data_6Y1Z # _model_server_result.job_id uY5hLiabk2UoBzvo9Bb5eA _model_server_result.datetime_utc '2025-02-05 16:58:24' _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 6y1z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"GA","auth_seq_id":502}' # _entry.id 6Y1Z # _exptl.entry_id 6Y1Z _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 204.225 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description TRYPTOPHAN _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 6Y1Z _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y1Z _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 _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 P N N ? 4 T N N ? 4 X N N ? 4 CA N N ? 4 GA 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 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG 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 A 505 NAG 2 n F NAG 2 F 2 NAG A 504 NAG 2 n F BMA 3 F 3 BMA A 503 BMA 3 n G NAG 1 G 1 NAG A 506 NAG 3 n G NAG 2 G 2 NAG A 507 NAG 2 n H NAG 1 H 1 NAG D 505 NAG 2 n H NAG 2 H 2 NAG D 504 NAG 2 n H BMA 3 H 3 BMA D 503 BMA 3 n I NAG 1 I 1 NAG D 506 NAG 3 n I NAG 2 I 2 NAG D 507 NAG 2 n J NAG 1 J 1 NAG B 505 NAG 2 n J NAG 2 J 2 NAG B 504 NAG 2 n J BMA 3 J 3 BMA B 503 BMA 3 n K NAG 1 K 1 NAG B 506 NAG 3 n K NAG 2 K 2 NAG B 507 NAG 2 n L NAG 1 L 1 NAG C 505 NAG 2 n L NAG 2 L 2 NAG C 504 NAG 2 n L BMA 3 L 3 BMA C 503 BMA 3 n M NAG 1 M 1 NAG C 506 NAG 3 n M NAG 2 M 2 NAG C 507 NAG 2 n N NAG 1 N 1 NAG E 505 NAG 2 n N NAG 2 N 2 NAG E 504 NAG 2 n N BMA 3 N 3 BMA E 503 BMA 3 n O NAG 1 O 1 NAG E 506 NAG 3 n O NAG 2 O 2 NAG E 507 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 239 A CYS 135 1_555 A SG CYS 253 A CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 239 D CYS 135 1_555 B SG CYS 253 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 C SG CYS 239 B CYS 135 1_555 C SG CYS 253 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 D SG CYS 239 C CYS 135 1_555 D SG CYS 253 C CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 E SG CYS 239 E CYS 135 1_555 E SG CYS 253 E CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 186 A ASN 82 1_555 R C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 252 A ASN 148 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 268 A ASN 164 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 B ND2 ASN 186 D ASN 82 1_555 V C1 NAG . D NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 B ND2 ASN 252 D ASN 148 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 B ND2 ASN 268 D ASN 164 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 C ND2 ASN 186 B ASN 82 1_555 Z C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 C ND2 ASN 252 B ASN 148 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 C ND2 ASN 268 B ASN 164 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 D ND2 ASN 186 C ASN 82 1_555 EA C1 NAG . C NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 D ND2 ASN 252 C ASN 148 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 D ND2 ASN 268 C ASN 164 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale13 E ND2 ASN 186 E ASN 82 1_555 IA C1 NAG . E NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 E ND2 ASN 252 E ASN 148 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale15 E ND2 ASN 268 E ASN 164 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale17 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale18 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale19 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale20 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale21 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale22 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale23 J O4 NAG . J NAG 2 1_555 J C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale24 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale25 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale26 L O4 NAG . L NAG 2 1_555 L C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale27 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale28 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale29 N O4 NAG . N NAG 2 1_555 N C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale30 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _chem_comp.formula 'C11 H12 N2 O2' _chem_comp.formula_weight 204.225 _chem_comp.id TRP _chem_comp.mon_nstd_flag y _chem_comp.name TRYPTOPHAN _chem_comp.type 'l-peptide linking' _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 N CA TRP sing 408 n n N H TRP sing 409 n n N H2 TRP sing 410 n n CA C TRP sing 411 n n CA CB TRP sing 412 n n CA HA TRP sing 413 n n C O TRP doub 414 n n C OXT TRP sing 415 n n CB CG TRP sing 416 n n CB HB2 TRP sing 417 n n CB HB3 TRP sing 418 n n CG CD1 TRP doub 419 n y CG CD2 TRP sing 420 n y CD1 NE1 TRP sing 421 n y CD1 HD1 TRP sing 422 n n CD2 CE2 TRP doub 423 n y CD2 CE3 TRP sing 424 n y NE1 CE2 TRP sing 425 n y NE1 HE1 TRP sing 426 n n CE2 CZ2 TRP sing 427 n y CE3 CZ3 TRP doub 428 n y CE3 HE3 TRP sing 429 n n CZ2 CH2 TRP doub 430 n y CZ2 HZ2 TRP sing 431 n n CZ3 CH2 TRP sing 432 n y CZ3 HZ3 TRP sing 433 n n CH2 HH2 TRP sing 434 n n OXT HXT TRP sing 435 n n # _atom_sites.entry_id 6Y1Z _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 P 4 TRP A 1 501 459 TRP TRP . Q 5 HIS A 1 502 460 HIS HIS . R 6 NAG A 1 503 501 NAG NAG . S 7 O7B A 1 504 903 O7B PAL . T 4 TRP D 1 501 459 TRP TRP . U 5 HIS D 1 502 460 HIS HIS . V 6 NAG D 1 503 501 NAG NAG . W 7 O7B D 1 504 903 O7B PAL . X 4 TRP B 1 501 459 TRP TRP . Y 5 HIS B 1 502 460 HIS HIS . Z 6 NAG B 1 503 501 NAG NAG . AA 7 O7B B 1 504 903 O7B PAL . BA 7 O7B C 1 501 903 O7B PAL . CA 4 TRP C 1 502 459 TRP TRP . DA 5 HIS C 1 503 460 HIS HIS . EA 6 NAG C 1 504 501 NAG NAG . FA 7 O7B E 1 501 903 O7B PAL . GA 4 TRP E 1 502 459 TRP TRP . HA 5 HIS E 1 503 460 HIS HIS . IA 6 NAG E 1 504 501 NAG NAG . # 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 N N TRP . . . GA 4 158.666 142.724 124.603 1 125.84 ? N TRP 502 E 1 HETATM 2 C CA TRP . . . GA 4 158.469 142.332 125.992 1 125.84 ? CA TRP 502 E 1 HETATM 3 C C TRP . . . GA 4 159.476 141.267 126.416 1 125.84 ? C TRP 502 E 1 HETATM 4 O O TRP . . . GA 4 160.336 141.514 127.261 1 125.84 ? O TRP 502 E 1 HETATM 5 C CB TRP . . . GA 4 157.042 141.822 126.203 1 125.84 ? CB TRP 502 E 1 HETATM 6 C CG TRP . . . GA 4 156.752 141.428 127.617 1 125.84 ? CG TRP 502 E 1 HETATM 7 C CD1 TRP . . . GA 4 156.45 142.261 128.654 1 125.84 ? CD1 TRP 502 E 1 HETATM 8 C CD2 TRP . . . GA 4 156.731 140.099 128.151 1 125.84 ? CD2 TRP 502 E 1 HETATM 9 N NE1 TRP . . . GA 4 156.245 141.534 129.801 1 125.84 ? NE1 TRP 502 E 1 HETATM 10 C CE2 TRP . . . GA 4 156.411 140.204 129.519 1 125.84 ? CE2 TRP 502 E 1 HETATM 11 C CE3 TRP . . . GA 4 156.951 138.83 127.605 1 125.84 ? CE3 TRP 502 E 1 HETATM 12 C CZ2 TRP . . . GA 4 156.308 139.09 130.349 1 125.84 ? CZ2 TRP 502 E 1 HETATM 13 C CZ3 TRP . . . GA 4 156.849 137.726 128.431 1 125.84 ? CZ3 TRP 502 E 1 HETATM 14 C CH2 TRP . . . GA 4 156.529 137.863 129.787 1 125.84 ? CH2 TRP 502 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 14 #