 HOH HOH . U 6 HOH A 10 293 280 HOH HOH . U 6 HOH A 11 294 281 HOH HOH . U 6 HOH A 12 295 282 HOH HOH . U 6 HOH A 13 296 283 HOH HOH . U 6 HOH A 14 297 284 HOH HOH . U 6 HOH A 15 298 285 HOH HOH . U 6 HOH A 16 299 286 HOH HOH . U 6 HOH A 17 300 287 HOH HOH . U 6 HOH A 18 301 288 HOH HOH . U 6 HOH A 19 302 289 HOH HOH . U 6 HOH A 20 303 290 HOH HOH . U 6 HOH A 21 304 291 HOH HOH . U 6 HOH A 22 305 292 HOH HOH . U 6 HOH A 23 306 293 HOH HOH . U 6 HOH A 24 307 284 HOH HOH . U 6 HOH A 25 308 285 HOH HOH . V 6 HOH B 1 284 271 HOH HOH . V 6 HOH B 2 285 272 HOH HOH . V 6 HOH B 3 286 273 HOH HOH . V 6 HOH B 4 287 274 HOH HOH . V 6 HOH B 5 288 275 HOH HOH . V 6 HOH B 6 289 276 HOH HOH . V 6 HOH B 7 290 277 HOH HOH . V 6 HOH B 8 291 278 HOH HOH . V 6 HOH B 9 292 279 HOH HOH . V 6 HOH B 10 293 280 HOH HOH . V 6 HOH B 11 294 281 HOH HOH . V 6 HOH B 12 295 282 HOH HOH . V 6 HOH B 13 296 283 HOH HOH . V 6 HOH B 14 297 284 HOH HOH . V 6 HOH B 15 298 285 HOH HOH . V 6 HOH B 16 299 286 HOH HOH . V 6 HOH B 17 300 287 HOH HOH . V 6 HOH B 18 301 288 HOH HOH . V 6 HOH B 19 302 289 HOH HOH . V 6 HOH B 20 303 290 HOH HOH . V 6 HOH B 21 304 291 HOH HOH . V 6 HOH B 22 305 292 HOH HOH . V 6 HOH B 23 306 293 HOH HOH . V 6 HOH B 24 307 294 HOH HOH . V 6 HOH B 25 308 295 HOH HOH . V 6 HOH B 26 309 296 HOH HOH . W 6 HOH D 1 287 271 HOH HOH . W 6 HOH D 2 288 272 HOH HOH . W 6 HOH D 3 289 273 HOH HOH . W 6 HOH D 4 290 274 HOH HOH . W 6 HOH D 5 291 275 HOH HOH . W 6 HOH D 6 292 276 HOH HOH . W 6 HOH D 7 293 277 HOH HOH . W 6 HOH D 8 294 278 HOH HOH . W 6 HOH D 9 295 279 HOH HOH . W 6 HOH D 10 296 280 HOH HOH . W 6 HOH D 11 297 281 HOH HOH . W 6 HOH D 12 298 282 HOH HOH . W 6 HOH D 13 299 283 HOH HOH . W 6 HOH D 14 300 284 HOH HOH . W 6 HOH D 15 301 285 HOH HOH . W 6 HOH D 16 302 286 HOH HOH . W 6 HOH D 17 303 287 HOH HOH . W 6 HOH D 18 304 288 HOH HOH . W 6 HOH D 19 305 289 HOH HOH . W 6 HOH D 20 306 290 HOH HOH . W 6 HOH D 21 307 291 HOH HOH . W 6 HOH D 22 308 284 HOH HOH . X 6 HOH E 1 281 271 HOH HOH . X 6 HOH E 2 282 272 HOH HOH . X 6 HOH E 3 283 273 HOH HOH . X 6 HOH E 4 284 274 HOH HOH . X 6 HOH E 5 285 275 HOH HOH . X 6 HOH E 6 286 276 HOH HOH . X 6 HOH E 7 287 277 HOH HOH . X 6 HOH E 8 288 278 HOH HOH . X 6 HOH E 9 289 279 HOH HOH . X 6 HOH E 10 290 280 HOH HOH . X 6 HOH E 11 291 281 HOH HOH . X 6 HOH E 12 292 282 HOH HOH . X 6 HOH E 13 293 283 HOH HOH . X 6 HOH E 14 294 284 HOH HOH . X 6 HOH E 15 295 285 HOH HOH . X 6 HOH E 16 296 286 HOH HOH . X 6 HOH E 17 297 287 HOH HOH . X 6 HOH E 18 298 288 HOH HOH . X 6 HOH E 19 299 289 HOH HOH . X 6 HOH E 20 300 290 HOH HOH . X 6 HOH E 21 301 291 HOH HOH . X 6 HOH E 22 302 292 HOH HOH . X 6 HOH E 23 303 293 HOH HOH . X 6 HOH E 24 304 294 HOH HOH . X 6 HOH E 25 305 295 HOH HOH . X 6 HOH E 26 306 296 HOH HOH . X 6 HOH E 27 307 297 HOH HOH . X 6 HOH E 28 308 298 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 . . . O 3 5.325 -45.382 53.061 1 36.17 ? C1 RET 260 D 1 HETATM 2 C C2 RET . . . O 3 6.296 -45.56 54.324 1 36.38 ? C2 RET 260 D 1 HETATM 3 C C3 RET . . . O 3 7.767 -45.585 54.175 1 36.31 ? C3 RET 260 D 1 HETATM 4 C C4 RET . . . O 3 8.367 -44.84 52.982 1 35.21 ? C4 RET 260 D 1 HETATM 5 C C5 RET . . . O 3 7.503 -44.643 51.716 1 35.62 ? C5 RET 260 D 1 HETATM 6 C C6 RET . . . O 3 6.031 -44.892 51.714 1 35.33 ? C6 RET 260 D 1 HETATM 7 C C7 RET . . . O 3 5.241 -44.647 50.342 1 34.74 ? C7 RET 260 D 1 HETATM 8 C C8 RET . . . O 3 3.888 -44.82 50.129 1 33.92 ? C8 RET 260 D 1 HETATM 9 C C9 RET . . . O 3 3.169 -44.589 48.896 1 34.44 ? C9 RET 260 D 1 HETATM 10 C C10 RET . . . O 3 1.818 -44.855 48.993 1 34.02 ? C10 RET 260 D 1 HETATM 11 C C11 RET . . . O 3 0.802 -44.729 47.975 1 33.65 ? C11 RET 260 D 1 HETATM 12 C C12 RET . . . O 3 -0.459 -45.095 48.325 1 33.03 ? C12 RET 260 D 1 HETATM 13 C C13 RET . . . O 3 -1.652 -45.051 47.449 1 30.94 ? C13 RET 260 D 1 HETATM 14 C C14 RET . . . O 3 -2.844 -45.511 48.013 1 30.25 ? C14 RET 260 D 1 HETATM 15 C C15 RET . . . O 3 -4.155 -45.591 47.343 1 30.2 ? C15 RET 260 D 1 HETATM 16 C C16 RET . . . O 3 4.678 -46.804 52.998 1 38.2 ? C16 RET 260 D 1 HETATM 17 C C17 RET . . . O 3 4.296 -44.389 53.655 1 34.03 ? C17 RET 260 D 1 HETATM 18 C C18 RET . . . O 3 8.249 -44.174 50.44 1 35.08 ? C18 RET 260 D 1 HETATM 19 C C19 RET . . . O 3 3.877 -44.094 47.615 1 31.21 ? C19 RET 260 D 1 HETATM 20 C C20 RET . . . O 3 -1.576 -44.554 46.017 1 31.8 ? C20 RET 260 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 378 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 20 #