data_6DG7 # _model_server_result.job_id aWauBwOqmPMaLz1737cPlA _model_server_result.datetime_utc '2024-11-04 22:34:24' _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 6dg7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":508}' # _entry.id 6DG7 # _exptl.entry_id 6DG7 _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 6DG7 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DG7 _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 E SG CYS 128 E CYS 135 1_555 E SG CYS 142 E CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 75 A ASN 82 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale2 A ND2 ASN 141 A ASN 148 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 B ND2 ASN 75 B ASN 82 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? covale ? covale4 B ND2 ASN 157 B ASN 164 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? covale ? covale5 C ND2 ASN 141 C ASN 148 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 D ND2 ASN 75 D ASN 82 1_555 P C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale7 D ND2 ASN 157 D ASN 164 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.487 ? covale ? covale8 E ND2 ASN 75 E ASN 82 1_555 S C1 NAG . S NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale9 E ND2 ASN 141 E ASN 148 1_555 T C1 NAG . T NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale11 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale12 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale13 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale15 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale16 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale17 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale18 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale19 L O4 NAG . L NAG 2 1_555 L C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale20 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale21 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale22 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale23 O O4 NAG . O NAG 2 1_555 O C1 BMA . O BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale24 P O4 NAG . P NAG 1 1_555 P C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale25 Q O4 NAG . Q NAG 1 1_555 Q C1 NAG . Q NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale26 R O4 NAG . R NAG 1 1_555 R C1 NAG . R NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale27 R O4 NAG . R NAG 2 1_555 R C1 BMA . R BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale28 S O4 NAG . S NAG 1 1_555 S C1 NAG . S NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale29 T O4 NAG . T NAG 1 1_555 T C1 NAG . T NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 # _atom_sites.entry_id 6DG7 _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 1 508 2 SRO SRO . V 4 SRO B 1 508 3 SRO SRO . W 4 SRO C 1 508 1 SRO SRO . X 4 SRO C 1 509 4 SRO SRO . Y 4 SRO E 1 508 5 SRO SRO . Z 5 HOH A 1 601 5 HOH HOH . AA 5 HOH B 1 601 4 HOH HOH . BA 5 HOH C 1 601 3 HOH HOH . CA 5 HOH D 1 601 2 HOH HOH . DA 5 HOH E 1 601 6 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 O OH SRO . . . Y 4 176.269 142.133 196.081 1 110.98 ? OH SRO 508 E 1 HETATM 2 C CZ3 SRO . . . Y 4 176.374 140.739 196.005 1 110.98 ? CZ3 SRO 508 E 1 HETATM 3 C CH2 SRO . . . Y 4 177.578 140.114 196.333 1 110.98 ? CH2 SRO 508 E 1 HETATM 4 C CZ2 SRO . . . Y 4 177.688 138.732 196.26 1 110.98 ? CZ2 SRO 508 E 1 HETATM 5 C CE2 SRO . . . Y 4 176.57 137.957 195.851 1 110.98 ? CE2 SRO 508 E 1 HETATM 6 N NE1 SRO . . . Y 4 176.413 136.618 195.698 1 110.98 ? NE1 SRO 508 E 1 HETATM 7 C CD1 SRO . . . Y 4 175.188 136.344 195.29 1 110.98 ? CD1 SRO 508 E 1 HETATM 8 C CG SRO . . . Y 4 174.478 137.533 195.165 1 110.98 ? CG SRO 508 E 1 HETATM 9 C CD2 SRO . . . Y 4 175.387 138.569 195.529 1 110.98 ? CD2 SRO 508 E 1 HETATM 10 C CE3 SRO . . . Y 4 175.278 139.979 195.604 1 110.98 ? CE3 SRO 508 E 1 HETATM 11 C CB SRO . . . Y 4 173.024 137.701 194.723 1 110.98 ? CB SRO 508 E 1 HETATM 12 C CA SRO . . . Y 4 172.031 137.006 195.651 1 110.98 ? CA SRO 508 E 1 HETATM 13 N NZ SRO . . . Y 4 171.949 135.592 195.334 1 110.98 ? NZ SRO 508 E 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 13 #