data_6DG8 # _model_server_result.job_id '_NAQaTXGX9Luiiw5t5K0zg' _model_server_result.datetime_utc '2024-11-18 02:41:14' _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 6dg8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":501}' # _entry.id 6DG8 # _exptl.entry_id 6DG8 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 176.215 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SEROTONIN _entity.pdbx_number_of_molecules 5 _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 6DG8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DG8 _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 _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 ? 4 U N N ? 4 V N N ? 4 W N N ? 4 X N N ? 4 Y N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . 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 F NAG 1 F 1 NAG J 501 NAG 2 n F NAG 2 F 2 NAG J 502 NAG 3 n G NAG 1 G 1 NAG J 505 NAG 3 n G NAG 2 G 2 NAG J 504 NAG 3 n G BMA 3 G 3 BMA J 503 BMA 2 n H NAG 1 H 1 NAG J 506 NAG 2 n H NAG 2 H 2 NAG J 507 NAG 3 n I NAG 1 I 1 NAG I 501 NAG 3 n I NAG 2 I 2 NAG I 502 NAG 3 n I BMA 3 I 3 BMA I 503 BMA 2 n J NAG 1 J 1 NAG I 505 NAG 2 n J NAG 2 J 2 NAG I 504 NAG 2 n K NAG 1 K 1 NAG I 507 NAG 2 n K NAG 2 K 2 NAG I 506 NAG 3 n L NAG 1 L 1 NAG H 503 NAG 3 n L NAG 2 L 2 NAG H 502 NAG 3 n L BMA 3 L 3 BMA H 501 BMA 2 n M NAG 1 M 1 NAG H 505 NAG 2 n M NAG 2 M 2 NAG H 504 NAG 2 n N NAG 1 N 1 NAG H 507 NAG 2 n N NAG 2 N 2 NAG H 506 NAG 3 n O NAG 1 O 1 NAG G 503 NAG 3 n O NAG 2 O 2 NAG G 502 NAG 3 n O BMA 3 O 3 BMA G 501 BMA 2 n P NAG 1 P 1 NAG G 505 NAG 2 n P NAG 2 P 2 NAG G 504 NAG 2 n Q NAG 1 Q 1 NAG G 507 NAG 2 n Q NAG 2 Q 2 NAG G 506 NAG 3 n R NAG 1 R 1 NAG F 503 NAG 3 n R NAG 2 R 2 NAG F 502 NAG 3 n R BMA 3 R 3 BMA F 501 BMA 2 n S NAG 1 S 1 NAG F 505 NAG 2 n S NAG 2 S 2 NAG F 504 NAG 2 n T NAG 1 T 1 NAG F 507 NAG 2 n T NAG 2 T 2 NAG F 506 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 128 A CYS 135 1_555 A SG CYS 142 A CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 128 B CYS 135 1_555 B SG CYS 142 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 C SG CYS 128 C CYS 135 1_555 C SG CYS 142 C CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 D SG CYS 128 D CYS 135 1_555 D SG CYS 142 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 E SG CYS 128 E CYS 135 1_555 E SG CYS 142 E CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 B ND2 ASN 157 B ASN 164 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.488 ? covale ? covale2 D ND2 ASN 75 D ASN 82 1_555 P C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale3 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale9 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale11 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale12 L O4 NAG . L NAG 2 1_555 L C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale13 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale15 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 O O4 NAG . O NAG 2 1_555 O C1 BMA . O BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale17 P O4 NAG . P NAG 1 1_555 P C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale18 Q O4 NAG . Q NAG 1 1_555 Q C1 NAG . Q NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale19 R O4 NAG . R NAG 1 1_555 R C1 NAG . R NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale20 R O4 NAG . R NAG 2 1_555 R C1 BMA . R BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale21 S O4 NAG . S NAG 1 1_555 S C1 NAG . S NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale22 T O4 NAG . T NAG 1 1_555 T C1 NAG . T NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _chem_comp.formula 'C10 H12 N2 O' _chem_comp.formula_weight 176.215 _chem_comp.id SRO _chem_comp.mon_nstd_flag . _chem_comp.name SEROTONIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 3-(2-AMINOETHYL)-1H-INDOL-5-OL # 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 OH CZ3 SRO sing 342 n n OH HOH SRO sing 343 n n CZ3 CE3 SRO doub 344 n y CZ3 CH2 SRO sing 345 n y CH2 CZ2 SRO doub 346 n y CH2 HH2 SRO sing 347 n n CZ2 CE2 SRO sing 348 n y CZ2 HZ2 SRO sing 349 n n CE2 NE1 SRO sing 350 n y CE2 CD2 SRO doub 351 n y NE1 CD1 SRO sing 352 n y NE1 HNE1 SRO sing 353 n n CD1 CG SRO doub 354 n y CD1 HD1 SRO sing 355 n n CG CB SRO sing 356 n n CG CD2 SRO sing 357 n y CD2 CE3 SRO sing 358 n y CE3 HE3 SRO sing 359 n n CB CA SRO sing 360 n n CB HB1 SRO sing 361 n n CB HB2 SRO sing 362 n n CA NZ SRO sing 363 n n CA HA1 SRO sing 364 n n CA HA2 SRO sing 365 n n NZ HNZ1 SRO sing 366 n n NZ HNZ2 SRO sing 367 n n # _atom_sites.entry_id 6DG8 _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 U 4 SRO A 1 501 5 SRO SRO . V 4 SRO B 1 501 3 SRO SRO . W 4 SRO B 1 502 4 SRO SRO . X 4 SRO D 1 501 2 SRO SRO . Y 4 SRO E 1 501 1 SRO SRO . # 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 O OH SRO . . . X 4 181.706 170.107 193.969 1 151.73 ? OH SRO 501 D 1 HETATM 2 C CZ3 SRO . . . X 4 183.065 169.771 194.009 1 151.73 ? CZ3 SRO 501 D 1 HETATM 3 C CH2 SRO . . . X 4 184.023 170.764 194.223 1 151.73 ? CH2 SRO 501 D 1 HETATM 4 C CZ2 SRO . . . X 4 185.37 170.427 194.262 1 151.73 ? CZ2 SRO 501 D 1 HETATM 5 C CE2 SRO . . . X 4 185.77 169.075 194.085 1 151.73 ? CE2 SRO 501 D 1 HETATM 6 N NE1 SRO . . . X 4 186.994 168.489 194.08 1 151.73 ? NE1 SRO 501 D 1 HETATM 7 C CD1 SRO . . . X 4 186.884 167.191 193.873 1 151.73 ? CD1 SRO 501 D 1 HETATM 8 C CG SRO . . . X 4 185.538 166.875 193.735 1 151.73 ? CG SRO 501 D 1 HETATM 9 C CD2 SRO . . . X 4 184.828 168.102 193.876 1 151.73 ? CD2 SRO 501 D 1 HETATM 10 C CE3 SRO . . . X 4 183.455 168.445 193.835 1 151.73 ? CE3 SRO 501 D 1 HETATM 11 C CB SRO . . . X 4 184.953 165.487 193.486 1 151.73 ? CB SRO 501 D 1 HETATM 12 C CA SRO . . . X 4 184.933 164.633 194.751 1 151.73 ? CA SRO 501 D 1 HETATM 13 N NZ SRO . . . X 4 185.074 163.23 194.407 1 151.73 ? NZ SRO 501 D 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 74 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 13 #