data_5WY8 # _model_server_result.job_id DpUW7rGtzA6UapYZCPZX0g _model_server_result.datetime_utc '2025-03-01 19:11:30' _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 5wy8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":413}' # _entry.id 5WY8 # _exptl.entry_id 5WY8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 65.409 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ZINC ION' _entity.pdbx_number_of_molecules 3 _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 5WY8 _cell.length_a 110.416 _cell.length_b 110.416 _cell.length_c 210.536 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WY8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 153 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 1 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 _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 x,y,z _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 ? 7 J N N ? 7 K N N ? 7 L N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide 5 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 FUC NAG C1 O1 . O3 HO3 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 5 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . 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 N 1101 NAG 3 n C FUC 2 C 2 FUC N 1112 FUC 4 n D NAG 1 D 1 NAG N 350 NAG 4 n D NAG 2 D 2 NAG N 351 NAG 4 n E NAG 1 E 1 NAG N 1401 NAG 4 n E NAG 2 E 2 NAG N 1402 NAG 5 n F NAG 1 F 1 NAG N 1501 NAG 5 n F NAG 2 F 2 NAG N 1502 NAG 5 n F BMA 3 F 3 BMA N 1503 BMA 5 n F MAN 4 F 4 MAN N 1504 MAN 4 n G NAG 1 G 1 NAG N 1601 NAG 4 n G NAG 2 G 2 NAG N 1602 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 25 A CYS 45 1_555 A SG CYS 78 A CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 127 A CYS 147 1_555 A SG CYS 187 A CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 237 A CYS 257 1_555 A SG CYS 282 A CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 B SG CYS 5 B CYS 31 1_555 B SG CYS 100 B CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 B SG CYS 27 B CYS 53 1_555 B SG CYS 92 B CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 B SG CYS 117 B CYS 143 1_555 B SG CYS 159 B CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf7 B SG CYS 138 B CYS 164 1_555 B SG CYS 190 B CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 B SG CYS 241 B CYS 267 1_555 B SG CYS 308 B CYS 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? covale ? covale1 A ND2 ASN 234 A ASN 254 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 279 A ASN 299 1_555 H C1 NAG . A NAG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 B ND2 ASN 37 B ASN 63 1_555 I C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B ND2 ASN 96 B ASN 122 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 B ND2 ASN 112 B ASN 138 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale6 B ND2 ASN 187 B ASN 213 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 sing covale ? covale7 B ND2 ASN 238 B ASN 264 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.639 sing covale ? covale8 C O3 NAG . C NAG 1 1_555 C C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale12 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? metalc ? metalc1 A OE1 GLU 86 A GLU 106 1_555 J ZN ZN . B ZN 412 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.789 ? metalc ? metalc2 A OE2 GLU 86 A GLU 106 1_555 J ZN ZN . B ZN 412 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc3 B OE1 GLU 182 B GLU 208 1_555 L ZN ZN . B ZN 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc4 B OE2 GLU 182 B GLU 208 1_555 L ZN ZN . B ZN 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? metalc ? metalc5 B OD1 ASP 183 B ASP 209 1_555 L ZN ZN . B ZN 414 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc6 B OD2 ASP 183 B ASP 209 1_555 L ZN ZN . B ZN 414 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.812 ? metalc ? metalc7 B NE2 HIS 283 B HIS 309 1_555 L ZN ZN . B ZN 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc8 B NE2 HIS 318 B HIS 344 1_555 J ZN ZN . B ZN 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? # _chem_comp.formula 'Zn 2' _chem_comp.formula_weight 65.409 _chem_comp.id ZN _chem_comp.mon_nstd_flag . _chem_comp.name 'ZINC ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5WY8 _atom_sites.fract_transf_matrix[1][1] 0.009057 _atom_sites.fract_transf_matrix[1][2] 0.005229 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010458 _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] 0.00475 _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 H 6 NAG A 1 1103 1201 NAG NAG . I 6 NAG B 1 403 1301 NAG NAG . J 7 ZN B 1 412 1 ZN ZN . K 7 ZN B 1 413 2 ZN ZN . L 7 ZN B 1 414 3 ZN ZN . M 8 HOH A 1 1201 1 HOH HOH . M 8 HOH A 2 1202 2 HOH HOH . N 8 HOH B 1 501 8 HOH HOH . N 8 HOH B 2 502 5 HOH HOH . N 8 HOH B 3 503 3 HOH HOH . N 8 HOH B 4 504 4 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol ZN _atom_site.label_atom_id ZN _atom_site.label_comp_id ZN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id K _atom_site.label_entity_id 7 _atom_site.Cartn_x -33.864 _atom_site.Cartn_y -16.914 _atom_site.Cartn_z 2.048 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 146.89 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id ZN _atom_site.auth_comp_id ZN _atom_site.auth_seq_id 413 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 1 #