data_2IYD # _entry.id 2IYD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2IYD PDBE EBI-29390 WWPDB D_1290029390 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 2CKG unspecified 'THE STRUCTURE OF SENP1 SUMO-2 CO-COMPLEX SUGGESTS A STRUCTURAL BASIS FOR DISCRIMINATION BETWEEN SUMO PARALOGUES DURING PROCESSING' PDB 2CKH unspecified 'SENP1-SUMO2 COMPLEX' PDB 1WM2 unspecified 'CRYSTAL STRUCTURE OF HUMAN SUMO-2 PROTEIN' PDB 1WM3 unspecified 'CRYSTAL STRUCTURE OF HUMAN SUMO-2 PROTEIN' PDB 1WZ0 unspecified 'SOLUTION STRUCTURE OF HUMAN SUMO-2 (SMT3B ), A UBIQUITIN-LIKE PROTEIN' PDB 2IY0 unspecified 'SENP1 (MUTANT) SUMO1 RANGAP' PDB 2IY1 unspecified 'SENP1 (MUTANT) FULL LENGTH SUMO1' PDB 2IYC unspecified 'SENP1 NATIVE STRUCTURE' PDB 2D07 unspecified 'CRYSTAL STRUCTURE OF SUMO-3-MODIFIED THYMINE -DNA GLYCOSYLASE' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2IYD _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2006-07-14 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Dong, C.' 1 'Naismith, J.H.' 2 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Senp1 Native Structure' 'To be Published' ? ? ? ? ? ? ? 0353 ? ? ? 1 'The Structure of Senp1 Sumo-2 Co-Complex Suggests a Structural Basis for Discrimination between Sumo Paralogues During Processing' Biochem.J. 397 279 ? 2006 BIJOAK UK 0264-6021 0043 ? 16553580 10.1042/BJ20052030 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Dong, C.' 1 primary 'Naismith, J.H.' 2 1 'Shen, L.' 3 1 'Dong, C.' 4 1 'Liu, H.' 5 1 'Naismith, J.H.' 6 1 'Hay, R.T.' 7 # _cell.entry_id 2IYD _cell.length_a 143.376 _cell.length_b 143.376 _cell.length_c 71.886 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2IYD _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'SENTRIN-SPECIFIC PROTEASE 1' 26932.211 1 3.4.22.- ? 'CATALYTIC FRAGMENT, RESIDUES 419-643' ? 2 polymer man 'SMALL UBIQUITIN-RELATED MODIFIER 2' 9325.474 1 ? ? 'CATALYTIC FRAGMENT, RESIDUES 15-95' ? # loop_ _entity_name_com.entity_id _entity_name_com.name 1 'SENP1, SENTRIN/SUMO-SPECIFIC PROTEASE SENP1' 2 'SUMO2, UBIQUITIN-LIKE PROTEIN SMT3B, SMT3 HOMOLOG 2, SENTRIN-2, HSMT3, SUMO-2' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ;EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFF TKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKE FDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL ; ;EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFF TKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKE FDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL ; A ? 2 'polypeptide(L)' no no ;NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGV Y ; ;NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGV Y ; B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLU n 1 2 PHE n 1 3 PRO n 1 4 GLU n 1 5 ILE n 1 6 THR n 1 7 GLU n 1 8 GLU n 1 9 MET n 1 10 GLU n 1 11 LYS n 1 12 GLU n 1 13 ILE n 1 14 LYS n 1 15 ASN n 1 16 VAL n 1 17 PHE n 1 18 ARG n 1 19 ASN n 1 20 GLY n 1 21 ASN n 1 22 GLN n 1 23 ASP n 1 24 GLU n 1 25 VAL n 1 26 LEU n 1 27 SER n 1 28 GLU n 1 29 ALA n 1 30 PHE n 1 31 ARG n 1 32 LEU n 1 33 THR n 1 34 ILE n 1 35 THR n 1 36 ARG n 1 37 LYS n 1 38 ASP n 1 39 ILE n 1 40 GLN n 1 41 THR n 1 42 LEU n 1 43 ASN n 1 44 HIS n 1 45 LEU n 1 46 ASN n 1 47 TRP n 1 48 LEU n 1 49 ASN n 1 50 ASP n 1 51 GLU n 1 52 ILE n 1 53 ILE n 1 54 ASN n 1 55 PHE n 1 56 TYR n 1 57 MET n 1 58 ASN n 1 59 MET n 1 60 LEU n 1 61 MET n 1 62 GLU n 1 63 ARG n 1 64 SER n 1 65 LYS n 1 66 GLU n 1 67 LYS n 1 68 GLY n 1 69 LEU n 1 70 PRO n 1 71 SER n 1 72 VAL n 1 73 HIS n 1 74 ALA n 1 75 PHE n 1 76 ASN n 1 77 THR n 1 78 PHE n 1 79 PHE n 1 80 PHE n 1 81 THR n 1 82 LYS n 1 83 LEU n 1 84 LYS n 1 85 THR n 1 86 ALA n 1 87 GLY n 1 88 TYR n 1 89 GLN n 1 90 ALA n 1 91 VAL n 1 92 LYS n 1 93 ARG n 1 94 TRP n 1 95 THR n 1 96 LYS n 1 97 LYS n 1 98 VAL n 1 99 ASP n 1 100 VAL n 1 101 PHE n 1 102 SER n 1 103 VAL n 1 104 ASP n 1 105 ILE n 1 106 LEU n 1 107 LEU n 1 108 VAL n 1 109 PRO n 1 110 ILE n 1 111 HIS n 1 112 LEU n 1 113 GLY n 1 114 VAL n 1 115 HIS n 1 116 TRP n 1 117 CYS n 1 118 LEU n 1 119 ALA n 1 120 VAL n 1 121 VAL n 1 122 ASP n 1 123 PHE n 1 124 ARG n 1 125 LYS n 1 126 LYS n 1 127 ASN n 1 128 ILE n 1 129 THR n 1 130 TYR n 1 131 TYR n 1 132 ASP n 1 133 SER n 1 134 MET n 1 135 GLY n 1 136 GLY n 1 137 ILE n 1 138 ASN n 1 139 ASN n 1 140 GLU n 1 141 ALA n 1 142 CYS n 1 143 ARG n 1 144 ILE n 1 145 LEU n 1 146 LEU n 1 147 GLN n 1 148 TYR n 1 149 LEU n 1 150 LYS n 1 151 GLN n 1 152 GLU n 1 153 SER n 1 154 ILE n 1 155 ASP n 1 156 LYS n 1 157 LYS n 1 158 ARG n 1 159 LYS n 1 160 GLU n 1 161 PHE n 1 162 ASP n 1 163 THR n 1 164 ASN n 1 165 GLY n 1 166 TRP n 1 167 GLN n 1 168 LEU n 1 169 PHE n 1 170 SER n 1 171 LYS n 1 172 LYS n 1 173 SER n 1 174 GLN n 1 175 GLU n 1 176 ILE n 1 177 PRO n 1 178 GLN n 1 179 GLN n 1 180 MET n 1 181 ASN n 1 182 GLY n 1 183 SER n 1 184 ASP n 1 185 CYS n 1 186 GLY n 1 187 MET n 1 188 PHE n 1 189 ALA n 1 190 CYS n 1 191 LYS n 1 192 TYR n 1 193 ALA n 1 194 ASP n 1 195 CYS n 1 196 ILE n 1 197 THR n 1 198 LYS n 1 199 ASP n 1 200 ARG n 1 201 PRO n 1 202 ILE n 1 203 ASN n 1 204 PHE n 1 205 THR n 1 206 GLN n 1 207 GLN n 1 208 HIS n 1 209 MET n 1 210 PRO n 1 211 TYR n 1 212 PHE n 1 213 ARG n 1 214 LYS n 1 215 ARG n 1 216 MET n 1 217 VAL n 1 218 TRP n 1 219 GLU n 1 220 ILE n 1 221 LEU n 1 222 HIS n 1 223 ARG n 1 224 LYS n 1 225 LEU n 1 226 LEU n 2 1 ASN n 2 2 ASP n 2 3 HIS n 2 4 ILE n 2 5 ASN n 2 6 LEU n 2 7 LYS n 2 8 VAL n 2 9 ALA n 2 10 GLY n 2 11 GLN n 2 12 ASP n 2 13 GLY n 2 14 SER n 2 15 VAL n 2 16 VAL n 2 17 GLN n 2 18 PHE n 2 19 LYS n 2 20 ILE n 2 21 LYS n 2 22 ARG n 2 23 HIS n 2 24 THR n 2 25 PRO n 2 26 LEU n 2 27 SER n 2 28 LYS n 2 29 LEU n 2 30 MET n 2 31 LYS n 2 32 ALA n 2 33 TYR n 2 34 CYS n 2 35 GLU n 2 36 ARG n 2 37 GLN n 2 38 GLY n 2 39 LEU n 2 40 SER n 2 41 MET n 2 42 ARG n 2 43 GLN n 2 44 ILE n 2 45 ARG n 2 46 PHE n 2 47 ARG n 2 48 PHE n 2 49 ASP n 2 50 GLY n 2 51 GLN n 2 52 PRO n 2 53 ILE n 2 54 ASN n 2 55 GLU n 2 56 THR n 2 57 ASP n 2 58 THR n 2 59 PRO n 2 60 ALA n 2 61 GLN n 2 62 LEU n 2 63 GLU n 2 64 MET n 2 65 GLU n 2 66 ASP n 2 67 GLU n 2 68 ASP n 2 69 THR n 2 70 ILE n 2 71 ASP n 2 72 VAL n 2 73 PHE n 2 74 GLN n 2 75 GLN n 2 76 GLN n 2 77 THR n 2 78 GLY n 2 79 GLY n 2 80 VAL n 2 81 TYR n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_variant _entity_src_gen.pdbx_gene_src_cell_line _entity_src_gen.pdbx_gene_src_atcc _entity_src_gen.pdbx_gene_src_organ _entity_src_gen.pdbx_gene_src_organelle _entity_src_gen.pdbx_gene_src_cell _entity_src_gen.pdbx_gene_src_cellular_location _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.host_org_genus _entity_src_gen.pdbx_host_org_gene _entity_src_gen.pdbx_host_org_organ _entity_src_gen.host_org_species _entity_src_gen.pdbx_host_org_tissue _entity_src_gen.pdbx_host_org_tissue_fraction _entity_src_gen.pdbx_host_org_strain _entity_src_gen.pdbx_host_org_variant _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_atcc _entity_src_gen.pdbx_host_org_culture_collection _entity_src_gen.pdbx_host_org_cell _entity_src_gen.pdbx_host_org_organelle _entity_src_gen.pdbx_host_org_cellular_location _entity_src_gen.pdbx_host_org_vector_type _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample ? ? ? HUMAN ? ? ? ? ? ? ? ? 'HOMO SAPIENS' 9606 ? ? ? ? ? ? ? ? 'ESCHERICHIA COLI' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample ? ? ? HUMAN ? ? ? ? ? ? ? ? 'HOMO SAPIENS' 9606 ? ? ? ? ? ? ? ? 'ESCHERICHIA COLI' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 UNP SENP1_HUMAN 1 ? ? Q9P0U3 ? 2 PDB 2IYD 1 ? ? 2IYD ? 3 UNP SUMO2_HUMAN 2 ? ? P61956 ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2IYD A 1 ? 174 ? Q9P0U3 419 ? 592 ? 419 592 2 2 2IYD A 175 ? 175 ? 2IYD 593 ? 593 ? 593 593 3 1 2IYD A 176 ? 226 ? Q9P0U3 593 ? 643 ? 594 644 4 3 2IYD B 1 ? 81 ? P61956 15 ? 95 ? 14 94 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2IYD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 6.04 _exptl_crystal.density_percent_sol 79.46 _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.933 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SRS BEAMLINE PX14.1' _diffrn_source.pdbx_synchrotron_site SRS _diffrn_source.pdbx_synchrotron_beamline PX14.1 _diffrn_source.pdbx_wavelength 0.933 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2IYD _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 120.000 _reflns.d_resolution_high 3.200 _reflns.number_obs 13469 _reflns.number_all ? _reflns.percent_possible_obs 100.0 _reflns.pdbx_Rmerge_I_obs 0.09000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 19.0000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.000 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 3.20 _reflns_shell.d_res_low 3.30 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.44000 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.000 _reflns_shell.pdbx_redundancy 8.00 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2IYD _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.ls_number_reflns_obs 13468 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 46.98 _refine.ls_d_res_high 3.20 _refine.ls_percent_reflns_obs 99.0 _refine.ls_R_factor_obs 0.273 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.272 _refine.ls_R_factor_R_free 0.288 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 714 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.926 _refine.correlation_coeff_Fo_to_Fc_free 0.913 _refine.B_iso_mean 107.26 _refine.aniso_B[1][1] 0.09000 _refine.aniso_B[2][2] 0.09000 _refine.aniso_B[3][3] -0.13000 _refine.aniso_B[1][2] 0.04000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY AN OVERALL B FACTOR REFINED THIS REPLACES PREVIOUS ENTRY WHICH HAD SEQUENCE CONFLICTS. THERE IS COVALENT LINK BETWEEN CYS A 603 (SENP1) AND GLY B 92 (SUMO) THE DICTIONARY IS INCLUDED IN ENTRY ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.581 _refine.pdbx_overall_ESU_R_Free 0.407 _refine.overall_SU_ML 0.378 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 54.553 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 2524 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 2524 _refine_hist.d_res_high 3.20 _refine_hist.d_res_low 46.98 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.008 0.022 ? 2577 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.081 1.942 ? 3462 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.353 5.000 ? 303 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 39.261 24.519 ? 135 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 20.814 15.000 ? 495 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 13.993 15.000 ? 17 'X-RAY DIFFRACTION' ? r_chiral_restr 0.077 0.200 ? 368 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.003 0.020 ? 1944 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.231 0.200 ? 1386 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.309 0.200 ? 1767 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.147 0.200 ? 94 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.240 0.200 ? 23 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.170 0.200 ? 4 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 3.20 _refine_ls_shell.d_res_low 3.28 _refine_ls_shell.number_reflns_R_work 1006 _refine_ls_shell.R_factor_R_work 0.3530 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.3520 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 52 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2IYD _struct.title 'SENP1 covalent complex with SUMO-2' _struct.pdbx_descriptor 'SENTRIN-SPECIFIC PROTEASE 1 (E.C.3.4.22.-), SMALL UBIQUITIN-RELATED MODIFIER 2' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2IYD _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'PROTEASE, HYDROLASE, THIOL PROTEASE, NUCLEAR PROTEIN, UBL CONJUGATION PATHWAY' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 THR A 6 ? ARG A 18 ? THR A 424 ARG A 436 1 ? 13 HELX_P HELX_P2 2 ARG A 36 ? THR A 41 ? ARG A 454 THR A 459 1 ? 6 HELX_P HELX_P3 3 ASN A 49 ? ARG A 63 ? ASN A 467 ARG A 481 1 ? 15 HELX_P HELX_P4 4 PHE A 78 ? GLY A 87 ? PHE A 496 GLY A 505 1 ? 10 HELX_P HELX_P5 5 GLY A 87 ? LYS A 92 ? GLY A 505 LYS A 510 1 ? 6 HELX_P HELX_P6 6 ARG A 93 ? LYS A 96 ? ARG A 511 LYS A 514 5 ? 4 HELX_P HELX_P7 7 ASN A 138 ? LYS A 157 ? ASN A 556 LYS A 575 1 ? 20 HELX_P HELX_P8 8 ASP A 184 ? LYS A 198 ? ASP A 602 LYS A 616 1 ? 15 HELX_P HELX_P9 9 HIS A 208 ? ARG A 223 ? HIS A 626 ARG A 641 1 ? 16 HELX_P HELX_P10 10 LEU B 26 ? ARG B 36 ? LEU B 39 ARG B 49 1 ? 11 HELX_P HELX_P11 11 PRO B 59 ? GLU B 63 ? PRO B 72 GLU B 76 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 2 ? AB ? 5 ? BA ? 5 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA 1 2 ? anti-parallel AB 1 2 ? parallel AB 2 3 ? anti-parallel AB 3 4 ? anti-parallel AB 4 5 ? parallel BA 1 2 ? anti-parallel BA 2 3 ? parallel BA 3 4 ? anti-parallel BA 4 5 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA 1 VAL A 25 ? ALA A 29 ? VAL A 443 ALA A 447 AA 2 LEU A 32 ? THR A 35 ? LEU A 450 THR A 453 AB 1 VAL A 72 ? ALA A 74 ? VAL A 490 ALA A 492 AB 2 ILE A 105 ? LEU A 112 ? ILE A 523 LEU A 530 AB 3 HIS A 115 ? ASP A 122 ? HIS A 533 ASP A 540 AB 4 ASN A 127 ? TYR A 131 ? ASN A 545 TYR A 549 AB 5 GLN A 167 ? SER A 170 ? GLN A 585 SER A 588 BA 1 SER B 14 ? LYS B 21 ? SER B 27 LYS B 34 BA 2 HIS B 3 ? GLY B 10 ? HIS B 16 GLY B 23 BA 3 ASP B 68 ? GLN B 74 ? ASP B 81 GLN B 87 BA 4 ILE B 44 ? PHE B 48 ? ILE B 57 PHE B 61 BA 5 GLN B 51 ? PRO B 52 ? GLN B 64 PRO B 65 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA 1 2 N ALA A 29 ? N ALA A 447 O LEU A 32 ? O LEU A 450 AB 1 2 N HIS A 73 ? N HIS A 491 O ILE A 105 ? O ILE A 523 AB 2 3 N LEU A 112 ? N LEU A 530 O HIS A 115 ? O HIS A 533 AB 3 4 N ASP A 122 ? N ASP A 540 O ASN A 127 ? O ASN A 545 AB 4 5 N ILE A 128 ? N ILE A 546 O GLN A 167 ? O GLN A 585 BA 1 2 N ILE B 20 ? N ILE B 33 O ILE B 4 ? O ILE B 17 BA 2 3 N LYS B 7 ? N LYS B 20 O ASP B 68 ? O ASP B 81 BA 3 4 N PHE B 73 ? N PHE B 86 O ARG B 45 ? O ARG B 58 BA 4 5 N PHE B 48 ? N PHE B 61 O GLN B 51 ? O GLN B 64 # _database_PDB_matrix.entry_id 2IYD _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2IYD _atom_sites.fract_transf_matrix[1][1] 0.006975 _atom_sites.fract_transf_matrix[1][2] 0.004027 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.008054 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.013911 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLU 1 419 419 GLU GLU A . n A 1 2 PHE 2 420 420 PHE PHE A . n A 1 3 PRO 3 421 421 PRO PRO A . n A 1 4 GLU 4 422 422 GLU GLU A . n A 1 5 ILE 5 423 423 ILE ILE A . n A 1 6 THR 6 424 424 THR THR A . n A 1 7 GLU 7 425 425 GLU GLU A . n A 1 8 GLU 8 426 426 GLU GLU A . n A 1 9 MET 9 427 427 MET MET A . n A 1 10 GLU 10 428 428 GLU GLU A . n A 1 11 LYS 11 429 429 LYS LYS A . n A 1 12 GLU 12 430 430 GLU GLU A . n A 1 13 ILE 13 431 431 ILE ILE A . n A 1 14 LYS 14 432 432 LYS LYS A . n A 1 15 ASN 15 433 433 ASN ASN A . n A 1 16 VAL 16 434 434 VAL VAL A . n A 1 17 PHE 17 435 435 PHE PHE A . n A 1 18 ARG 18 436 436 ARG ARG A . n A 1 19 ASN 19 437 437 ASN ASN A . n A 1 20 GLY 20 438 438 GLY GLY A . n A 1 21 ASN 21 439 439 ASN ASN A . n A 1 22 GLN 22 440 440 GLN GLN A . n A 1 23 ASP 23 441 441 ASP ASP A . n A 1 24 GLU 24 442 442 GLU GLU A . n A 1 25 VAL 25 443 443 VAL VAL A . n A 1 26 LEU 26 444 444 LEU LEU A . n A 1 27 SER 27 445 445 SER SER A . n A 1 28 GLU 28 446 446 GLU GLU A . n A 1 29 ALA 29 447 447 ALA ALA A . n A 1 30 PHE 30 448 448 PHE PHE A . n A 1 31 ARG 31 449 449 ARG ARG A . n A 1 32 LEU 32 450 450 LEU LEU A . n A 1 33 THR 33 451 451 THR THR A . n A 1 34 ILE 34 452 452 ILE ILE A . n A 1 35 THR 35 453 453 THR THR A . n A 1 36 ARG 36 454 454 ARG ARG A . n A 1 37 LYS 37 455 455 LYS LYS A . n A 1 38 ASP 38 456 456 ASP ASP A . n A 1 39 ILE 39 457 457 ILE ILE A . n A 1 40 GLN 40 458 458 GLN GLN A . n A 1 41 THR 41 459 459 THR THR A . n A 1 42 LEU 42 460 460 LEU LEU A . n A 1 43 ASN 43 461 461 ASN ASN A . n A 1 44 HIS 44 462 462 HIS HIS A . n A 1 45 LEU 45 463 463 LEU LEU A . n A 1 46 ASN 46 464 464 ASN ASN A . n A 1 47 TRP 47 465 465 TRP TRP A . n A 1 48 LEU 48 466 466 LEU LEU A . n A 1 49 ASN 49 467 467 ASN ASN A . n A 1 50 ASP 50 468 468 ASP ASP A . n A 1 51 GLU 51 469 469 GLU GLU A . n A 1 52 ILE 52 470 470 ILE ILE A . n A 1 53 ILE 53 471 471 ILE ILE A . n A 1 54 ASN 54 472 472 ASN ASN A . n A 1 55 PHE 55 473 473 PHE PHE A . n A 1 56 TYR 56 474 474 TYR TYR A . n A 1 57 MET 57 475 475 MET MET A . n A 1 58 ASN 58 476 476 ASN ASN A . n A 1 59 MET 59 477 477 MET MET A . n A 1 60 LEU 60 478 478 LEU LEU A . n A 1 61 MET 61 479 479 MET MET A . n A 1 62 GLU 62 480 480 GLU GLU A . n A 1 63 ARG 63 481 481 ARG ARG A . n A 1 64 SER 64 482 482 SER SER A . n A 1 65 LYS 65 483 483 LYS LYS A . n A 1 66 GLU 66 484 484 GLU GLU A . n A 1 67 LYS 67 485 485 LYS LYS A . n A 1 68 GLY 68 486 486 GLY GLY A . n A 1 69 LEU 69 487 487 LEU LEU A . n A 1 70 PRO 70 488 488 PRO PRO A . n A 1 71 SER 71 489 489 SER SER A . n A 1 72 VAL 72 490 490 VAL VAL A . n A 1 73 HIS 73 491 491 HIS HIS A . n A 1 74 ALA 74 492 492 ALA ALA A . n A 1 75 PHE 75 493 493 PHE PHE A . n A 1 76 ASN 76 494 494 ASN ASN A . n A 1 77 THR 77 495 495 THR THR A . n A 1 78 PHE 78 496 496 PHE PHE A . n A 1 79 PHE 79 497 497 PHE PHE A . n A 1 80 PHE 80 498 498 PHE PHE A . n A 1 81 THR 81 499 499 THR THR A . n A 1 82 LYS 82 500 500 LYS LYS A . n A 1 83 LEU 83 501 501 LEU LEU A . n A 1 84 LYS 84 502 502 LYS LYS A . n A 1 85 THR 85 503 503 THR THR A . n A 1 86 ALA 86 504 504 ALA ALA A . n A 1 87 GLY 87 505 505 GLY GLY A . n A 1 88 TYR 88 506 506 TYR TYR A . n A 1 89 GLN 89 507 507 GLN GLN A . n A 1 90 ALA 90 508 508 ALA ALA A . n A 1 91 VAL 91 509 509 VAL VAL A . n A 1 92 LYS 92 510 510 LYS LYS A . n A 1 93 ARG 93 511 511 ARG ARG A . n A 1 94 TRP 94 512 512 TRP TRP A . n A 1 95 THR 95 513 513 THR THR A . n A 1 96 LYS 96 514 514 LYS LYS A . n A 1 97 LYS 97 515 515 LYS LYS A . n A 1 98 VAL 98 516 516 VAL VAL A . n A 1 99 ASP 99 517 517 ASP ASP A . n A 1 100 VAL 100 518 518 VAL VAL A . n A 1 101 PHE 101 519 519 PHE PHE A . n A 1 102 SER 102 520 520 SER SER A . n A 1 103 VAL 103 521 521 VAL VAL A . n A 1 104 ASP 104 522 522 ASP ASP A . n A 1 105 ILE 105 523 523 ILE ILE A . n A 1 106 LEU 106 524 524 LEU LEU A . n A 1 107 LEU 107 525 525 LEU LEU A . n A 1 108 VAL 108 526 526 VAL VAL A . n A 1 109 PRO 109 527 527 PRO PRO A . n A 1 110 ILE 110 528 528 ILE ILE A . n A 1 111 HIS 111 529 529 HIS HIS A . n A 1 112 LEU 112 530 530 LEU LEU A . n A 1 113 GLY 113 531 531 GLY GLY A . n A 1 114 VAL 114 532 532 VAL VAL A . n A 1 115 HIS 115 533 533 HIS HIS A . n A 1 116 TRP 116 534 534 TRP TRP A . n A 1 117 CYS 117 535 535 CYS CYS A . n A 1 118 LEU 118 536 536 LEU LEU A . n A 1 119 ALA 119 537 537 ALA ALA A . n A 1 120 VAL 120 538 538 VAL VAL A . n A 1 121 VAL 121 539 539 VAL VAL A . n A 1 122 ASP 122 540 540 ASP ASP A . n A 1 123 PHE 123 541 541 PHE PHE A . n A 1 124 ARG 124 542 542 ARG ARG A . n A 1 125 LYS 125 543 543 LYS LYS A . n A 1 126 LYS 126 544 544 LYS LYS A . n A 1 127 ASN 127 545 545 ASN ASN A . n A 1 128 ILE 128 546 546 ILE ILE A . n A 1 129 THR 129 547 547 THR THR A . n A 1 130 TYR 130 548 548 TYR TYR A . n A 1 131 TYR 131 549 549 TYR TYR A . n A 1 132 ASP 132 550 550 ASP ASP A . n A 1 133 SER 133 551 551 SER SER A . n A 1 134 MET 134 552 552 MET MET A . n A 1 135 GLY 135 553 553 GLY GLY A . n A 1 136 GLY 136 554 554 GLY GLY A . n A 1 137 ILE 137 555 555 ILE ILE A . n A 1 138 ASN 138 556 556 ASN ASN A . n A 1 139 ASN 139 557 557 ASN ASN A . n A 1 140 GLU 140 558 558 GLU GLU A . n A 1 141 ALA 141 559 559 ALA ALA A . n A 1 142 CYS 142 560 560 CYS CYS A . n A 1 143 ARG 143 561 561 ARG ARG A . n A 1 144 ILE 144 562 562 ILE ILE A . n A 1 145 LEU 145 563 563 LEU LEU A . n A 1 146 LEU 146 564 564 LEU LEU A . n A 1 147 GLN 147 565 565 GLN GLN A . n A 1 148 TYR 148 566 566 TYR TYR A . n A 1 149 LEU 149 567 567 LEU LEU A . n A 1 150 LYS 150 568 568 LYS LYS A . n A 1 151 GLN 151 569 569 GLN GLN A . n A 1 152 GLU 152 570 570 GLU GLU A . n A 1 153 SER 153 571 571 SER SER A . n A 1 154 ILE 154 572 572 ILE ILE A . n A 1 155 ASP 155 573 573 ASP ASP A . n A 1 156 LYS 156 574 574 LYS LYS A . n A 1 157 LYS 157 575 575 LYS LYS A . n A 1 158 ARG 158 576 576 ARG ARG A . n A 1 159 LYS 159 577 577 LYS LYS A . n A 1 160 GLU 160 578 578 GLU GLU A . n A 1 161 PHE 161 579 579 PHE PHE A . n A 1 162 ASP 162 580 580 ASP ASP A . n A 1 163 THR 163 581 581 THR THR A . n A 1 164 ASN 164 582 582 ASN ASN A . n A 1 165 GLY 165 583 583 GLY GLY A . n A 1 166 TRP 166 584 584 TRP TRP A . n A 1 167 GLN 167 585 585 GLN GLN A . n A 1 168 LEU 168 586 586 LEU LEU A . n A 1 169 PHE 169 587 587 PHE PHE A . n A 1 170 SER 170 588 588 SER SER A . n A 1 171 LYS 171 589 589 LYS LYS A . n A 1 172 LYS 172 590 590 LYS LYS A . n A 1 173 SER 173 591 591 SER SER A . n A 1 174 GLN 174 592 592 GLN GLN A . n A 1 175 GLU 175 593 593 GLU GLU A . n A 1 176 ILE 176 594 594 ILE ILE A . n A 1 177 PRO 177 595 595 PRO PRO A . n A 1 178 GLN 178 596 596 GLN GLN A . n A 1 179 GLN 179 597 597 GLN GLN A . n A 1 180 MET 180 598 598 MET MET A . n A 1 181 ASN 181 599 599 ASN ASN A . n A 1 182 GLY 182 600 600 GLY GLY A . n A 1 183 SER 183 601 601 SER SER A . n A 1 184 ASP 184 602 602 ASP ASP A . n A 1 185 CYS 185 603 603 CYS CYS A . n A 1 186 GLY 186 604 604 GLY GLY A . n A 1 187 MET 187 605 605 MET MET A . n A 1 188 PHE 188 606 606 PHE PHE A . n A 1 189 ALA 189 607 607 ALA ALA A . n A 1 190 CYS 190 608 608 CYS CYS A . n A 1 191 LYS 191 609 609 LYS LYS A . n A 1 192 TYR 192 610 610 TYR TYR A . n A 1 193 ALA 193 611 611 ALA ALA A . n A 1 194 ASP 194 612 612 ASP ASP A . n A 1 195 CYS 195 613 613 CYS CYS A . n A 1 196 ILE 196 614 614 ILE ILE A . n A 1 197 THR 197 615 615 THR THR A . n A 1 198 LYS 198 616 616 LYS LYS A . n A 1 199 ASP 199 617 617 ASP ASP A . n A 1 200 ARG 200 618 618 ARG ARG A . n A 1 201 PRO 201 619 619 PRO PRO A . n A 1 202 ILE 202 620 620 ILE ILE A . n A 1 203 ASN 203 621 621 ASN ASN A . n A 1 204 PHE 204 622 622 PHE PHE A . n A 1 205 THR 205 623 623 THR THR A . n A 1 206 GLN 206 624 624 GLN GLN A . n A 1 207 GLN 207 625 625 GLN GLN A . n A 1 208 HIS 208 626 626 HIS HIS A . n A 1 209 MET 209 627 627 MET MET A . n A 1 210 PRO 210 628 628 PRO PRO A . n A 1 211 TYR 211 629 629 TYR TYR A . n A 1 212 PHE 212 630 630 PHE PHE A . n A 1 213 ARG 213 631 631 ARG ARG A . n A 1 214 LYS 214 632 632 LYS LYS A . n A 1 215 ARG 215 633 633 ARG ARG A . n A 1 216 MET 216 634 634 MET MET A . n A 1 217 VAL 217 635 635 VAL VAL A . n A 1 218 TRP 218 636 636 TRP TRP A . n A 1 219 GLU 219 637 637 GLU GLU A . n A 1 220 ILE 220 638 638 ILE ILE A . n A 1 221 LEU 221 639 639 LEU LEU A . n A 1 222 HIS 222 640 640 HIS HIS A . n A 1 223 ARG 223 641 641 ARG ARG A . n A 1 224 LYS 224 642 642 LYS LYS A . n A 1 225 LEU 225 643 643 LEU LEU A . n A 1 226 LEU 226 644 644 LEU LEU A . n B 2 1 ASN 1 14 14 ASN ASN B . n B 2 2 ASP 2 15 15 ASP ASP B . n B 2 3 HIS 3 16 16 HIS HIS B . n B 2 4 ILE 4 17 17 ILE ILE B . n B 2 5 ASN 5 18 18 ASN ASN B . n B 2 6 LEU 6 19 19 LEU LEU B . n B 2 7 LYS 7 20 20 LYS LYS B . n B 2 8 VAL 8 21 21 VAL VAL B . n B 2 9 ALA 9 22 22 ALA ALA B . n B 2 10 GLY 10 23 23 GLY GLY B . n B 2 11 GLN 11 24 24 GLN GLN B . n B 2 12 ASP 12 25 25 ASP ASP B . n B 2 13 GLY 13 26 26 GLY GLY B . n B 2 14 SER 14 27 27 SER SER B . n B 2 15 VAL 15 28 28 VAL VAL B . n B 2 16 VAL 16 29 29 VAL VAL B . n B 2 17 GLN 17 30 30 GLN GLN B . n B 2 18 PHE 18 31 31 PHE PHE B . n B 2 19 LYS 19 32 32 LYS LYS B . n B 2 20 ILE 20 33 33 ILE ILE B . n B 2 21 LYS 21 34 34 LYS LYS B . n B 2 22 ARG 22 35 35 ARG ARG B . n B 2 23 HIS 23 36 36 HIS HIS B . n B 2 24 THR 24 37 37 THR THR B . n B 2 25 PRO 25 38 38 PRO PRO B . n B 2 26 LEU 26 39 39 LEU LEU B . n B 2 27 SER 27 40 40 SER SER B . n B 2 28 LYS 28 41 41 LYS LYS B . n B 2 29 LEU 29 42 42 LEU LEU B . n B 2 30 MET 30 43 43 MET MET B . n B 2 31 LYS 31 44 44 LYS LYS B . n B 2 32 ALA 32 45 45 ALA ALA B . n B 2 33 TYR 33 46 46 TYR TYR B . n B 2 34 CYS 34 47 47 CYS CYS B . n B 2 35 GLU 35 48 48 GLU GLU B . n B 2 36 ARG 36 49 49 ARG ARG B . n B 2 37 GLN 37 50 50 GLN GLN B . n B 2 38 GLY 38 51 51 GLY GLY B . n B 2 39 LEU 39 52 52 LEU LEU B . n B 2 40 SER 40 53 53 SER SER B . n B 2 41 MET 41 54 54 MET MET B . n B 2 42 ARG 42 55 55 ARG ARG B . n B 2 43 GLN 43 56 56 GLN GLN B . n B 2 44 ILE 44 57 57 ILE ILE B . n B 2 45 ARG 45 58 58 ARG ARG B . n B 2 46 PHE 46 59 59 PHE PHE B . n B 2 47 ARG 47 60 60 ARG ARG B . n B 2 48 PHE 48 61 61 PHE PHE B . n B 2 49 ASP 49 62 62 ASP ASP B . n B 2 50 GLY 50 63 63 GLY GLY B . n B 2 51 GLN 51 64 64 GLN GLN B . n B 2 52 PRO 52 65 65 PRO PRO B . n B 2 53 ILE 53 66 66 ILE ILE B . n B 2 54 ASN 54 67 67 ASN ASN B . n B 2 55 GLU 55 68 68 GLU GLU B . n B 2 56 THR 56 69 69 THR THR B . n B 2 57 ASP 57 70 70 ASP ASP B . n B 2 58 THR 58 71 71 THR THR B . n B 2 59 PRO 59 72 72 PRO PRO B . n B 2 60 ALA 60 73 73 ALA ALA B . n B 2 61 GLN 61 74 74 GLN GLN B . n B 2 62 LEU 62 75 75 LEU LEU B . n B 2 63 GLU 63 76 76 GLU GLU B . n B 2 64 MET 64 77 77 MET MET B . n B 2 65 GLU 65 78 78 GLU GLU B . n B 2 66 ASP 66 79 79 ASP ASP B . n B 2 67 GLU 67 80 80 GLU GLU B . n B 2 68 ASP 68 81 81 ASP ASP B . n B 2 69 THR 69 82 82 THR THR B . n B 2 70 ILE 70 83 83 ILE ILE B . n B 2 71 ASP 71 84 84 ASP ASP B . n B 2 72 VAL 72 85 85 VAL VAL B . n B 2 73 PHE 73 86 86 PHE PHE B . n B 2 74 GLN 74 87 87 GLN GLN B . n B 2 75 GLN 75 88 88 GLN GLN B . n B 2 76 GLN 76 89 89 GLN GLN B . n B 2 77 THR 77 90 90 THR THR B . n B 2 78 GLY 78 91 91 GLY GLY B . n B 2 79 GLY 79 92 92 GLY GLY B . n B 2 80 VAL 80 93 ? ? ? B . n B 2 81 TYR 81 94 ? ? ? B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2006-08-08 2 'Structure model' 1 1 2011-07-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' Advisory 2 2 'Structure model' 'Version format compliance' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 67.7985 -16.3022 18.3553 -0.0604 -0.3356 -0.5749 0.0643 0.1063 0.0852 5.9434 9.7263 2.9872 -0.8523 -1.2751 -0.4233 -0.3692 -0.5039 -0.3427 0.7041 0.2495 0.4621 0.3100 -0.0507 0.1197 'X-RAY DIFFRACTION' 2 ? refined 54.1951 -23.1124 -1.5351 0.2177 -0.1873 -0.2598 -0.2746 -0.1054 -0.0067 5.6794 7.5373 11.1390 -2.4032 5.7171 0.5961 -0.3804 0.5824 -0.6515 -1.1167 0.0152 1.3855 -1.0442 -0.0727 0.3652 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 A 419 ? ? A 644 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 B 14 ? ? B 92 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 MOSFLM 'data reduction' . ? 2 SCALA 'data scaling' . ? 3 CCP4 phasing . ? 4 # _pdbx_entry_details.entry_id 2IYD _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE EXTRA RESIDUE AT POSITION 593 IN CHAINS A AND B IS A KNOWN CONFLICT IN UNIPROT AND IS DESCRIBED IN PUBMED ID: 12477932. ; # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 SG A CYS 603 ? ? C B GLY 92 ? ? 1.71 2 1 SG A CYS 603 ? ? CA B GLY 92 ? ? 2.08 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASN A 439 ? ? 60.86 96.87 2 1 SER A 445 ? ? 161.18 113.51 3 1 ARG A 449 ? ? 48.69 12.78 4 1 HIS A 462 ? ? 49.09 -103.32 5 1 SER A 482 ? ? -65.05 -167.17 6 1 LYS A 483 ? ? 51.40 -13.11 7 1 ASN A 494 ? ? -29.94 149.82 8 1 PHE A 496 ? ? -59.54 -9.61 9 1 PHE A 497 ? ? -54.62 -71.15 10 1 LYS A 510 ? ? -26.76 -74.41 11 1 VAL A 516 ? ? -172.54 113.11 12 1 VAL A 518 ? ? -59.84 -9.21 13 1 ASN A 599 ? ? -113.87 -168.63 14 1 ASP A 617 ? ? 51.60 -1.94 15 1 THR A 623 ? ? -119.57 -161.18 16 1 GLN A 625 ? ? -25.67 -53.37 17 1 ARG A 641 ? ? 63.34 67.40 18 1 GLU B 48 ? ? -58.32 -73.26 19 1 SER B 53 ? ? -42.95 -78.21 20 1 MET B 54 ? ? 119.99 -70.29 21 1 ARG B 55 ? ? -79.00 37.14 22 1 GLN B 56 ? ? -153.70 9.72 23 1 ILE B 57 ? ? -124.18 -169.86 24 1 GLN B 74 ? ? -82.77 35.30 25 1 LEU B 75 ? ? -141.07 -6.54 26 1 GLU B 80 ? ? 52.06 7.54 27 1 GLN B 89 ? ? 73.63 120.90 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 B VAL 93 ? B VAL 80 2 1 Y 1 B TYR 94 ? B TYR 81 #