data_8A6D # _model_server_result.job_id T9AbD1fQI-fhUwRQq7IQIg _model_server_result.datetime_utc '2024-11-22 20:42:00' _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 8a6d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 8A6D # _exptl.entry_id 8A6D _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 2 _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 90 _cell.entry_id 8A6D _cell.length_a 61.51 _cell.length_b 91.01 _cell.length_c 151.11 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8A6D _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab (z,x,y)' _symmetry.space_group_name_H-M 'P 2 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,AA 1 1 B,D,S,T,U,V,W,X,Y,Z,BA 1 2 # 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' 3_545 -x,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 -45.505 75.555 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 T N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 C NAG 1 C 1 NAG A 501 NAG 2 n C NAG 2 C 2 NAG A 601 NAG 2 n D NAG 1 D 1 NAG B 501 NAG 2 n D NAG 2 D 2 NAG B 601 NAG # 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 disulf ? disulf1 A SG CYS 110 A CYS 110 1_555 A SG CYS 187 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 B SG CYS 110 B CYS 110 1_555 B SG CYS 187 B CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? covale ? covale1 A N MET 1 A MET 1 1_555 E C ACE . A ACE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale2 A ND2 ASN 2 A ASN 2 1_555 G C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 A ND2 ASN 15 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A NZ LYS 296 A LYS 296 1_555 F C15 RET . A RET 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 A SG CYS 322 A CYS 322 1_555 N C1 PLM . A PLM 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale6 B N MET 1 B MET 1 1_555 S C ACE . B ACE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale7 B ND2 ASN 2 B ASN 2 1_555 U C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale8 B ND2 ASN 15 B ASN 15 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale9 B NZ LYS 296 B LYS 296 1_555 T C15 RET . B RET 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale10 B SG CYS 322 B CYS 322 1_555 Y C1 PLM . B PLM 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale11 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale12 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _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 463 n n C1 C6 RET sing 464 n n C1 C16 RET sing 465 n n C1 C17 RET sing 466 n n C2 C3 RET sing 467 n n C2 H21 RET sing 468 n n C2 H22 RET sing 469 n n C3 C4 RET sing 470 n n C3 H31 RET sing 471 n n C3 H32 RET sing 472 n n C4 C5 RET sing 473 n n C4 H41 RET sing 474 n n C4 H42 RET sing 475 n n C5 C6 RET doub 476 n n C5 C18 RET sing 477 n n C6 C7 RET sing 478 n n C7 C8 RET doub 479 e n C7 H7 RET sing 480 n n C8 C9 RET sing 481 n n C8 H8 RET sing 482 n n C9 C10 RET doub 483 e n C9 C19 RET sing 484 n n C10 C11 RET sing 485 n n C10 H10 RET sing 486 n n C11 C12 RET doub 487 e n C11 H11 RET sing 488 n n C12 C13 RET sing 489 n n C12 H12 RET sing 490 n n C13 C14 RET doub 491 e n C13 C20 RET sing 492 n n C14 C15 RET sing 493 n n C14 H14 RET sing 494 n n C15 O1 RET doub 495 n n C15 H15 RET sing 496 n n C16 H161 RET sing 497 n n C16 H162 RET sing 498 n n C16 H163 RET sing 499 n n C17 H171 RET sing 500 n n C17 H172 RET sing 501 n n C17 H173 RET sing 502 n n C18 H181 RET sing 503 n n C18 H182 RET sing 504 n n C18 H183 RET sing 505 n n C19 H191 RET sing 506 n n C19 H192 RET sing 507 n n C19 H193 RET sing 508 n n C20 H201 RET sing 509 n n C20 H202 RET sing 510 n n C20 H203 RET sing 511 n n # _atom_sites.entry_id 8A6D _atom_sites.fract_transf_matrix[1][1] 0.016258 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010988 _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] 0.006618 _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 ACE A 1 401 0 ACE ACE . F 4 RET A 1 402 401 RET RET . G 5 NAG A 1 403 701 NAG NAG . H 6 DAO A 1 404 702 DAO DAO . I 7 OLC A 1 405 801 OLC OLC . J 7 OLC A 1 406 802 OLC OLC . K 7 OLC A 1 407 805 OLC OLC . L 7 OLC A 1 408 806 OLC OLC . M 7 OLC A 1 409 808 OLC OLC . N 8 PLM A 1 410 809 PLM PLM . O 7 OLC A 1 411 811 OLC OLC . P 7 OLC A 1 412 702 OLC OLC . Q 7 OLC A 1 413 705 OLC OLC . R 7 OLC A 1 414 709 OLC OLC . S 3 ACE B 1 401 0 ACE ACE . T 4 RET B 1 402 401 RET RET . U 5 NAG B 1 403 701 NAG NAG . V 7 OLC B 1 404 704 OLC OLC . W 7 OLC B 1 405 706 OLC OLC . X 7 OLC B 1 406 707 OLC OLC . Y 8 PLM B 1 407 708 PLM PLM . Z 7 OLC B 1 408 801 OLC OLC . AA 9 HOH A 1 501 27 HOH HOH . AA 9 HOH A 2 502 38 HOH HOH . AA 9 HOH A 3 503 63 HOH HOH . AA 9 HOH A 4 504 100 HOH HOH . AA 9 HOH A 5 505 28 HOH HOH . AA 9 HOH A 6 506 103 HOH HOH . AA 9 HOH A 7 507 2 HOH HOH . AA 9 HOH A 8 508 19 HOH HOH . AA 9 HOH A 9 509 52 HOH HOH . AA 9 HOH A 10 510 45 HOH HOH . AA 9 HOH A 11 511 55 HOH HOH . AA 9 HOH A 12 512 20 HOH HOH . AA 9 HOH A 13 513 64 HOH HOH . AA 9 HOH A 14 514 33 HOH HOH . AA 9 HOH A 15 515 24 HOH HOH . AA 9 HOH A 16 516 46 HOH HOH . AA 9 HOH A 17 517 1 HOH HOH . AA 9 HOH A 18 518 30 HOH HOH . AA 9 HOH A 19 519 44 HOH HOH . AA 9 HOH A 20 520 9 HOH HOH . AA 9 HOH A 21 521 185 HOH HOH . AA 9 HOH A 22 522 131 HOH HOH . AA 9 HOH A 23 523 15 HOH HOH . AA 9 HOH A 24 524 23 HOH HOH . AA 9 HOH A 25 525 50 HOH HOH . AA 9 HOH A 26 526 68 HOH HOH . AA 9 HOH A 27 527 14 HOH HOH . AA 9 HOH A 28 528 13 HOH HOH . AA 9 HOH A 29 529 49 HOH HOH . AA 9 HOH A 30 530 29 HOH HOH . AA 9 HOH A 31 531 138 HOH HOH . AA 9 HOH A 32 532 184 HOH HOH . AA 9 HOH A 33 533 62 HOH HOH . AA 9 HOH A 34 534 6 HOH HOH . AA 9 HOH A 35 535 169 HOH HOH . AA 9 HOH A 36 536 179 HOH HOH . AA 9 HOH A 37 537 164 HOH HOH . AA 9 HOH A 38 538 59 HOH HOH . AA 9 HOH A 39 539 147 HOH HOH . AA 9 HOH A 40 540 56 HOH HOH . AA 9 HOH A 41 541 84 HOH HOH . AA 9 HOH A 42 542 93 HOH HOH . AA 9 HOH A 43 543 142 HOH HOH . AA 9 HOH A 44 544 75 HOH HOH . AA 9 HOH A 45 545 161 HOH HOH . AA 9 HOH A 46 546 133 HOH HOH . AA 9 HOH A 47 547 116 HOH HOH . AA 9 HOH A 48 548 41 HOH HOH . AA 9 HOH A 49 549 21 HOH HOH . AA 9 HOH A 50 550 88 HOH HOH . AA 9 HOH A 51 551 70 HOH HOH . AA 9 HOH A 52 552 97 HOH HOH . AA 9 HOH A 53 553 81 HOH HOH . AA 9 HOH A 54 554 157 HOH HOH . AA 9 HOH A 55 555 71 HOH HOH . BA 9 HOH B 1 501 39 HOH HOH . BA 9 HOH B 2 502 37 HOH HOH . BA 9 HOH B 3 503 82 HOH HOH . BA 9 HOH B 4 504 128 HOH HOH . BA 9 HOH B 5 505 165 HOH HOH . BA 9 HOH B 6 506 54 HOH HOH . BA 9 HOH B 7 507 113 HOH HOH . BA 9 HOH B 8 508 4 HOH HOH . BA 9 HOH B 9 509 76 HOH HOH . BA 9 HOH B 10 510 102 HOH HOH . BA 9 HOH B 11 511 42 HOH HOH . BA 9 HOH B 12 512 18 HOH HOH . BA 9 HOH B 13 513 163 HOH HOH . BA 9 HOH B 14 514 151 HOH HOH . BA 9 HOH B 15 515 85 HOH HOH . BA 9 HOH B 16 516 11 HOH HOH . BA 9 HOH B 17 517 25 HOH HOH . BA 9 HOH B 18 518 26 HOH HOH . BA 9 HOH B 19 519 205 HOH HOH . BA 9 HOH B 20 520 60 HOH HOH . BA 9 HOH B 21 521 124 HOH HOH . BA 9 HOH B 22 522 47 HOH HOH . BA 9 HOH B 23 523 127 HOH HOH . BA 9 HOH B 24 524 79 HOH HOH . BA 9 HOH B 25 525 17 HOH HOH . BA 9 HOH B 26 526 69 HOH HOH . BA 9 HOH B 27 527 51 HOH HOH . BA 9 HOH B 28 528 10 HOH HOH . BA 9 HOH B 29 529 109 HOH HOH . BA 9 HOH B 30 530 43 HOH HOH . BA 9 HOH B 31 531 36 HOH HOH . BA 9 HOH B 32 532 173 HOH HOH . BA 9 HOH B 33 533 48 HOH HOH . BA 9 HOH B 34 534 3 HOH HOH . BA 9 HOH B 35 535 89 HOH HOH . BA 9 HOH B 36 536 16 HOH HOH . BA 9 HOH B 37 537 171 HOH HOH . BA 9 HOH B 38 538 12 HOH HOH . BA 9 HOH B 39 539 95 HOH HOH . BA 9 HOH B 40 540 211 HOH HOH . BA 9 HOH B 41 541 31 HOH HOH . BA 9 HOH B 42 542 22 HOH HOH . BA 9 HOH B 43 543 112 HOH HOH . BA 9 HOH B 44 544 65 HOH HOH . BA 9 HOH B 45 545 94 HOH HOH . BA 9 HOH B 46 546 192 HOH HOH . BA 9 HOH B 47 547 40 HOH HOH . BA 9 HOH B 48 548 77 HOH HOH . BA 9 HOH B 49 549 72 HOH HOH . BA 9 HOH B 50 550 57 HOH HOH . BA 9 HOH B 51 551 177 HOH HOH . BA 9 HOH B 52 552 5 HOH HOH . BA 9 HOH B 53 553 148 HOH HOH . BA 9 HOH B 54 554 106 HOH HOH . BA 9 HOH B 55 555 35 HOH HOH . BA 9 HOH B 56 556 210 HOH HOH . BA 9 HOH B 57 557 141 HOH HOH . BA 9 HOH B 58 558 193 HOH HOH . BA 9 HOH B 59 559 86 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 . . . F 4 10.735 31.693 31.007 1 36.37 ? C1 RET 402 A 1 HETATM 2 C C2 RET . . . F 4 11.436 32.167 32.281 1 39.97 ? C2 RET 402 A 1 HETATM 3 C C3 RET . . . F 4 11.926 31.047 33.121 1 42.4 ? C3 RET 402 A 1 HETATM 4 C C4 RET . . . F 4 10.749 30.181 33.541 1 34.8 ? C4 RET 402 A 1 HETATM 5 C C5 RET . . . F 4 9.849 29.806 32.399 1 36.67 ? C5 RET 402 A 1 HETATM 6 C C6 RET . . . F 4 9.98 30.39 31.185 1 35.31 ? C6 RET 402 A 1 HETATM 7 C C7 RET . . . F 4 9.387 29.877 29.968 1 37.44 ? C7 RET 402 A 1 HETATM 8 C C8 RET . . . F 4 9.012 28.602 29.693 1 33.97 ? C8 RET 402 A 1 HETATM 9 C C9 RET . . . F 4 8.728 28.021 28.465 1 36.59 ? C9 RET 402 A 1 HETATM 10 C C10 RET . . . F 4 8.511 26.635 28.384 1 33.69 ? C10 RET 402 A 1 HETATM 11 C C11 RET . . . F 4 9.175 25.714 27.606 1 26.55 ? C11 RET 402 A 1 HETATM 12 C C12 RET . . . F 4 8.992 24.35 27.599 1 26.66 ? C12 RET 402 A 1 HETATM 13 C C13 RET . . . F 4 9.866 23.388 27.068 1 31.12 ? C13 RET 402 A 1 HETATM 14 C C14 RET . . . F 4 9.545 22.039 26.943 1 26.75 ? C14 RET 402 A 1 HETATM 15 C C15 RET . . . F 4 10.493 21.069 26.638 1 25.37 ? C15 RET 402 A 1 HETATM 16 C C16 RET . . . F 4 9.768 32.802 30.563 1 37.32 ? C16 RET 402 A 1 HETATM 17 C C17 RET . . . F 4 11.81 31.514 29.924 1 36.57 ? C17 RET 402 A 1 HETATM 18 C C18 RET . . . F 4 8.831 28.771 32.79 1 32.91 ? C18 RET 402 A 1 HETATM 19 C C19 RET . . . F 4 8.631 28.808 27.214 1 28.28 ? C19 RET 402 A 1 HETATM 20 C C20 RET . . . F 4 11.206 23.873 26.656 1 32.79 ? C20 RET 402 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #