data_5L31 # _model_server_result.job_id 7NaiSTfOAHRCMrr1coFxVA _model_server_result.datetime_utc '2025-07-08 06:20:53' _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 5l31 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":202}' # _entry.id 5L31 # _exptl.entry_id 5L31 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 4 _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 5L31 _cell.length_a 62.594 _cell.length_b 77.534 _cell.length_c 88.063 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L31 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 4 G N N ? 4 I 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 38 A CYS 38 1_555 C SG CYS 38 C CYS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 81 A CYS 81 1_555 D SG CYS 81 D CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf3 A SG CYS 96 A CYS 96 1_555 B SG CYS 96 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf4 B SG CYS 81 B CYS 81 1_555 C SG CYS 81 C CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf5 C SG CYS 96 C CYS 96 1_555 D SG CYS 96 D CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? covale ? covale1 A SG CYS 98 A CYS 98 1_555 E CAB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.684 ? covale ? covale2 A SG CYS 101 A CYS 101 1_555 E CAC HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.7 ? covale ? covale3 B C ALA 37 B ALA 37 1_555 B N CSO 38 B CSO 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale4 B C CSO 38 B CSO 38 1_555 B N ASP 39 B ASP 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? covale ? covale5 B SG CYS 98 B CYS 98 1_555 F CAB HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.662 ? covale ? covale6 B SG CYS 101 B CYS 101 1_555 F CAC HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.668 ? covale ? covale7 C SG CYS 98 C CYS 98 1_555 H CAB HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.637 ? covale ? covale8 C SG CYS 101 C CYS 101 1_555 H CAC HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.675 ? covale ? covale9 D SG CYS 98 D CYS 98 1_555 J CAB HEC . D HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.641 ? covale ? covale10 D SG CYS 101 D CYS 101 1_555 J CAC HEC . D HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.675 ? metalc ? metalc1 A SD MET 7 A MET 7 1_555 E FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc2 A NE2 HIS 102 A HIS 102 1_555 E FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc3 B SD MET 7 B MET 7 1_555 F FE HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc4 B OD1 ASP 50 B ASP 50 1_555 G NA NA . B NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc5 B NE2 HIS 102 B HIS 102 1_555 F FE HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc6 G NA NA . B NA 202 1_555 L O HOH . B HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc7 C OE1 GLU 4 C GLU 4 1_555 I NA NA . C NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? metalc ? metalc8 C SD MET 7 C MET 7 1_555 H FE HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc9 C NE2 HIS 102 C HIS 102 1_555 H FE HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc10 D SD MET 7 D MET 7 1_555 J FE HEC . D HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc11 D NE2 HIS 102 D HIS 102 1_555 J FE HEC . D HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? # _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 5L31 _atom_sites.fract_transf_matrix[1][1] 0.015976 _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] 0.012898 _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] 0.011356 _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 3 HEC A 1 201 150 HEC HEM . F 3 HEC B 1 201 150 HEC HEM . G 4 NA B 1 202 2 NA NA . H 3 HEC C 1 201 150 HEC HEM . I 4 NA C 1 202 1 NA NA . J 3 HEC D 1 201 150 HEC HEM . K 5 HOH A 1 301 34 HOH HOH . K 5 HOH A 2 302 16 HOH HOH . K 5 HOH A 3 303 62 HOH HOH . K 5 HOH A 4 304 32 HOH HOH . K 5 HOH A 5 305 10 HOH HOH . K 5 HOH A 6 306 47 HOH HOH . K 5 HOH A 7 307 50 HOH HOH . K 5 HOH A 8 308 20 HOH HOH . K 5 HOH A 9 309 35 HOH HOH . K 5 HOH A 10 310 56 HOH HOH . K 5 HOH A 11 311 58 HOH HOH . K 5 HOH A 12 312 36 HOH HOH . K 5 HOH A 13 313 1 HOH HOH . K 5 HOH A 14 314 9 HOH HOH . K 5 HOH A 15 315 4 HOH HOH . K 5 HOH A 16 316 52 HOH HOH . K 5 HOH A 17 317 3 HOH HOH . K 5 HOH A 18 318 49 HOH HOH . K 5 HOH A 19 319 5 HOH HOH . K 5 HOH A 20 320 21 HOH HOH . L 5 HOH B 1 301 22 HOH HOH . L 5 HOH B 2 302 48 HOH HOH . L 5 HOH B 3 303 53 HOH HOH . L 5 HOH B 4 304 25 HOH HOH . L 5 HOH B 5 305 19 HOH HOH . L 5 HOH B 6 306 6 HOH HOH . L 5 HOH B 7 307 61 HOH HOH . L 5 HOH B 8 308 7 HOH HOH . L 5 HOH B 9 309 55 HOH HOH . L 5 HOH B 10 310 23 HOH HOH . L 5 HOH B 11 311 39 HOH HOH . L 5 HOH B 12 312 17 HOH HOH . L 5 HOH B 13 313 38 HOH HOH . L 5 HOH B 14 314 54 HOH HOH . L 5 HOH B 15 315 31 HOH HOH . L 5 HOH B 16 316 13 HOH HOH . L 5 HOH B 17 317 11 HOH HOH . L 5 HOH B 18 318 59 HOH HOH . L 5 HOH B 19 319 57 HOH HOH . L 5 HOH B 20 320 42 HOH HOH . L 5 HOH B 21 321 18 HOH HOH . L 5 HOH B 22 322 26 HOH HOH . M 5 HOH C 1 301 40 HOH HOH . M 5 HOH C 2 302 27 HOH HOH . M 5 HOH C 3 303 33 HOH HOH . M 5 HOH C 4 304 46 HOH HOH . M 5 HOH C 5 305 29 HOH HOH . M 5 HOH C 6 306 45 HOH HOH . M 5 HOH C 7 307 2 HOH HOH . M 5 HOH C 8 308 37 HOH HOH . M 5 HOH C 9 309 8 HOH HOH . N 5 HOH D 1 301 63 HOH HOH . N 5 HOH D 2 302 51 HOH HOH . N 5 HOH D 3 303 28 HOH HOH . N 5 HOH D 4 304 12 HOH HOH . N 5 HOH D 5 305 60 HOH HOH . N 5 HOH D 6 306 24 HOH HOH . N 5 HOH D 7 307 15 HOH HOH . N 5 HOH D 8 308 43 HOH HOH . N 5 HOH D 9 309 44 HOH HOH . N 5 HOH D 10 310 41 HOH HOH . N 5 HOH D 11 311 30 HOH HOH . N 5 HOH D 12 312 64 HOH HOH . N 5 HOH D 13 313 14 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 I _atom_site.label_entity_id 4 _atom_site.Cartn_x 28.254 _atom_site.Cartn_y -27.577 _atom_site.Cartn_z 15.649 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 63.58 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 202 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #