data_8TOT # _model_server_result.job_id 8oEk-5IQi0aQKFZU-CC8-w _model_server_result.datetime_utc '2025-01-13 16:54:23' _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 8tot # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":701}' # _entry.id 8TOT # _exptl.entry_id 8TOT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 65.409 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ZINC ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 116.93 _cell.angle_gamma 90 _cell.entry_id 8TOT _cell.length_a 111.661 _cell.length_b 89.308 _cell.length_c 118.508 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TOT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,J,K,L,M,T 1 1 B,D,H,I,N,O,P,Q,R,S 2 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 ? 5 J N N ? 5 R N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 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 3 n E NAG 1 E 1 NAG A 712 NAG 3 n E NAG 2 E 2 NAG A 713 NAG 3 n F NAG 1 F 1 NAG A 714 NAG 3 n F NAG 2 F 2 NAG A 715 NAG 3 n G NAG 1 G 1 NAG A 718 NAG 3 n G NAG 2 G 2 NAG A 719 NAG 3 n H NAG 1 H 1 NAG B 629 NAG 3 n H NAG 2 H 2 NAG B 630 NAG 4 n I NAG 1 I 1 NAG B 633 NAG 4 n I NAG 2 I 2 NAG B 634 NAG 4 n I BMA 3 I 3 BMA B 635 BMA # 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 116 A CYS 133 1_555 A SG CYS 124 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf2 A SG CYS 327 A CYS 344 1_555 A SG CYS 344 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 A SG CYS 513 A CYS 530 1_555 A SG CYS 525 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf4 B SG CYS 116 B CYS 133 1_555 B SG CYS 124 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 B SG CYS 327 B CYS 344 1_555 B SG CYS 344 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 B SG CYS 513 B CYS 530 1_555 B SG CYS 525 B CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? covale ? covale1 A ND2 ASN 36 A ASN 53 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.368 ? covale ? covale2 A ND2 ASN 73 A ASN 90 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 A ND2 ASN 86 A ASN 103 1_555 K C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 A ND2 ASN 305 A ASN 322 1_555 L C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale5 A ND2 ASN 529 A ASN 546 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale6 B ND2 ASN 36 B ASN 53 1_555 N C1 NAG . B NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale7 B ND2 ASN 73 B ASN 90 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale8 B ND2 ASN 86 B ASN 103 1_555 O C1 NAG . B NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale9 B ND2 ASN 305 B ASN 322 1_555 P C1 NAG . B NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.567 ? covale ? covale10 B ND2 ASN 415 B ASN 432 1_555 Q C1 NAG . B NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale11 B ND2 ASN 529 B ASN 546 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale12 C C ACE 1 C ACE 0 1_555 C N TYR 2 C TYR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale13 C C CYS 14 C CYS 13 1_555 C N NH2 15 C NH2 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale14 D C ACE 1 D ACE 0 1_555 D N TYR 2 D TYR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale15 D C CYS 14 D CYS 13 1_555 D N NH2 15 D NH2 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale16 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale17 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale18 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale19 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale20 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale21 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? metalc ? metalc1 A NE2 HIS 357 A HIS 374 1_555 J ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc2 A NE2 HIS 361 A HIS 378 1_555 J ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc3 A OE1 GLU 385 A GLU 402 1_555 J ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc4 A OE2 GLU 385 A GLU 402 1_555 J ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc5 B NE2 HIS 357 B HIS 374 1_555 R ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc6 B OE2 GLU 358 B GLU 375 1_555 R ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc7 B NE2 HIS 361 B HIS 378 1_555 R ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc8 B OE2 GLU 385 B GLU 402 1_555 R ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? # _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 8TOT _atom_sites.fract_transf_matrix[1][1] 0.008956 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004549 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011197 _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] 0.009465 _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 J 5 ZN A 1 701 701 ZN ZN . K 6 NAG A 1 702 716 NAG NAG . L 6 NAG A 1 703 717 NAG NAG . M 7 CL A 1 704 2 CL CL . N 6 NAG B 1 701 628 NAG NAG . O 6 NAG B 1 702 632 NAG NAG . P 6 NAG B 1 703 637 NAG NAG . Q 6 NAG B 1 704 638 NAG NAG . R 5 ZN B 1 705 7 ZN ZN . S 7 CL B 1 706 1 CL CL . T 8 HOH A 1 801 1 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 J _atom_site.label_entity_id 5 _atom_site.Cartn_x 24.199 _atom_site.Cartn_y -3.046 _atom_site.Cartn_z 8.486 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 114.11 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id ZN _atom_site.auth_comp_id ZN _atom_site.auth_seq_id 701 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #