data_4D8K # _entry.id 4D8K # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.365 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4D8K pdb_00004d8k 10.2210/pdb4d8k/pdb RCSB RCSB070017 ? ? WWPDB D_1000070017 ? ? # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.db_id JCSG-422603 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 4D8K _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-01-10 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Joint Center for Structural Genomics (JCSG)' 1 'Partnership for T-Cell Biology (TCELL)' 2 # _citation.id primary _citation.title ;Crystal structure of a SH3-SH2 domains of a lymphocyte-specific protein tyrosine kinase (LCK) from Homo sapiens at 2.36 A resolution ; _citation.journal_abbrev 'To be published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Joint Center for Structural Genomics (JCSG)' 1 ? primary 'Partnership for T-Cell Biology' 2 ? # _cell.entry_id 4D8K _cell.length_a 68.899 _cell.length_b 68.899 _cell.length_c 80.283 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 6 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4D8K _symmetry.Int_Tables_number 152 _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # 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 'Tyrosine-protein kinase Lck' 19586.670 1 2.7.10.2 ? 'UNP residues 53-226' ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 non-polymer syn GLYCEROL 92.094 2 ? ? ? ? 4 water nat water 18.015 43 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;Leukocyte C-terminal Src kinase, LSK, Lymphocyte cell-specific protein-tyrosine kinase, Protein YT16, Proto-oncogene Lck, T cell-specific protein-tyrosine kinase, p56-LCK ; # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;GGSNPPASPLQDNLVIALHSYEPSHDGDLGFEKGEQLRILEQSGEWWKAQSLTTGQEGFIPFNFVAKANSLEPEPWFFKN LSRKDAERQLLAPGNTHGSFLIRESESTAGSFSLSVRDFDQNQGEVVKHYKIRNLDNGGFYISPRITFPGLHELVRHYTN ASDGLCTRLSRPCQT ; _entity_poly.pdbx_seq_one_letter_code_can ;GGSNPPASPLQDNLVIALHSYEPSHDGDLGFEKGEQLRILEQSGEWWKAQSLTTGQEGFIPFNFVAKANSLEPEPWFFKN LSRKDAERQLLAPGNTHGSFLIRESESTAGSFSLSVRDFDQNQGEVVKHYKIRNLDNGGFYISPRITFPGLHELVRHYTN ASDGLCTRLSRPCQT ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier JCSG-422603 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 GLY n 1 3 SER n 1 4 ASN n 1 5 PRO n 1 6 PRO n 1 7 ALA n 1 8 SER n 1 9 PRO n 1 10 LEU n 1 11 GLN n 1 12 ASP n 1 13 ASN n 1 14 LEU n 1 15 VAL n 1 16 ILE n 1 17 ALA n 1 18 LEU n 1 19 HIS n 1 20 SER n 1 21 TYR n 1 22 GLU n 1 23 PRO n 1 24 SER n 1 25 HIS n 1 26 ASP n 1 27 GLY n 1 28 ASP n 1 29 LEU n 1 30 GLY n 1 31 PHE n 1 32 GLU n 1 33 LYS n 1 34 GLY n 1 35 GLU n 1 36 GLN n 1 37 LEU n 1 38 ARG n 1 39 ILE n 1 40 LEU n 1 41 GLU n 1 42 GLN n 1 43 SER n 1 44 GLY n 1 45 GLU n 1 46 TRP n 1 47 TRP n 1 48 LYS n 1 49 ALA n 1 50 GLN n 1 51 SER n 1 52 LEU n 1 53 THR n 1 54 THR n 1 55 GLY n 1 56 GLN n 1 57 GLU n 1 58 GLY n 1 59 PHE n 1 60 ILE n 1 61 PRO n 1 62 PHE n 1 63 ASN n 1 64 PHE n 1 65 VAL n 1 66 ALA n 1 67 LYS n 1 68 ALA n 1 69 ASN n 1 70 SER n 1 71 LEU n 1 72 GLU n 1 73 PRO n 1 74 GLU n 1 75 PRO n 1 76 TRP n 1 77 PHE n 1 78 PHE n 1 79 LYS n 1 80 ASN n 1 81 LEU n 1 82 SER n 1 83 ARG n 1 84 LYS n 1 85 ASP n 1 86 ALA n 1 87 GLU n 1 88 ARG n 1 89 GLN n 1 90 LEU n 1 91 LEU n 1 92 ALA n 1 93 PRO n 1 94 GLY n 1 95 ASN n 1 96 THR n 1 97 HIS n 1 98 GLY n 1 99 SER n 1 100 PHE n 1 101 LEU n 1 102 ILE n 1 103 ARG n 1 104 GLU n 1 105 SER n 1 106 GLU n 1 107 SER n 1 108 THR n 1 109 ALA n 1 110 GLY n 1 111 SER n 1 112 PHE n 1 113 SER n 1 114 LEU n 1 115 SER n 1 116 VAL n 1 117 ARG n 1 118 ASP n 1 119 PHE n 1 120 ASP n 1 121 GLN n 1 122 ASN n 1 123 GLN n 1 124 GLY n 1 125 GLU n 1 126 VAL n 1 127 VAL n 1 128 LYS n 1 129 HIS n 1 130 TYR n 1 131 LYS n 1 132 ILE n 1 133 ARG n 1 134 ASN n 1 135 LEU n 1 136 ASP n 1 137 ASN n 1 138 GLY n 1 139 GLY n 1 140 PHE n 1 141 TYR n 1 142 ILE n 1 143 SER n 1 144 PRO n 1 145 ARG n 1 146 ILE n 1 147 THR n 1 148 PHE n 1 149 PRO n 1 150 GLY n 1 151 LEU n 1 152 HIS n 1 153 GLU n 1 154 LEU n 1 155 VAL n 1 156 ARG n 1 157 HIS n 1 158 TYR n 1 159 THR n 1 160 ASN n 1 161 ALA n 1 162 SER n 1 163 ASP n 1 164 GLY n 1 165 LEU n 1 166 CYS n 1 167 THR n 1 168 ARG n 1 169 LEU n 1 170 SER n 1 171 ARG n 1 172 PRO n 1 173 CYS n 1 174 GLN n 1 175 THR n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _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 human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'BC013200, LCK' _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 'Escherichia Coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _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 HK100 _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 Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code LCK_HUMAN _struct_ref.pdbx_db_accession P06239 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;GSNPPASPLQDNLVIALHSYEPSHDGDLGFEKGEQLRILEQSGEWWKAQSLTTGQEGFIPFNFVAKANSLEPEPWFFKNL SRKDAERQLLAPGNTHGSFLIRESESTAGSFSLSVRDFDQNQGEVVKHYKIRNLDNGGFYISPRITFPGLHELVRHYTNA SDGLCTRLSRPCQT ; _struct_ref.pdbx_align_begin 53 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4D8K _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 175 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P06239 _struct_ref_seq.db_align_beg 53 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 226 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 53 _struct_ref_seq.pdbx_auth_seq_align_end 226 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4D8K _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code P06239 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 52 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 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 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 4D8K # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.81 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 56.20 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '1.5M lithium sulfate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.details 'KOHZU: Double Crystal Si(111)' _diffrn_detector.pdbx_collection_date 2011-10-16 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Double Crystal Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.pdbx_wavelength 0.9795 _diffrn_source.pdbx_wavelength_list ? _diffrn_source.pdbx_synchrotron_site ALS # _reflns.entry_id 4D8K _reflns.d_resolution_high 2.36 _reflns.d_resolution_low 29.834 _reflns.number_all 9434 _reflns.number_obs 9434 _reflns.pdbx_netI_over_sigmaI 9.300 _reflns.pdbx_Rsym_value 0.129 _reflns.pdbx_redundancy 4.900 _reflns.percent_possible_obs 99.900 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.pdbx_Rmerge_I_obs ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.360 2.420 ? 3254 ? 0.865 0.9 0.865 ? 4.800 ? 674 100.000 1 1 2.420 2.490 ? 3222 ? 0.812 1.0 0.812 ? 4.800 ? 668 99.500 2 1 2.490 2.560 ? 3167 ? 0.592 1.2 0.592 ? 4.900 ? 643 99.900 3 1 2.560 2.640 ? 3148 ? 0.481 1.6 0.481 ? 4.900 ? 636 99.800 4 1 2.640 2.730 ? 3035 ? 0.465 1.6 0.465 ? 5.000 ? 612 100.000 5 1 2.730 2.820 ? 2930 ? 0.342 2.2 0.342 ? 5.000 ? 582 100.000 6 1 2.820 2.930 ? 2936 ? 0.330 2.4 0.330 ? 5.000 ? 586 100.000 7 1 2.930 3.050 ? 2677 ? 0.233 3.3 0.233 ? 5.000 ? 539 100.000 8 1 3.050 3.180 ? 2683 ? 0.170 4.4 0.170 ? 4.900 ? 543 100.000 9 1 3.180 3.340 ? 2487 ? 0.122 6.0 0.122 ? 4.900 ? 507 100.000 10 1 3.340 3.520 ? 2409 ? 0.116 6.4 0.116 ? 4.900 ? 496 100.000 11 1 3.520 3.730 ? 2206 ? 0.089 7.8 0.089 ? 4.800 ? 462 100.000 12 1 3.730 3.990 ? 2078 ? 0.073 9.5 0.073 ? 4.800 ? 437 100.000 13 1 3.990 4.310 ? 1897 ? 0.061 10.6 0.061 ? 4.700 ? 403 100.000 14 1 4.310 4.720 ? 1658 ? 0.056 12.6 0.056 ? 4.300 ? 384 100.000 15 1 4.720 5.280 ? 1635 ? 0.052 12.6 0.052 ? 4.700 ? 349 100.000 16 1 5.280 6.090 ? 1496 ? 0.062 11.0 0.062 ? 4.900 ? 303 100.000 17 1 6.090 7.460 ? 1301 ? 0.062 11.0 0.062 ? 4.900 ? 268 100.000 18 1 7.460 10.550 ? 1021 ? 0.029 23.5 0.029 ? 4.700 ? 215 100.000 19 1 10.550 29.834 ? 527 ? 0.024 23.9 0.024 ? 4.100 ? 127 95.500 20 1 # _refine.entry_id 4D8K _refine.ls_d_res_high 2.3600 _refine.ls_d_res_low 29.834 _refine.pdbx_ls_sigma_F 1.350 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.8400 _refine.ls_number_reflns_obs 9408 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.details ;1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. SULFATE (SO4) FROM THE CRYSTALLIZATION AND GLYCEROL (GOL) USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1940 _refine.ls_R_factor_R_work 0.1911 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2513 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.7800 _refine.ls_number_reflns_R_free 450 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 47.5713 _refine.solvent_model_param_bsol 36.2270 _refine.solvent_model_param_ksol 0.3760 _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 6.0335 _refine.aniso_B[2][2] 6.0335 _refine.aniso_B[3][3] -12.0670 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.6100 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 130.390 _refine.B_iso_min 8.070 _refine.pdbx_overall_phase_error 26.1800 _refine.occupancy_max 1.000 _refine.occupancy_min 0.470 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _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 1297 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 17 _refine_hist.number_atoms_solvent 43 _refine_hist.number_atoms_total 1357 _refine_hist.d_res_high 2.3600 _refine_hist.d_res_low 29.834 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 1349 0.008 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 1826 1.176 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 187 0.071 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 243 0.005 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 490 14.718 ? ? ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 2.3601 2.7014 3 100.0000 2915 . 0.2608 0.3334 . 150 . 3065 . . 'X-RAY DIFFRACTION' 2.7014 3.4027 3 100.0000 2950 . 0.2077 0.2864 . 156 . 3106 . . 'X-RAY DIFFRACTION' 3.4027 29.8366 3 100.0000 3093 . 0.1631 0.2073 . 144 . 3237 . . 'X-RAY DIFFRACTION' # _struct.entry_id 4D8K _struct.title ;Crystal structure of a SH3-SH2 domains of a lymphocyte-specific protein tyrosine kinase (LCK) from Homo sapiens at 2.36 A resolution ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;Protein kinases, SH2 domain, SH3 domain, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, Partnership for T-Cell Biology, TCELL, TRANSFERASE ; _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.entry_id 4D8K # 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 ? C N N 3 ? D N N 3 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.details ;ANALYTICAL SIZE EXCLUSION CHROMATOGRPAHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. HOWEVER, CRYSTAL PACKING ANALYSIS SUGGESTS THAT THE PROTEIN HAS ASSOCIATED INTO TRIMERS THAT ARE PREDICTED TO BE STABLE. ; # 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 SER A 82 ? ALA A 92 ? SER A 133 ALA A 143 1 ? 11 HELX_P HELX_P2 2 GLY A 150 ? ALA A 161 ? GLY A 201 ALA A 212 1 ? 12 # _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 A ? 5 ? B ? 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 A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 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 A 1 GLU A 57 ? PRO A 61 ? GLU A 108 PRO A 112 A 2 TRP A 46 ? SER A 51 ? TRP A 97 SER A 102 A 3 GLN A 36 ? GLU A 41 ? GLN A 87 GLU A 92 A 4 LEU A 14 ? ALA A 17 ? LEU A 65 ALA A 68 A 5 VAL A 65 ? LYS A 67 ? VAL A 116 LYS A 118 B 1 PHE A 100 ? GLU A 104 ? PHE A 151 GLU A 155 B 2 PHE A 112 ? PHE A 119 ? PHE A 163 PHE A 170 B 3 GLU A 125 ? ASN A 134 ? GLU A 176 ASN A 185 B 4 PHE A 140 ? TYR A 141 ? PHE A 191 TYR A 192 B 5 THR A 147 ? PHE A 148 ? THR A 198 PHE A 199 # 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 A 1 2 O GLY A 58 ? O GLY A 109 N ALA A 49 ? N ALA A 100 A 2 3 O GLN A 50 ? O GLN A 101 N ARG A 38 ? N ARG A 89 A 3 4 O LEU A 37 ? O LEU A 88 N VAL A 15 ? N VAL A 66 A 4 5 N ILE A 16 ? N ILE A 67 O ALA A 66 ? O ALA A 117 B 1 2 N LEU A 101 ? N LEU A 152 O SER A 115 ? O SER A 166 B 2 3 N ASP A 118 ? N ASP A 169 O VAL A 126 ? O VAL A 177 B 3 4 N ARG A 133 ? N ARG A 184 O TYR A 141 ? O TYR A 192 B 4 5 N PHE A 140 ? N PHE A 191 O PHE A 148 ? O PHE A 199 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SO4 301 ? 5 'BINDING SITE FOR RESIDUE SO4 A 301' AC2 Software A GOL 302 ? 4 'BINDING SITE FOR RESIDUE GOL A 302' AC3 Software A GOL 303 ? 5 'BINDING SITE FOR RESIDUE GOL A 303' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 5 ARG A 103 ? ARG A 154 . ? 1_555 ? 2 AC1 5 SER A 105 ? SER A 156 . ? 1_555 ? 3 AC1 5 GLU A 106 ? GLU A 157 . ? 1_555 ? 4 AC1 5 SER A 107 ? SER A 158 . ? 1_555 ? 5 AC1 5 HOH E . ? HOH A 406 . ? 1_555 ? 6 AC2 4 HIS A 19 ? HIS A 70 . ? 1_555 ? 7 AC2 4 ASN A 63 ? ASN A 114 . ? 1_555 ? 8 AC2 4 SER A 162 ? SER A 213 . ? 3_654 ? 9 AC2 4 ASP A 163 ? ASP A 214 . ? 3_654 ? 10 AC3 5 LYS A 67 ? LYS A 118 . ? 2_545 ? 11 AC3 5 PHE A 119 ? PHE A 170 . ? 1_555 ? 12 AC3 5 ASP A 120 ? ASP A 171 . ? 1_555 ? 13 AC3 5 GLN A 121 ? GLN A 172 . ? 1_555 ? 14 AC3 5 LYS A 128 ? LYS A 179 . ? 1_555 ? # _atom_sites.entry_id 4D8K _atom_sites.fract_transf_matrix[1][1] 0.014514 _atom_sites.fract_transf_matrix[1][2] 0.008380 _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] 0.016759 _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] 0.012456 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # 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 GLY 1 52 ? ? ? A . n A 1 2 GLY 2 53 ? ? ? A . n A 1 3 SER 3 54 ? ? ? A . n A 1 4 ASN 4 55 ? ? ? A . n A 1 5 PRO 5 56 ? ? ? A . n A 1 6 PRO 6 57 ? ? ? A . n A 1 7 ALA 7 58 ? ? ? A . n A 1 8 SER 8 59 ? ? ? A . n A 1 9 PRO 9 60 ? ? ? A . n A 1 10 LEU 10 61 ? ? ? A . n A 1 11 GLN 11 62 ? ? ? A . n A 1 12 ASP 12 63 ? ? ? A . n A 1 13 ASN 13 64 64 ASN ASN A . n A 1 14 LEU 14 65 65 LEU LEU A . n A 1 15 VAL 15 66 66 VAL VAL A . n A 1 16 ILE 16 67 67 ILE ILE A . n A 1 17 ALA 17 68 68 ALA ALA A . n A 1 18 LEU 18 69 69 LEU LEU A . n A 1 19 HIS 19 70 70 HIS HIS A . n A 1 20 SER 20 71 71 SER SER A . n A 1 21 TYR 21 72 72 TYR TYR A . n A 1 22 GLU 22 73 73 GLU GLU A . n A 1 23 PRO 23 74 74 PRO PRO A . n A 1 24 SER 24 75 75 SER SER A . n A 1 25 HIS 25 76 76 HIS HIS A . n A 1 26 ASP 26 77 77 ASP ASP A . n A 1 27 GLY 27 78 78 GLY GLY A . n A 1 28 ASP 28 79 79 ASP ASP A . n A 1 29 LEU 29 80 80 LEU LEU A . n A 1 30 GLY 30 81 81 GLY GLY A . n A 1 31 PHE 31 82 82 PHE PHE A . n A 1 32 GLU 32 83 83 GLU GLU A . n A 1 33 LYS 33 84 84 LYS LYS A . n A 1 34 GLY 34 85 85 GLY GLY A . n A 1 35 GLU 35 86 86 GLU GLU A . n A 1 36 GLN 36 87 87 GLN GLN A . n A 1 37 LEU 37 88 88 LEU LEU A . n A 1 38 ARG 38 89 89 ARG ARG A . n A 1 39 ILE 39 90 90 ILE ILE A . n A 1 40 LEU 40 91 91 LEU LEU A . n A 1 41 GLU 41 92 92 GLU GLU A . n A 1 42 GLN 42 93 93 GLN GLN A . n A 1 43 SER 43 94 94 SER SER A . n A 1 44 GLY 44 95 95 GLY GLY A . n A 1 45 GLU 45 96 96 GLU GLU A . n A 1 46 TRP 46 97 97 TRP TRP A . n A 1 47 TRP 47 98 98 TRP TRP A . n A 1 48 LYS 48 99 99 LYS LYS A . n A 1 49 ALA 49 100 100 ALA ALA A . n A 1 50 GLN 50 101 101 GLN GLN A . n A 1 51 SER 51 102 102 SER SER A . n A 1 52 LEU 52 103 103 LEU LEU A . n A 1 53 THR 53 104 104 THR THR A . n A 1 54 THR 54 105 105 THR THR A . n A 1 55 GLY 55 106 106 GLY GLY A . n A 1 56 GLN 56 107 107 GLN GLN A . n A 1 57 GLU 57 108 108 GLU GLU A . n A 1 58 GLY 58 109 109 GLY GLY A . n A 1 59 PHE 59 110 110 PHE PHE A . n A 1 60 ILE 60 111 111 ILE ILE A . n A 1 61 PRO 61 112 112 PRO PRO A . n A 1 62 PHE 62 113 113 PHE PHE A . n A 1 63 ASN 63 114 114 ASN ASN A . n A 1 64 PHE 64 115 115 PHE PHE A . n A 1 65 VAL 65 116 116 VAL VAL A . n A 1 66 ALA 66 117 117 ALA ALA A . n A 1 67 LYS 67 118 118 LYS LYS A . n A 1 68 ALA 68 119 119 ALA ALA A . n A 1 69 ASN 69 120 120 ASN ASN A . n A 1 70 SER 70 121 121 SER SER A . n A 1 71 LEU 71 122 122 LEU LEU A . n A 1 72 GLU 72 123 123 GLU GLU A . n A 1 73 PRO 73 124 124 PRO PRO A . n A 1 74 GLU 74 125 125 GLU GLU A . n A 1 75 PRO 75 126 126 PRO PRO A . n A 1 76 TRP 76 127 127 TRP TRP A . n A 1 77 PHE 77 128 128 PHE PHE A . n A 1 78 PHE 78 129 129 PHE PHE A . n A 1 79 LYS 79 130 130 LYS LYS A . n A 1 80 ASN 80 131 131 ASN ASN A . n A 1 81 LEU 81 132 132 LEU LEU A . n A 1 82 SER 82 133 133 SER SER A . n A 1 83 ARG 83 134 134 ARG ARG A . n A 1 84 LYS 84 135 135 LYS LYS A . n A 1 85 ASP 85 136 136 ASP ASP A . n A 1 86 ALA 86 137 137 ALA ALA A . n A 1 87 GLU 87 138 138 GLU GLU A . n A 1 88 ARG 88 139 139 ARG ARG A . n A 1 89 GLN 89 140 140 GLN GLN A . n A 1 90 LEU 90 141 141 LEU LEU A . n A 1 91 LEU 91 142 142 LEU LEU A . n A 1 92 ALA 92 143 143 ALA ALA A . n A 1 93 PRO 93 144 144 PRO PRO A . n A 1 94 GLY 94 145 145 GLY GLY A . n A 1 95 ASN 95 146 146 ASN ASN A . n A 1 96 THR 96 147 147 THR THR A . n A 1 97 HIS 97 148 148 HIS HIS A . n A 1 98 GLY 98 149 149 GLY GLY A . n A 1 99 SER 99 150 150 SER SER A . n A 1 100 PHE 100 151 151 PHE PHE A . n A 1 101 LEU 101 152 152 LEU LEU A . n A 1 102 ILE 102 153 153 ILE ILE A . n A 1 103 ARG 103 154 154 ARG ARG A . n A 1 104 GLU 104 155 155 GLU GLU A . n A 1 105 SER 105 156 156 SER SER A . n A 1 106 GLU 106 157 157 GLU GLU A . n A 1 107 SER 107 158 158 SER SER A . n A 1 108 THR 108 159 159 THR THR A . n A 1 109 ALA 109 160 160 ALA ALA A . n A 1 110 GLY 110 161 161 GLY GLY A . n A 1 111 SER 111 162 162 SER SER A . n A 1 112 PHE 112 163 163 PHE PHE A . n A 1 113 SER 113 164 164 SER SER A . n A 1 114 LEU 114 165 165 LEU LEU A . n A 1 115 SER 115 166 166 SER SER A . n A 1 116 VAL 116 167 167 VAL VAL A . n A 1 117 ARG 117 168 168 ARG ARG A . n A 1 118 ASP 118 169 169 ASP ASP A . n A 1 119 PHE 119 170 170 PHE PHE A . n A 1 120 ASP 120 171 171 ASP ASP A . n A 1 121 GLN 121 172 172 GLN GLN A . n A 1 122 ASN 122 173 173 ASN ASN A . n A 1 123 GLN 123 174 174 GLN GLN A . n A 1 124 GLY 124 175 175 GLY GLY A . n A 1 125 GLU 125 176 176 GLU GLU A . n A 1 126 VAL 126 177 177 VAL VAL A . n A 1 127 VAL 127 178 178 VAL VAL A . n A 1 128 LYS 128 179 179 LYS LYS A . n A 1 129 HIS 129 180 180 HIS HIS A . n A 1 130 TYR 130 181 181 TYR TYR A . n A 1 131 LYS 131 182 182 LYS LYS A . n A 1 132 ILE 132 183 183 ILE ILE A . n A 1 133 ARG 133 184 184 ARG ARG A . n A 1 134 ASN 134 185 185 ASN ASN A . n A 1 135 LEU 135 186 186 LEU LEU A . n A 1 136 ASP 136 187 187 ASP ASP A . n A 1 137 ASN 137 188 188 ASN ASN A . n A 1 138 GLY 138 189 189 GLY GLY A . n A 1 139 GLY 139 190 190 GLY GLY A . n A 1 140 PHE 140 191 191 PHE PHE A . n A 1 141 TYR 141 192 192 TYR TYR A . n A 1 142 ILE 142 193 193 ILE ILE A . n A 1 143 SER 143 194 194 SER SER A . n A 1 144 PRO 144 195 195 PRO PRO A . n A 1 145 ARG 145 196 196 ARG ARG A . n A 1 146 ILE 146 197 197 ILE ILE A . n A 1 147 THR 147 198 198 THR THR A . n A 1 148 PHE 148 199 199 PHE PHE A . n A 1 149 PRO 149 200 200 PRO PRO A . n A 1 150 GLY 150 201 201 GLY GLY A . n A 1 151 LEU 151 202 202 LEU LEU A . n A 1 152 HIS 152 203 203 HIS HIS A . n A 1 153 GLU 153 204 204 GLU GLU A . n A 1 154 LEU 154 205 205 LEU LEU A . n A 1 155 VAL 155 206 206 VAL VAL A . n A 1 156 ARG 156 207 207 ARG ARG A . n A 1 157 HIS 157 208 208 HIS HIS A . n A 1 158 TYR 158 209 209 TYR TYR A . n A 1 159 THR 159 210 210 THR THR A . n A 1 160 ASN 160 211 211 ASN ASN A . n A 1 161 ALA 161 212 212 ALA ALA A . n A 1 162 SER 162 213 213 SER SER A . n A 1 163 ASP 163 214 214 ASP ASP A . n A 1 164 GLY 164 215 215 GLY GLY A . n A 1 165 LEU 165 216 216 LEU LEU A . n A 1 166 CYS 166 217 217 CYS CYS A . n A 1 167 THR 167 218 218 THR THR A . n A 1 168 ARG 168 219 219 ARG ARG A . n A 1 169 LEU 169 220 220 LEU LEU A . n A 1 170 SER 170 221 221 SER SER A . n A 1 171 ARG 171 222 222 ARG ARG A . n A 1 172 PRO 172 223 223 PRO PRO A . n A 1 173 CYS 173 224 224 CYS CYS A . n A 1 174 GLN 174 225 225 GLN GLN A . n A 1 175 THR 175 226 226 THR THR A . n # loop_ _pdbx_SG_project.project_name _pdbx_SG_project.full_name_of_center _pdbx_SG_project.id _pdbx_SG_project.initial_of_center PSI:Biology 'Joint Center for Structural Genomics' 1 JCSG PSI:Biology 'Partnership for T-Cell Biology' 2 TCELL # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_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_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SO4 1 301 227 SO4 SO4 A . C 3 GOL 1 302 228 GOL GOL A . D 3 GOL 1 303 229 GOL GOL A . E 4 HOH 1 401 230 HOH HOH A . E 4 HOH 2 402 231 HOH HOH A . E 4 HOH 3 403 232 HOH HOH A . E 4 HOH 4 404 233 HOH HOH A . E 4 HOH 5 405 234 HOH HOH A . E 4 HOH 6 406 235 HOH HOH A . E 4 HOH 7 407 236 HOH HOH A . E 4 HOH 8 408 237 HOH HOH A . E 4 HOH 9 409 238 HOH HOH A . E 4 HOH 10 410 239 HOH HOH A . E 4 HOH 11 411 240 HOH HOH A . E 4 HOH 12 412 241 HOH HOH A . E 4 HOH 13 413 242 HOH HOH A . E 4 HOH 14 414 243 HOH HOH A . E 4 HOH 15 415 244 HOH HOH A . E 4 HOH 16 416 245 HOH HOH A . E 4 HOH 17 417 246 HOH HOH A . E 4 HOH 18 418 247 HOH HOH A . E 4 HOH 19 419 248 HOH HOH A . E 4 HOH 20 420 249 HOH HOH A . E 4 HOH 21 421 250 HOH HOH A . E 4 HOH 22 422 251 HOH HOH A . E 4 HOH 23 423 252 HOH HOH A . E 4 HOH 24 424 253 HOH HOH A . E 4 HOH 25 425 254 HOH HOH A . E 4 HOH 26 426 255 HOH HOH A . E 4 HOH 27 427 256 HOH HOH A . E 4 HOH 28 428 257 HOH HOH A . E 4 HOH 29 429 258 HOH HOH A . E 4 HOH 30 430 259 HOH HOH A . E 4 HOH 31 431 260 HOH HOH A . E 4 HOH 32 432 261 HOH HOH A . E 4 HOH 33 433 262 HOH HOH A . E 4 HOH 34 434 263 HOH HOH A . E 4 HOH 35 435 264 HOH HOH A . E 4 HOH 36 436 265 HOH HOH A . E 4 HOH 37 437 266 HOH HOH A . E 4 HOH 38 438 267 HOH HOH A . E 4 HOH 39 439 268 HOH HOH A . E 4 HOH 40 440 269 HOH HOH A . E 4 HOH 41 441 270 HOH HOH A . E 4 HOH 42 442 271 HOH HOH A . E 4 HOH 43 443 272 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 438 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 2012-01-25 2 'Structure model' 1 1 2012-08-29 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 2018-01-24 5 'Structure model' 1 4 2023-02-01 # _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 ? _pdbx_audit_revision_details.details ? # 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' 'Structure summary' 2 3 'Structure model' 'Author supporting evidence' 3 3 'Structure model' 'Refinement description' 4 4 'Structure model' 'Database references' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' pdbx_struct_assembly_auth_evidence 2 3 'Structure model' software 3 4 'Structure model' citation_author 4 5 'Structure model' database_2 5 5 'Structure model' struct_ref_seq_dif 6 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_citation_author.name' 4 5 'Structure model' '_database_2.pdbx_DOI' 5 5 'Structure model' '_database_2.pdbx_database_accession' 6 5 'Structure model' '_struct_ref_seq_dif.details' 7 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 8 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 9 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # 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[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 59.1958 -7.1906 11.3458 0.6104 0.3416 0.3608 -0.1171 -0.1229 -0.0643 2.4757 2.8842 3.1537 0.1412 -0.6464 0.6091 -0.0799 0.0334 -0.0835 -0.5299 0.8110 -0.3454 0.7285 -0.9308 0.7727 'X-RAY DIFFRACTION' 2 ? refined 29.9311 -18.9955 21.1831 0.1743 0.1018 0.1098 -0.0196 -0.0005 -0.0119 0.7298 1.9025 4.1716 -0.1586 -0.1436 -0.5795 -0.0124 0.0775 -0.0604 0.0875 -0.0908 -0.0701 -0.2753 0.4703 -0.0830 'X-RAY DIFFRACTION' 3 ? refined 29.4964 -7.0298 22.9802 0.0939 0.0776 0.0771 -0.0043 -0.0151 -0.0533 4.8810 4.7456 4.2263 -0.8357 -0.5391 0.0608 0.0544 -0.0556 -0.0011 -0.0101 0.2645 0.0422 0.0477 -0.1716 -0.1612 # 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.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 0 A 0 ;chain 'A' and (resseq 64:118) ; ? ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 0 A 0 ;chain 'A' and (resseq 119:183) ; ? ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 0 A 0 ;chain 'A' and (resseq 184:226) ; ? ? ? ? ? # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 2 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 PHASER 2.3.0 ? program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 4 SCALA 3.3.20 ? package 'Phil Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' ? ? ? 5 PHENIX 1.7.2 ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 6 MOSFLM . ? ? ? ? 'data reduction' ? ? ? # _pdbx_entry_details.entry_id 4D8K _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 53-226 OF THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 GLU _pdbx_validate_symm_contact.auth_seq_id_1 73 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 NH2 _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 ARG _pdbx_validate_symm_contact.auth_seq_id_2 184 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 6_655 _pdbx_validate_symm_contact.dist 2.18 # 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 SER A 75 ? ? -99.13 -65.34 2 1 ASN A 120 ? ? 74.48 -0.77 3 1 ASN A 188 ? ? -109.45 -79.98 4 1 SER A 221 ? ? -119.03 -83.66 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A LEU 65 ? CG ? A LEU 14 CG 2 1 Y 1 A LEU 65 ? CD1 ? A LEU 14 CD1 3 1 Y 1 A LEU 65 ? CD2 ? A LEU 14 CD2 4 1 Y 1 A LYS 99 ? CE ? A LYS 48 CE 5 1 Y 1 A LYS 99 ? NZ ? A LYS 48 NZ 6 1 Y 1 A LYS 135 ? CG ? A LYS 84 CG 7 1 Y 1 A LYS 135 ? CD ? A LYS 84 CD 8 1 Y 1 A LYS 135 ? CE ? A LYS 84 CE 9 1 Y 1 A LYS 135 ? NZ ? A LYS 84 NZ # 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 A GLY 52 ? A GLY 1 2 1 Y 1 A GLY 53 ? A GLY 2 3 1 Y 1 A SER 54 ? A SER 3 4 1 Y 1 A ASN 55 ? A ASN 4 5 1 Y 1 A PRO 56 ? A PRO 5 6 1 Y 1 A PRO 57 ? A PRO 6 7 1 Y 1 A ALA 58 ? A ALA 7 8 1 Y 1 A SER 59 ? A SER 8 9 1 Y 1 A PRO 60 ? A PRO 9 10 1 Y 1 A LEU 61 ? A LEU 10 11 1 Y 1 A GLN 62 ? A GLN 11 12 1 Y 1 A ASP 63 ? A ASP 12 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 GLYCEROL GOL 4 water HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'gel filtration' _pdbx_struct_assembly_auth_evidence.details ? #