data_2V5Y # _model_server_result.job_id jmCvVVIbpnuiK0GxyvfZvQ _model_server_result.datetime_utc '2024-11-25 19:12:50' _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 2v5y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1576}' # _entry.id 2V5Y # _exptl.entry_id 2V5Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _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 113.52 _cell.angle_gamma 90 _cell.entry_id 2V5Y _cell.length_a 167.336 _cell.length_b 69.325 _cell.length_c 97.487 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2V5Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_755 -x+2,y,-z -1 0 0 0 1 0 0 0 -1 334.672 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 J 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 7 A CYS 7 1_555 A SG CYS 16 A CYS 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 76 A CYS 76 1_555 A SG CYS 162 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 186 A CYS 186 1_555 A SG CYS 240 A CYS 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 A SG CYS 356 A CYS 356 1_555 A SG CYS 390 A CYS 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 52 A ASN 52 1_555 E C1 NAG . A NAG 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 72 A ASN 72 1_555 C C1 NAG . A NAG 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 111 A ASN 111 1_555 D C1 NAG . A NAG 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 A ND2 ASN 386 A ASN 386 1_555 B C1 NAG . A NAG 1569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 A ND2 ASN 394 A ASN 394 1_555 G C1 NAG . A NAG 1574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 A ND2 ASN 434 A ASN 434 1_555 F C1 NAG . A NAG 1573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 A ND2 ASN 524 A ASN 524 1_555 H C1 NAG . A NAG 1575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? metalc ? metalc1 A OD1 ASP 24 A ASP 24 1_555 I NA NA . A NA 1576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc2 A OD1 ASN 27 A ASN 27 1_555 I NA NA . A NA 1576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc3 A OD1 ASP 153 A ASP 153 1_555 J NA NA . A NA 1577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? # _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 2V5Y _atom_sites.fract_transf_matrix[1][1] 0.005976 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002601 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014425 _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] 0.011187 _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 B 2 NAG A 1 1569 1569 NAG NAG . C 2 NAG A 1 1570 1570 NAG NAG . D 2 NAG A 1 1571 1571 NAG NAG . E 2 NAG A 1 1572 1572 NAG NAG . F 2 NAG A 1 1573 1573 NAG NAG . G 2 NAG A 1 1574 1574 NAG NAG . H 2 NAG A 1 1575 1575 NAG NAG . I 3 NA A 1 1576 1576 NA NA . J 3 NA A 1 1577 1577 NA NA . # _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 3 _atom_site.Cartn_x 214.956 _atom_site.Cartn_y 77.535 _atom_site.Cartn_z 18.181 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 39.02 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1576 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 357 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #