data_3PQR # _model_server_result.job_id RqUerXON5omfGuEmZ0UtsA _model_server_result.datetime_utc '2024-11-13 01:31:31' _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 3pqr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 3PQR # _exptl.entry_id 3PQR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 1 _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 3PQR _cell.length_a 241.55 _cell.length_b 241.55 _cell.length_c 109.87 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PQR _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 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,C,D,E,F,G,H,I,J,K,L,M,N 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N 2 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' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 109.87 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 4 1 2 GLC GLC C1 O1 . O1 HO1 . 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 3 n C NAG 1 C 1 NAG A 402 NAG 3 n C NAG 2 C 2 NAG A 403 NAG 3 n C BMA 3 C 3 BMA A 404 BMA 3 n C MAN 4 C 4 MAN A 405 MAN 4 n D GLC 1 D 1 GLC A 1001 TRE 4 n D GLC 2 D 2 GLC A 1001 TRE # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? covale ? covale1 A ND2 ASN 2 A ASN 2 1_555 F C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A ND2 ASN 15 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 A NZ LYS 296 A LYS 296 1_555 E C15 RET . A RET 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 A SG CYS 323 A CYS 323 1_555 I C1 PLM . A PLM 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.833 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale8 D C1 GLC . D GLC 1 1_555 D O1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 sing # _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 482 n n C1 C6 RET sing 483 n n C1 C16 RET sing 484 n n C1 C17 RET sing 485 n n C2 C3 RET sing 486 n n C2 H21 RET sing 487 n n C2 H22 RET sing 488 n n C3 C4 RET sing 489 n n C3 H31 RET sing 490 n n C3 H32 RET sing 491 n n C4 C5 RET sing 492 n n C4 H41 RET sing 493 n n C4 H42 RET sing 494 n n C5 C6 RET doub 495 n n C5 C18 RET sing 496 n n C6 C7 RET sing 497 n n C7 C8 RET doub 498 e n C7 H7 RET sing 499 n n C8 C9 RET sing 500 n n C8 H8 RET sing 501 n n C9 C10 RET doub 502 e n C9 C19 RET sing 503 n n C10 C11 RET sing 504 n n C10 H10 RET sing 505 n n C11 C12 RET doub 506 e n C11 H11 RET sing 507 n n C12 C13 RET sing 508 n n C12 H12 RET sing 509 n n C13 C14 RET doub 510 e n C13 C20 RET sing 511 n n C14 C15 RET sing 512 n n C14 H14 RET sing 513 n n C15 O1 RET doub 514 n n C15 H15 RET sing 515 n n C16 H161 RET sing 516 n n C16 H162 RET sing 517 n n C16 H163 RET sing 518 n n C17 H171 RET sing 519 n n C17 H172 RET sing 520 n n C17 H173 RET sing 521 n n C18 H181 RET sing 522 n n C18 H182 RET sing 523 n n C18 H183 RET sing 524 n n C19 H191 RET sing 525 n n C19 H192 RET sing 526 n n C19 H193 RET sing 527 n n C20 H201 RET sing 528 n n C20 H202 RET sing 529 n n C20 H203 RET sing 530 n n # _atom_sites.entry_id 3PQR _atom_sites.fract_transf_matrix[1][1] 0.00414 _atom_sites.fract_transf_matrix[1][2] 0.00239 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00478 _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] 0.009102 _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 5 RET A 1 401 401 RET RET . F 6 NAG A 1 501 501 NAG NAG . G 7 BOG A 1 601 601 BOG BOG . H 7 BOG A 1 602 602 BOG BOG . I 8 PLM A 1 701 701 PLM PLM . J 9 SO4 A 1 801 801 SO4 SO4 . K 10 ACT A 1 901 901 ACT ACT . L 10 ACT A 1 902 902 ACT ACT . M 11 HOH A 1 349 1 HOH HOH . M 11 HOH A 2 350 2 HOH HOH . M 11 HOH A 3 351 3 HOH HOH . M 11 HOH A 4 352 6 HOH HOH . M 11 HOH A 5 353 7 HOH HOH . M 11 HOH A 6 354 8 HOH HOH . M 11 HOH A 7 355 9 HOH HOH . M 11 HOH A 8 356 10 HOH HOH . M 11 HOH A 9 357 11 HOH HOH . M 11 HOH A 10 358 12 HOH HOH . M 11 HOH A 11 359 13 HOH HOH . M 11 HOH A 12 360 14 HOH HOH . M 11 HOH A 13 361 15 HOH HOH . M 11 HOH A 14 362 16 HOH HOH . M 11 HOH A 15 363 17 HOH HOH . M 11 HOH A 16 364 18 HOH HOH . M 11 HOH A 17 365 19 HOH HOH . M 11 HOH A 18 366 20 HOH HOH . M 11 HOH A 19 367 22 HOH HOH . N 11 HOH B 1 4 4 HOH HOH . N 11 HOH B 2 5 5 HOH HOH . N 11 HOH B 3 21 21 HOH HOH . N 11 HOH B 4 23 23 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 . . . E 5 -43.073 -16.462 33.951 1 80.74 ? C1 RET 401 A 1 HETATM 2 C C2 RET . . . E 5 -43.304 -18.013 34.059 1 76.14 ? C2 RET 401 A 1 HETATM 3 C C3 RET . . . E 5 -44.521 -18.5 33.462 1 74.48 ? C3 RET 401 A 1 HETATM 4 C C4 RET . . . E 5 -45.742 -17.753 33.836 1 80.23 ? C4 RET 401 A 1 HETATM 5 C C5 RET . . . E 5 -45.593 -16.265 33.697 1 83.7 ? C5 RET 401 A 1 HETATM 6 C C6 RET . . . E 5 -44.401 -15.674 33.85 1 83.94 ? C6 RET 401 A 1 HETATM 7 C C7 RET . . . E 5 -44.254 -14.2 33.942 1 80.57 ? C7 RET 401 A 1 HETATM 8 C C8 RET . . . E 5 -44.906 -13.384 34.761 1 75.14 ? C8 RET 401 A 1 HETATM 9 C C9 RET . . . E 5 -44.76 -11.929 34.871 1 72.83 ? C9 RET 401 A 1 HETATM 10 C C10 RET . . . E 5 -45.287 -11.337 35.963 1 68.27 ? C10 RET 401 A 1 HETATM 11 C C11 RET . . . E 5 -45.276 -9.952 36.341 1 68.18 ? C11 RET 401 A 1 HETATM 12 C C12 RET . . . E 5 -45.947 -9.448 37.401 1 74.87 ? C12 RET 401 A 1 HETATM 13 C C13 RET . . . E 5 -45.955 -8.076 37.866 1 78.46 ? C13 RET 401 A 1 HETATM 14 C C14 RET . . . E 5 -46.815 -7.72 38.854 1 81.05 ? C14 RET 401 A 1 HETATM 15 C C15 RET . . . E 5 -46.969 -6.414 39.472 1 76.45 ? C15 RET 401 A 1 HETATM 16 C C16 RET . . . E 5 -42.118 -16.005 32.896 1 74.97 ? C16 RET 401 A 1 HETATM 17 C C17 RET . . . E 5 -42.415 -16.25 35.302 1 84.84 ? C17 RET 401 A 1 HETATM 18 C C18 RET . . . E 5 -46.886 -15.543 33.37 1 78.74 ? C18 RET 401 A 1 HETATM 19 C C19 RET . . . E 5 -44.041 -11.212 33.759 1 61.89 ? C19 RET 401 A 1 HETATM 20 C C20 RET . . . E 5 -44.978 -7.104 37.265 1 82.68 ? C20 RET 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #