data_5KXI # _model_server_result.job_id V8cGqRk514ujwxp-ZBDvPQ _model_server_result.datetime_utc '2024-11-21 10:32:24' _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 5kxi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":403}' # _entry.id 5KXI # _exptl.entry_id 5KXI _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 1 _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 5KXI _cell.length_a 127.099 _cell.length_b 132.633 _cell.length_c 202.44 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KXI _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 PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,O,P,Q,R _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 135 A CYS 135 1_555 A SG CYS 149 A CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 199 A CYS 199 1_555 A SG CYS 200 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 B SG CYS 130 B CYS 130 1_555 B SG CYS 144 B CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 C SG CYS 130 C CYS 130 1_555 C SG CYS 144 C CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 D SG CYS 135 D CYS 135 1_555 D SG CYS 149 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 D SG CYS 199 D CYS 199 1_555 D SG CYS 200 D CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf7 E SG CYS 130 E CYS 130 1_555 E SG CYS 144 E CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 148 A ASN 148 1_555 F C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 B ND2 ASN 143 B ASN 143 1_555 I C1 NAG . B NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 C ND2 ASN 143 C ASN 143 1_555 J C1 NAG . C NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 D ND2 ASN 148 D ASN 148 1_555 K C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 E ND2 ASN 143 E ASN 143 1_555 M C1 NAG . E NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 H NA NA . A NA 403 1_555 N O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc2 H NA NA . A NA 403 1_555 O O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc3 H NA NA . A NA 403 1_555 P O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc4 H NA NA . A NA 403 1_555 Q O HOH . D HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc5 H NA NA . A NA 403 1_555 R O HOH . E HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? # _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 5KXI _atom_sites.fract_transf_matrix[1][1] 0.007868 _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] 0.00754 _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] 0.00494 _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 F 3 NAG A 1 401 500 NAG NAG . G 4 NCT A 1 402 600 NCT NCT . H 5 NA A 1 403 1 NA NA . I 3 NAG B 1 500 500 NAG NAG . J 3 NAG C 1 500 500 NAG NAG . K 3 NAG D 1 401 500 NAG NAG . L 4 NCT D 1 402 600 NCT NCT . M 3 NAG E 1 500 500 NAG NAG . N 6 HOH A 1 501 2 HOH HOH . O 6 HOH B 1 601 3 HOH HOH . P 6 HOH C 1 601 4 HOH HOH . Q 6 HOH D 1 501 5 HOH HOH . R 6 HOH E 1 601 1 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 H _atom_site.label_entity_id 5 _atom_site.Cartn_x 19.642 _atom_site.Cartn_y -2.034 _atom_site.Cartn_z -12.031 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 84.19 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 403 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 55 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #