data_5VLP # _model_server_result.job_id mj2MlbB4RPdJV8b3_SvB6w _model_server_result.datetime_utc '2025-07-06 15:40:51' _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 5vlp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 5VLP # _exptl.entry_id 5VLP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM 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 90 _cell.angle_gamma 90 _cell.entry_id 5VLP _cell.length_a 110.865 _cell.length_b 142.168 _cell.length_c 239.365 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VLP _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 5 E N N ? 5 F N N # 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 223 A CYS 223 1_555 A SG CYS 255 A CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 323 A CYS 323 1_555 A SG CYS 358 A CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 375 A CYS 375 1_555 A SG CYS 378 A CYS 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf4 A SG CYS 457 A CYS 457 1_555 A SG CYS 527 A CYS 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 477 A CYS 477 1_555 A SG CYS 526 A CYS 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 A SG CYS 486 A CYS 486 1_555 A SG CYS 509 A CYS 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 A SG CYS 534 A CYS 534 1_555 A SG CYS 601 A CYS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf8 A SG CYS 552 A CYS 552 1_555 A SG CYS 600 A CYS 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf9 A SG CYS 562 A CYS 562 1_555 A SG CYS 588 A CYS 588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 A SG CYS 608 A CYS 608 1_555 A SG CYS 679 A CYS 679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf11 A SG CYS 626 A CYS 626 1_555 A SG CYS 678 A CYS 678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 A SG CYS 635 A CYS 635 1_555 A SG CYS 654 A CYS 654 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf13 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf14 B SG CYS 139 H CYS 139 1_555 C SG CYS 214 L CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf15 B SG CYS 151 H CYS 151 1_555 B SG CYS 206 H CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf16 C SG CYS 23 L CYS 23 1_555 C SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf17 C SG CYS 134 L CYS 134 1_555 C SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 D C ACE 1 Z ACE -6 1_555 D N MET 2 Z MET -5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale2 D C VAL 11 Z VAL 4 1_555 D N HRG 12 Z HRG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale3 D C HRG 12 Z HRG 5 1_555 D N ILE 13 Z ILE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A O GLY 106 A GLY 106 1_555 E NA NA . A NA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? metalc ? metalc2 A O ALA 330 A ALA 330 1_555 F NA NA . A NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc3 A OG1 THR 335 A THR 335 1_555 F NA NA . A NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.109 ? metalc ? metalc4 A O CYS 358 A CYS 358 1_555 F NA NA . A NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc5 A OD1 ASP 360 A ASP 360 1_555 F NA NA . A NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc6 A O CYS 552 A CYS 552 1_555 E NA NA . A NA 801 7_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc7 A O GLN 554 A GLN 554 1_555 E NA NA . A NA 801 7_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc8 A O HIS 557 A HIS 557 1_555 E NA NA . A NA 801 7_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5VLP _atom_sites.fract_transf_matrix[1][1] 0.00902 _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] 0.007034 _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] 0.004178 _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 E 5 NA A 1 801 1 NA NA . F 5 NA A 1 802 2 NA NA . G 6 HOH A 1 901 1 HOH HOH . G 6 HOH A 2 902 5 HOH HOH . G 6 HOH A 3 903 2 HOH HOH . H 6 HOH H 1 301 4 HOH HOH . I 6 HOH L 1 301 3 HOH HOH . I 6 HOH L 2 302 6 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id E _atom_site.label_entity_id 5 _atom_site.Cartn_x -36.277 _atom_site.Cartn_y -71.961 _atom_site.Cartn_z -51.537 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 39.19 _atom_site.pdbx_formal_charge 1 _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 801 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #