data_8DN5 # _model_server_result.job_id CU7lxXo5Uott2wdqRMHkVA _model_server_result.datetime_utc '2024-11-22 20:42:28' _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 8dn5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":509}' # _entry.id 8DN5 # _exptl.entry_id 8DN5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 128.255 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description nonane _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 90 _cell.entry_id 8DN5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DN5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB _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 ? _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 ? 5 H N N ? 5 V N N ? 5 Z N N ? 5 EA 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 disulf ? disulf1 A SG CYS 138 D CYS 138 1_555 A SG CYS 152 D CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 198 D CYS 198 1_555 A SG CYS 209 D CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 138 A CYS 138 1_555 B SG CYS 152 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 198 A CYS 198 1_555 B SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 C SG CYS 138 B CYS 138 1_555 C SG CYS 152 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 C SG CYS 198 B CYS 198 1_555 C SG CYS 209 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 D SG CYS 138 C CYS 138 1_555 D SG CYS 152 C CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 D SG CYS 198 C CYS 198 1_555 D SG CYS 209 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 E SG CYS 159 E CYS 161 1_555 E SG CYS 173 E CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 E SG CYS 219 E CYS 221 1_555 E SG CYS 231 E CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A ND2 ASN 38 D ASN 38 1_555 G C1 NAG . D NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 B ND2 ASN 38 A ASN 38 1_555 S C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 C ND2 ASN 38 B ASN 38 1_555 GA C1 NAG . B NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 E ND2 ASN 218 E ASN 220 1_555 YA C1 NAG . E NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _chem_comp.formula 'C9 H20' _chem_comp.formula_weight 128.255 _chem_comp.id DD9 _chem_comp.mon_nstd_flag . _chem_comp.name nonane _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 C2 C1 DD9 sing 114 n n C1 H1 DD9 sing 115 n n C1 H1A DD9 sing 116 n n C1 H1B DD9 sing 117 n n C3 C2 DD9 sing 118 n n C2 H2 DD9 sing 119 n n C2 H2A DD9 sing 120 n n C4 C3 DD9 sing 121 n n C3 H3 DD9 sing 122 n n C3 H3A DD9 sing 123 n n C5 C4 DD9 sing 124 n n C4 H4 DD9 sing 125 n n C4 H4A DD9 sing 126 n n C6 C5 DD9 sing 127 n n C5 H5 DD9 sing 128 n n C5 H5A DD9 sing 129 n n C7 C6 DD9 sing 130 n n C6 H6 DD9 sing 131 n n C6 H6A DD9 sing 132 n n C8 C7 DD9 sing 133 n n C7 H7 DD9 sing 134 n n C7 H7A DD9 sing 135 n n C9 C8 DD9 sing 136 n n C8 H8 DD9 sing 137 n n C8 H8A DD9 sing 138 n n C9 H9 DD9 sing 139 n n C9 H9A DD9 sing 140 n n C9 H9B DD9 sing 141 n n # _atom_sites.entry_id 8DN5 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 3 GLY D 1 501 501 GLY GLY . G 4 NAG D 1 502 502 NAG NAG . H 5 DD9 D 1 503 503 DD9 DD9 . I 6 HP6 D 1 504 504 HP6 HP6 . J 7 HEX D 1 505 505 HEX HEX . K 6 HP6 D 1 506 506 HP6 HP6 . L 6 HP6 D 1 507 507 HP6 HP6 . M 7 HEX D 1 508 508 HEX HEX . N 7 HEX D 1 509 510 HEX HEX . O 7 HEX D 1 510 511 HEX HEX . P 7 HEX D 1 511 512 HEX HEX . Q 8 UND D 1 512 509 UND UND . R 3 GLY A 1 501 501 GLY GLY . S 4 NAG A 1 502 502 NAG NAG . T 8 UND A 1 503 503 UND UND . U 8 UND A 1 504 504 UND UND . V 5 DD9 A 1 505 505 DD9 DD9 . W 6 HP6 A 1 506 506 HP6 HP6 . X 7 HEX A 1 507 509 HEX HEX . Y 9 NBU A 1 508 510 NBU NBU . Z 5 DD9 A 1 509 511 DD9 DD9 . AA 9 NBU A 1 510 512 NBU NBU . BA 8 UND A 1 511 504 UND UND . CA 8 UND A 1 512 505 UND UND . DA 10 D10 B 1 501 507 D10 D10 . EA 5 DD9 B 1 502 508 DD9 DD9 . FA 3 GLY B 1 503 501 GLY GLY . GA 4 NAG B 1 504 502 NAG NAG . HA 7 HEX B 1 505 503 HEX HEX . IA 7 HEX B 1 506 504 HEX HEX . JA 9 NBU B 1 507 505 NBU NBU . KA 10 D10 B 1 508 506 D10 D10 . LA 9 NBU B 1 509 507 NBU NBU . MA 9 NBU B 1 510 508 NBU NBU . NA 7 HEX B 1 511 509 HEX HEX . OA 3 GLY C 1 501 501 GLY GLY . PA 4 NAG C 1 502 502 NAG NAG . QA 6 HP6 C 1 503 503 HP6 HP6 . RA 6 HP6 C 1 504 504 HP6 HP6 . SA 9 NBU C 1 505 505 NBU NBU . TA 7 HEX C 1 506 506 HEX HEX . UA 7 HEX C 1 507 507 HEX HEX . VA 9 NBU C 1 508 508 NBU NBU . WA 9 NBU E 1 501 509 NBU NBU . XA 3 GLY E 1 502 501 GLY GLY . YA 4 NAG E 1 503 502 NAG NAG . ZA 10 D10 E 1 504 503 D10 D10 . AB 8 UND E 1 505 506 UND UND . BB 11 OCT E 1 506 507 OCT OCT . CB 11 OCT E 1 507 508 OCT OCT . DB 7 HEX E 1 508 509 HEX HEX . EB 7 HEX E 1 509 510 HEX HEX . # 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 DD9 . . . Z 5 87.987 143.635 130.928 1 20 ? C1 DD9 509 A 1 HETATM 2 C C2 DD9 . . . Z 5 88.768 142.369 130.661 1 20 ? C2 DD9 509 A 1 HETATM 3 C C3 DD9 . . . Z 5 89.803 142.516 129.575 1 20 ? C3 DD9 509 A 1 HETATM 4 C C4 DD9 . . . Z 5 90.592 141.262 129.294 1 20 ? C4 DD9 509 A 1 HETATM 5 C C5 DD9 . . . Z 5 91.628 141.413 128.206 1 20 ? C5 DD9 509 A 1 HETATM 6 C C6 DD9 . . . Z 5 92.418 140.158 127.925 1 20 ? C6 DD9 509 A 1 HETATM 7 C C7 DD9 . . . Z 5 93.453 140.31 126.837 1 20 ? C7 DD9 509 A 1 HETATM 8 C C8 DD9 . . . Z 5 94.245 139.057 126.551 1 20 ? C8 DD9 509 A 1 HETATM 9 C C9 DD9 . . . Z 5 95.291 139.192 125.462 1 20 ? C9 DD9 509 A 1 HETATM 10 H H1 DD9 . . . Z 5 87.339 143.473 131.635 1 20 ? H1 DD9 509 A 1 HETATM 11 H H1A DD9 . . . Z 5 87.522 143.907 130.119 1 20 ? H1A DD9 509 A 1 HETATM 12 H H1B DD9 . . . Z 5 88.597 144.341 131.205 1 20 ? H1B DD9 509 A 1 HETATM 13 H H2 DD9 . . . Z 5 88.142 141.657 130.405 1 20 ? H2 DD9 509 A 1 HETATM 14 H H2A DD9 . . . Z 5 89.216 142.091 131.488 1 20 ? H2A DD9 509 A 1 HETATM 15 H H3 DD9 . . . Z 5 90.427 143.229 129.831 1 20 ? H3 DD9 509 A 1 HETATM 16 H H3A DD9 . . . Z 5 89.354 142.797 128.749 1 20 ? H3A DD9 509 A 1 HETATM 17 H H4 DD9 . . . Z 5 89.969 140.549 129.038 1 20 ? H4 DD9 509 A 1 HETATM 18 H H4A DD9 . . . Z 5 91.042 140.981 130.12 1 20 ? H4A DD9 509 A 1 HETATM 19 H H5 DD9 . . . Z 5 92.251 142.126 128.463 1 20 ? H5 DD9 509 A 1 HETATM 20 H H5A DD9 . . . Z 5 91.179 141.693 127.381 1 20 ? H5A DD9 509 A 1 HETATM 21 H H6 DD9 . . . Z 5 91.795 139.445 127.668 1 20 ? H6 DD9 509 A 1 HETATM 22 H H6A DD9 . . . Z 5 92.868 139.878 128.75 1 20 ? H6A DD9 509 A 1 HETATM 23 H H7 DD9 . . . Z 5 94.077 141.024 127.094 1 20 ? H7 DD9 509 A 1 HETATM 24 H H7A DD9 . . . Z 5 93.004 140.592 126.012 1 20 ? H7A DD9 509 A 1 HETATM 25 H H8 DD9 . . . Z 5 93.619 138.345 126.298 1 20 ? H8 DD9 509 A 1 HETATM 26 H H8A DD9 . . . Z 5 94.692 138.775 127.379 1 20 ? H8A DD9 509 A 1 HETATM 27 H H9 DD9 . . . Z 5 96.171 139.003 125.831 1 20 ? H9 DD9 509 A 1 HETATM 28 H H9A DD9 . . . Z 5 95.281 140.097 125.102 1 20 ? H9A DD9 509 A 1 HETATM 29 H H9B DD9 . . . Z 5 95.099 138.56 124.748 1 20 ? H9B DD9 509 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 400 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #