data_3IN8 # _entry.id 3IN8 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3IN8 RCSB RCSB054622 WWPDB D_1000054622 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2HUW . unspecified PDB 3C7I . unspecified PDB 3IMD . unspecified PDB 3IMJ . unspecified PDB 3IN7 . unspecified # _pdbx_database_status.entry_id 3IN8 _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-08-11 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Benfield, A.P.' 1 'Clements, 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 ;Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization. ; J.Am.Chem.Soc. 131 16758 16770 2009 JACSAT US 0002-7863 0004 ? 19886660 10.1021/ja904698q 1 'Ligand Preorganization May Be Accompanied by Entropic Penalties in Protein-Ligand Interactions' Angew.Chem.Int.Ed.Engl. 45 6830 6835 2006 ? GE 1433-7851 9999 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Delorbe, J.E.' 1 primary 'Clements, J.H.' 2 primary 'Teresk, M.G.' 3 primary 'Benfield, A.P.' 4 primary 'Plake, H.R.' 5 primary 'Millspaugh, L.E.' 6 primary 'Martin, S.F.' 7 1 'Benfield, A.P.' 8 1 'Teresk, M.G.' 9 1 'Plake, H.R.' 10 1 'DeLorbe, J.E.' 11 1 'Millspaugh, L.E.' 12 1 'Martin, S.F.' 13 # _cell.entry_id 3IN8 _cell.length_a 42.034 _cell.length_b 42.034 _cell.length_c 109.757 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _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 3IN8 _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _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 'Growth factor receptor-bound protein 2' 13758.543 1 ? ? 'SH2 domain' ? 2 non-polymer syn 'N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-isoleucyl-L-aspartamide' 543.507 1 ? ? ? ? 3 non-polymer syn 'FORMIC ACID' 46.025 1 ? ? ? ? 4 water nat water 18.015 116 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Adapter protein GRB2, SH2/SH3 adapter GRB2, Protein Ash' # _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 ;IEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELV DYHRSTSVSRNQQIFLRDIEQVPQQPTYVQAHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;IEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELV DYHRSTSVSRNQQIFLRDIEQVPQQPTYVQAHHHHHH ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ILE n 1 2 GLU n 1 3 MET n 1 4 LYS n 1 5 PRO n 1 6 HIS n 1 7 PRO n 1 8 TRP n 1 9 PHE n 1 10 PHE n 1 11 GLY n 1 12 LYS n 1 13 ILE n 1 14 PRO n 1 15 ARG n 1 16 ALA n 1 17 LYS n 1 18 ALA n 1 19 GLU n 1 20 GLU n 1 21 MET n 1 22 LEU n 1 23 SER n 1 24 LYS n 1 25 GLN n 1 26 ARG n 1 27 HIS n 1 28 ASP n 1 29 GLY n 1 30 ALA n 1 31 PHE n 1 32 LEU n 1 33 ILE n 1 34 ARG n 1 35 GLU n 1 36 SER n 1 37 GLU n 1 38 SER n 1 39 ALA n 1 40 PRO n 1 41 GLY n 1 42 ASP n 1 43 PHE n 1 44 SER n 1 45 LEU n 1 46 SER n 1 47 VAL n 1 48 LYS n 1 49 PHE n 1 50 GLY n 1 51 ASN n 1 52 ASP n 1 53 VAL n 1 54 GLN n 1 55 HIS n 1 56 PHE n 1 57 LYS n 1 58 VAL n 1 59 LEU n 1 60 ARG n 1 61 ASP n 1 62 GLY n 1 63 ALA n 1 64 GLY n 1 65 LYS n 1 66 TYR n 1 67 PHE n 1 68 LEU n 1 69 TRP n 1 70 VAL n 1 71 VAL n 1 72 LYS n 1 73 PHE n 1 74 ASN n 1 75 SER n 1 76 LEU n 1 77 ASN n 1 78 GLU n 1 79 LEU n 1 80 VAL n 1 81 ASP n 1 82 TYR n 1 83 HIS n 1 84 ARG n 1 85 SER n 1 86 THR n 1 87 SER n 1 88 VAL n 1 89 SER n 1 90 ARG n 1 91 ASN n 1 92 GLN n 1 93 GLN n 1 94 ILE n 1 95 PHE n 1 96 LEU n 1 97 ARG n 1 98 ASP n 1 99 ILE n 1 100 GLU n 1 101 GLN n 1 102 VAL n 1 103 PRO n 1 104 GLN n 1 105 GLN n 1 106 PRO n 1 107 THR n 1 108 TYR n 1 109 VAL n 1 110 GLN n 1 111 ALA n 1 112 HIS n 1 113 HIS n 1 114 HIS n 1 115 HIS n 1 116 HIS n 1 117 HIS 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 'GRB2, ASH' _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 'residues 53-163 were expressed in addition to a C-terminal 6-his tag' _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 SG13009 _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 pQE-60 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code GRB2_HUMAN _struct_ref.pdbx_db_accession P62993 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;IEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELV DYHRSTSVSRNQQIFLRDIEQVPQQPTYVQA ; _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 3IN8 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 111 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P62993 _struct_ref_seq.db_align_beg 53 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 163 _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 163 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3IN8 HIS A 112 ? UNP P62993 ? ? 'EXPRESSION TAG' 164 1 1 3IN8 HIS A 113 ? UNP P62993 ? ? 'EXPRESSION TAG' 165 2 1 3IN8 HIS A 114 ? UNP P62993 ? ? 'EXPRESSION TAG' 166 3 1 3IN8 HIS A 115 ? UNP P62993 ? ? 'EXPRESSION TAG' 167 4 1 3IN8 HIS A 116 ? UNP P62993 ? ? 'EXPRESSION TAG' 168 5 1 3IN8 HIS A 117 ? UNP P62993 ? ? 'EXPRESSION TAG' 169 6 # 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 FMT non-polymer . 'FORMIC ACID' ? 'C H2 O2' 46.025 FYI peptide-like . 'N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-isoleucyl-L-aspartamide' ? 'C22 H34 N5 O9 P' 543.507 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 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 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.crystals_number 1 _exptl.entry_id 3IN8 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.762 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 30.187 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;Ligand in lyophilized powder form was dissolved in a 15.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1. 3.5 uL of this solution was mixed with 3.5 uL of 5.0 M sodium formate, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after six weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K ; _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 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV++' _diffrn_detector.pdbx_collection_date 2005-03-17 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'blue max-flux confocal' _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _reflns.entry_id 3IN8 _reflns.d_resolution_high 1.700 _reflns.d_resolution_low 30.000 _reflns.number_obs 11224 _reflns.pdbx_Rmerge_I_obs 0.054 _reflns.pdbx_netI_over_sigmaI 23.300 _reflns.pdbx_chi_squared 1.545 _reflns.pdbx_redundancy 5.200 _reflns.percent_possible_obs 97.200 _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.number_all 11547 _reflns.pdbx_Rsym_value ? _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_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.70 _reflns_shell.d_res_low 1.76 _reflns_shell.number_measured_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_unique_obs ? _reflns_shell.Rmerge_I_obs 0.174 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared 1.423 _reflns_shell.pdbx_redundancy 2.60 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 889 _reflns_shell.percent_possible_all 79.70 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3IN8 _refine.ls_d_res_high 1.700 _refine.ls_d_res_low 20.000 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 97.200 _refine.ls_number_reflns_obs 11165 _refine.ls_number_reflns_all 11487 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details random _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.189 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.211 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.900 _refine.ls_number_reflns_R_free 560 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 17.748 _refine.solvent_model_param_bsol 48.876 _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 1.481 _refine.aniso_B[2][2] 1.481 _refine.aniso_B[3][3] -2.963 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _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_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.solvent_model_details ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 'pdb entry 1JYR' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.883 _refine.B_iso_max 56.50 _refine.B_iso_min 7.31 _refine.occupancy_max 1.00 _refine.occupancy_min 0.50 _refine.pdbx_ls_sigma_I 0 _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _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 832 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 40 _refine_hist.number_atoms_solvent 116 _refine_hist.number_atoms_total 988 _refine_hist.d_res_high 1.700 _refine_hist.d_res_low 20.000 # 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_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d ? 0.005 ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? 1.328 ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? 1.211 1.500 ? 'X-RAY DIFFRACTION' ? c_scbond_it ? 1.914 2.000 ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? 1.929 2.000 ? 'X-RAY DIFFRACTION' ? c_scangle_it ? 2.858 2.500 ? 'X-RAY DIFFRACTION' ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 CNS_TOPPAR:protein_rep.param CNS_TOPPAR:protein.top 'X-RAY DIFFRACTION' 2 fpyin.param fpyin.top 'X-RAY DIFFRACTION' 3 CNS_TOPPAR:water_rep.param CNS_TOPPAR:water.top 'X-RAY DIFFRACTION' 4 CNS_TOPPAR:ion.param CNS_TOPPAR:ion.top 'X-RAY DIFFRACTION' 5 formate.param formate.top 'X-RAY DIFFRACTION' # _struct.entry_id 3IN8 _struct.title 'Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic' _struct.pdbx_descriptor 'Growth factor receptor-bound protein 2' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3IN8 _struct_keywords.text ;ligand preorganization, Golgi apparatus, PEPTIDE MIMICS, Host-virus interaction, Phosphoprotein, SH2 domain, SH3, SIGNALING PROTEIN, SIGNALING PROTEIN-pseudopeptide ligand complex, SIGNALING PROTEIN-PEPTIDE COMPLEX ; _struct_keywords.pdbx_keywords 'SIGNALING PROTEIN/PEPTIDE' # 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 4 ? # _struct_biol.id 1 _struct_biol.details ? # 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 PRO A 14 ? LYS A 24 ? PRO A 66 LYS A 76 1 ? 11 HELX_P HELX_P2 2 SER A 75 ? HIS A 83 ? SER A 127 HIS A 135 1 ? 9 # _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 ? 3 ? B ? 3 ? # 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 B 1 2 ? anti-parallel B 2 3 ? 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 PHE A 31 ? GLU A 35 ? PHE A 83 GLU A 87 A 2 PHE A 43 ? PHE A 49 ? PHE A 95 PHE A 101 A 3 ASP A 52 ? LYS A 57 ? ASP A 104 LYS A 109 B 1 LEU A 59 ? ARG A 60 ? LEU A 111 ARG A 112 B 2 TYR A 66 ? PHE A 67 ? TYR A 118 PHE A 119 B 3 LYS A 72 ? PHE A 73 ? LYS A 124 PHE A 125 # 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 N ARG A 34 ? N ARG A 86 O SER A 44 ? O SER A 96 A 2 3 N LEU A 45 ? N LEU A 97 O PHE A 56 ? O PHE A 108 B 1 2 N LEU A 59 ? N LEU A 111 O PHE A 67 ? O PHE A 119 B 2 3 N TYR A 66 ? N TYR A 118 O PHE A 73 ? O PHE A 125 # 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 ? ? ? ? 20 'BINDING SITE FOR RESIDUE FYI A 1' AC2 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE FMT A 170' # 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 20 HOH D . ? HOH A 12 . ? 1_555 ? 2 AC1 20 HOH D . ? HOH A 37 . ? 1_555 ? 3 AC1 20 HOH D . ? HOH A 38 . ? 1_555 ? 4 AC1 20 ARG A 15 ? ARG A 67 . ? 1_555 ? 5 AC1 20 ARG A 26 ? ARG A 78 . ? 7_565 ? 6 AC1 20 ARG A 34 ? ARG A 86 . ? 1_555 ? 7 AC1 20 SER A 36 ? SER A 88 . ? 1_555 ? 8 AC1 20 SER A 38 ? SER A 90 . ? 1_555 ? 9 AC1 20 SER A 44 ? SER A 96 . ? 1_555 ? 10 AC1 20 HIS A 55 ? HIS A 107 . ? 1_555 ? 11 AC1 20 PHE A 56 ? PHE A 108 . ? 1_555 ? 12 AC1 20 LYS A 57 ? LYS A 109 . ? 1_555 ? 13 AC1 20 LEU A 68 ? LEU A 120 . ? 1_555 ? 14 AC1 20 TRP A 69 ? TRP A 121 . ? 1_555 ? 15 AC1 20 GLU A 100 ? GLU A 152 . ? 7_565 ? 16 AC1 20 VAL A 102 ? VAL A 154 . ? 7_565 ? 17 AC1 20 PRO A 103 ? PRO A 155 . ? 7_565 ? 18 AC1 20 HOH D . ? HOH A 189 . ? 1_555 ? 19 AC1 20 HOH D . ? HOH A 207 . ? 1_555 ? 20 AC1 20 HOH D . ? HOH A 230 . ? 1_555 ? 21 AC2 7 HOH D . ? HOH A 4 . ? 1_555 ? 22 AC2 7 HOH D . ? HOH A 35 . ? 7_455 ? 23 AC2 7 GLN A 25 ? GLN A 77 . ? 1_555 ? 24 AC2 7 ARG A 26 ? ARG A 78 . ? 1_555 ? 25 AC2 7 HIS A 27 ? HIS A 79 . ? 1_555 ? 26 AC2 7 LYS A 57 ? LYS A 109 . ? 7_455 ? 27 AC2 7 GLU A 100 ? GLU A 152 . ? 1_555 ? # _atom_sites.entry_id 3IN8 _atom_sites.fract_transf_matrix[1][1] 0.023790 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.023790 _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] 0.009111 _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 P 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 ILE 1 53 ? ? ? A . n A 1 2 GLU 2 54 ? ? ? A . n A 1 3 MET 3 55 55 MET MET A . n A 1 4 LYS 4 56 56 LYS LYS A . n A 1 5 PRO 5 57 57 PRO PRO A . n A 1 6 HIS 6 58 58 HIS HIS A . n A 1 7 PRO 7 59 59 PRO PRO A . n A 1 8 TRP 8 60 60 TRP TRP A . n A 1 9 PHE 9 61 61 PHE PHE A . n A 1 10 PHE 10 62 62 PHE PHE A . n A 1 11 GLY 11 63 63 GLY GLY A . n A 1 12 LYS 12 64 64 LYS LYS A . n A 1 13 ILE 13 65 65 ILE ILE A . n A 1 14 PRO 14 66 66 PRO PRO A . n A 1 15 ARG 15 67 67 ARG ARG A . n A 1 16 ALA 16 68 68 ALA ALA A . n A 1 17 LYS 17 69 69 LYS LYS A . n A 1 18 ALA 18 70 70 ALA ALA A . n A 1 19 GLU 19 71 71 GLU GLU A . n A 1 20 GLU 20 72 72 GLU GLU A . n A 1 21 MET 21 73 73 MET MET A . n A 1 22 LEU 22 74 74 LEU LEU A . n A 1 23 SER 23 75 75 SER SER A . n A 1 24 LYS 24 76 76 LYS LYS A . n A 1 25 GLN 25 77 77 GLN GLN A . n A 1 26 ARG 26 78 78 ARG ARG A . n A 1 27 HIS 27 79 79 HIS HIS A . n A 1 28 ASP 28 80 80 ASP ASP A . n A 1 29 GLY 29 81 81 GLY GLY A . n A 1 30 ALA 30 82 82 ALA ALA A . n A 1 31 PHE 31 83 83 PHE PHE A . n A 1 32 LEU 32 84 84 LEU LEU A . n A 1 33 ILE 33 85 85 ILE ILE A . n A 1 34 ARG 34 86 86 ARG ARG A . n A 1 35 GLU 35 87 87 GLU GLU A . n A 1 36 SER 36 88 88 SER SER A . n A 1 37 GLU 37 89 89 GLU GLU A . n A 1 38 SER 38 90 90 SER SER A . n A 1 39 ALA 39 91 91 ALA ALA A . n A 1 40 PRO 40 92 92 PRO PRO A . n A 1 41 GLY 41 93 93 GLY GLY A . n A 1 42 ASP 42 94 94 ASP ASP A . n A 1 43 PHE 43 95 95 PHE PHE A . n A 1 44 SER 44 96 96 SER SER A . n A 1 45 LEU 45 97 97 LEU LEU A . n A 1 46 SER 46 98 98 SER SER A . n A 1 47 VAL 47 99 99 VAL VAL A . n A 1 48 LYS 48 100 100 LYS LYS A . n A 1 49 PHE 49 101 101 PHE PHE A . n A 1 50 GLY 50 102 102 GLY GLY A . n A 1 51 ASN 51 103 103 ASN ASN A . n A 1 52 ASP 52 104 104 ASP ASP A . n A 1 53 VAL 53 105 105 VAL VAL A . n A 1 54 GLN 54 106 106 GLN GLN A . n A 1 55 HIS 55 107 107 HIS HIS A . n A 1 56 PHE 56 108 108 PHE PHE A . n A 1 57 LYS 57 109 109 LYS LYS A . n A 1 58 VAL 58 110 110 VAL VAL A . n A 1 59 LEU 59 111 111 LEU LEU A . n A 1 60 ARG 60 112 112 ARG ARG A . n A 1 61 ASP 61 113 113 ASP ASP A . n A 1 62 GLY 62 114 114 GLY GLY A . n A 1 63 ALA 63 115 115 ALA ALA A . n A 1 64 GLY 64 116 116 GLY GLY A . n A 1 65 LYS 65 117 117 LYS LYS A . n A 1 66 TYR 66 118 118 TYR TYR A . n A 1 67 PHE 67 119 119 PHE PHE A . n A 1 68 LEU 68 120 120 LEU LEU A . n A 1 69 TRP 69 121 121 TRP TRP A . n A 1 70 VAL 70 122 122 VAL VAL A . n A 1 71 VAL 71 123 123 VAL VAL A . n A 1 72 LYS 72 124 124 LYS LYS A . n A 1 73 PHE 73 125 125 PHE PHE A . n A 1 74 ASN 74 126 126 ASN ASN A . n A 1 75 SER 75 127 127 SER SER A . n A 1 76 LEU 76 128 128 LEU LEU A . n A 1 77 ASN 77 129 129 ASN ASN A . n A 1 78 GLU 78 130 130 GLU GLU A . n A 1 79 LEU 79 131 131 LEU LEU A . n A 1 80 VAL 80 132 132 VAL VAL A . n A 1 81 ASP 81 133 133 ASP ASP A . n A 1 82 TYR 82 134 134 TYR TYR A . n A 1 83 HIS 83 135 135 HIS HIS A . n A 1 84 ARG 84 136 136 ARG ARG A . n A 1 85 SER 85 137 137 SER SER A . n A 1 86 THR 86 138 138 THR THR A . n A 1 87 SER 87 139 139 SER SER A . n A 1 88 VAL 88 140 140 VAL VAL A . n A 1 89 SER 89 141 141 SER SER A . n A 1 90 ARG 90 142 142 ARG ARG A . n A 1 91 ASN 91 143 143 ASN ASN A . n A 1 92 GLN 92 144 144 GLN GLN A . n A 1 93 GLN 93 145 145 GLN GLN A . n A 1 94 ILE 94 146 146 ILE ILE A . n A 1 95 PHE 95 147 147 PHE PHE A . n A 1 96 LEU 96 148 148 LEU LEU A . n A 1 97 ARG 97 149 149 ARG ARG A . n A 1 98 ASP 98 150 150 ASP ASP A . n A 1 99 ILE 99 151 151 ILE ILE A . n A 1 100 GLU 100 152 152 GLU GLU A . n A 1 101 GLN 101 153 153 GLN GLN A . n A 1 102 VAL 102 154 154 VAL VAL A . n A 1 103 PRO 103 155 155 PRO PRO A . n A 1 104 GLN 104 156 ? ? ? A . n A 1 105 GLN 105 157 ? ? ? A . n A 1 106 PRO 106 158 ? ? ? A . n A 1 107 THR 107 159 ? ? ? A . n A 1 108 TYR 108 160 ? ? ? A . n A 1 109 VAL 109 161 ? ? ? A . n A 1 110 GLN 110 162 ? ? ? A . n A 1 111 ALA 111 163 ? ? ? A . n A 1 112 HIS 112 164 ? ? ? A . n A 1 113 HIS 113 165 ? ? ? A . n A 1 114 HIS 114 166 ? ? ? A . n A 1 115 HIS 115 167 ? ? ? A . n A 1 116 HIS 116 168 ? ? ? A . n A 1 117 HIS 117 169 ? ? ? A . n # 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 FYI 1 1 1 FYI FYI A . C 3 FMT 1 170 170 FMT FMT A . D 4 HOH 1 2 2 HOH HOH A . D 4 HOH 2 3 3 HOH HOH A . D 4 HOH 3 4 4 HOH HOH A . D 4 HOH 4 5 5 HOH HOH A . D 4 HOH 5 6 6 HOH HOH A . D 4 HOH 6 7 7 HOH HOH A . D 4 HOH 7 8 8 HOH HOH A . D 4 HOH 8 9 9 HOH HOH A . D 4 HOH 9 10 10 HOH HOH A . D 4 HOH 10 11 11 HOH HOH A . D 4 HOH 11 12 12 HOH HOH A . D 4 HOH 12 13 13 HOH HOH A . D 4 HOH 13 14 14 HOH HOH A . D 4 HOH 14 15 15 HOH HOH A . D 4 HOH 15 16 16 HOH HOH A . D 4 HOH 16 17 17 HOH HOH A . D 4 HOH 17 18 18 HOH HOH A . D 4 HOH 18 19 19 HOH HOH A . D 4 HOH 19 20 20 HOH HOH A . D 4 HOH 20 21 21 HOH HOH A . D 4 HOH 21 22 22 HOH HOH A . D 4 HOH 22 23 23 HOH HOH A . D 4 HOH 23 24 24 HOH HOH A . D 4 HOH 24 25 25 HOH HOH A . D 4 HOH 25 26 26 HOH HOH A . D 4 HOH 26 27 27 HOH HOH A . D 4 HOH 27 28 28 HOH HOH A . D 4 HOH 28 29 29 HOH HOH A . D 4 HOH 29 30 30 HOH HOH A . D 4 HOH 30 31 31 HOH HOH A . D 4 HOH 31 32 32 HOH HOH A . D 4 HOH 32 33 33 HOH HOH A . D 4 HOH 33 34 34 HOH HOH A . D 4 HOH 34 35 35 HOH HOH A . D 4 HOH 35 36 36 HOH HOH A . D 4 HOH 36 37 37 HOH HOH A . D 4 HOH 37 38 38 HOH HOH A . D 4 HOH 38 39 39 HOH HOH A . D 4 HOH 39 40 40 HOH HOH A . D 4 HOH 40 41 41 HOH HOH A . D 4 HOH 41 42 42 HOH HOH A . D 4 HOH 42 43 43 HOH HOH A . D 4 HOH 43 44 44 HOH HOH A . D 4 HOH 44 45 45 HOH HOH A . D 4 HOH 45 46 46 HOH HOH A . D 4 HOH 46 47 47 HOH HOH A . D 4 HOH 47 48 48 HOH HOH A . D 4 HOH 48 49 49 HOH HOH A . D 4 HOH 49 50 50 HOH HOH A . D 4 HOH 50 51 51 HOH HOH A . D 4 HOH 51 52 52 HOH HOH A . D 4 HOH 52 171 171 HOH HOH A . D 4 HOH 53 172 172 HOH HOH A . D 4 HOH 54 173 173 HOH HOH A . D 4 HOH 55 174 174 HOH HOH A . D 4 HOH 56 175 175 HOH HOH A . D 4 HOH 57 176 176 HOH HOH A . D 4 HOH 58 177 177 HOH HOH A . D 4 HOH 59 178 178 HOH HOH A . D 4 HOH 60 179 179 HOH HOH A . D 4 HOH 61 180 180 HOH HOH A . D 4 HOH 62 181 181 HOH HOH A . D 4 HOH 63 182 182 HOH HOH A . D 4 HOH 64 183 183 HOH HOH A . D 4 HOH 65 184 184 HOH HOH A . D 4 HOH 66 185 185 HOH HOH A . D 4 HOH 67 186 186 HOH HOH A . D 4 HOH 68 187 187 HOH HOH A . D 4 HOH 69 188 188 HOH HOH A . D 4 HOH 70 189 189 HOH HOH A . D 4 HOH 71 190 190 HOH HOH A . D 4 HOH 72 191 191 HOH HOH A . D 4 HOH 73 192 192 HOH HOH A . D 4 HOH 74 193 193 HOH HOH A . D 4 HOH 75 194 194 HOH HOH A . D 4 HOH 76 195 195 HOH HOH A . D 4 HOH 77 196 196 HOH HOH A . D 4 HOH 78 197 197 HOH HOH A . D 4 HOH 79 198 198 HOH HOH A . D 4 HOH 80 199 199 HOH HOH A . D 4 HOH 81 200 200 HOH HOH A . D 4 HOH 82 201 201 HOH HOH A . D 4 HOH 83 202 202 HOH HOH A . D 4 HOH 84 203 203 HOH HOH A . D 4 HOH 85 204 204 HOH HOH A . D 4 HOH 86 205 205 HOH HOH A . D 4 HOH 87 206 206 HOH HOH A . D 4 HOH 88 207 207 HOH HOH A . D 4 HOH 89 208 208 HOH HOH A . D 4 HOH 90 209 209 HOH HOH A . D 4 HOH 91 210 210 HOH HOH A . D 4 HOH 92 211 211 HOH HOH A . D 4 HOH 93 212 212 HOH HOH A . D 4 HOH 94 213 213 HOH HOH A . D 4 HOH 95 214 214 HOH HOH A . D 4 HOH 96 215 215 HOH HOH A . D 4 HOH 97 216 216 HOH HOH A . D 4 HOH 98 217 217 HOH HOH A . D 4 HOH 99 218 218 HOH HOH A . D 4 HOH 100 219 219 HOH HOH A . D 4 HOH 101 220 220 HOH HOH A . D 4 HOH 102 221 221 HOH HOH A . D 4 HOH 103 222 222 HOH HOH A . D 4 HOH 104 223 223 HOH HOH A . D 4 HOH 105 224 224 HOH HOH A . D 4 HOH 106 225 225 HOH HOH A . D 4 HOH 107 226 226 HOH HOH A . D 4 HOH 108 227 227 HOH HOH A . D 4 HOH 109 228 228 HOH HOH A . D 4 HOH 110 229 229 HOH HOH A . D 4 HOH 111 230 230 HOH HOH A . D 4 HOH 112 231 231 HOH HOH A . D 4 HOH 113 232 232 HOH HOH A . D 4 HOH 114 233 233 HOH HOH A . D 4 HOH 115 234 234 HOH HOH A . D 4 HOH 116 235 235 HOH HOH A . # _pdbx_molecule_features.prd_id PRD_000634 _pdbx_molecule_features.name 'AC-PTYR-ILE-ASN-NH2 TRIPEPTIDE MIMIC' _pdbx_molecule_features.type Peptide-like _pdbx_molecule_features.class Inhibitor _pdbx_molecule_features.details ? # _pdbx_molecule.instance_id 1 _pdbx_molecule.prd_id PRD_000634 _pdbx_molecule.asym_id B # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2700 ? 1 MORE -18 ? 1 'SSA (A^2)' 10320 ? # 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.vector[1] _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.vector[2] _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[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 7_555 y,x,-z 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 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 2009-11-17 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-12-12 4 'Structure model' 1 3 2017-11-01 # _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 ? # 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' 'Atomic model' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 2 'Structure model' 'Non-polymer description' 5 2 'Structure model' 'Structure summary' 6 2 'Structure model' 'Version format compliance' 7 3 'Structure model' Other 8 4 'Structure model' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 4 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # _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 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 MOLREP . ? program 'Alexei Vaguine' alexei@ysbl.york.ac.uk phasing http://www.ccp4.ac.uk/dist/html/molrep.html Fortran_77 ? 4 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns-online.org/ Fortran_77 ? 5 PDB_EXTRACT 3.005 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 CrystalClear . ? ? ? ? 'data collection' ? ? ? 7 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 8 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 CB _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 PRO _pdbx_validate_close_contact.auth_seq_id_1 59 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 NE2 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 GLN _pdbx_validate_close_contact.auth_seq_id_2 153 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.99 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id TRP _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 121 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -122.91 _pdbx_validate_torsion.psi -70.25 # _pdbx_validate_chiral.id 1 _pdbx_validate_chiral.PDB_model_num 1 _pdbx_validate_chiral.auth_atom_id C8 _pdbx_validate_chiral.label_alt_id ? _pdbx_validate_chiral.auth_asym_id A _pdbx_validate_chiral.auth_comp_id FYI _pdbx_validate_chiral.auth_seq_id 1 _pdbx_validate_chiral.PDB_ins_code ? _pdbx_validate_chiral.details 'WRONG HAND' _pdbx_validate_chiral.omega . # 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 ILE 53 ? A ILE 1 2 1 Y 1 A GLU 54 ? A GLU 2 3 1 Y 1 A GLN 156 ? A GLN 104 4 1 Y 1 A GLN 157 ? A GLN 105 5 1 Y 1 A PRO 158 ? A PRO 106 6 1 Y 1 A THR 159 ? A THR 107 7 1 Y 1 A TYR 160 ? A TYR 108 8 1 Y 1 A VAL 161 ? A VAL 109 9 1 Y 1 A GLN 162 ? A GLN 110 10 1 Y 1 A ALA 163 ? A ALA 111 11 1 Y 1 A HIS 164 ? A HIS 112 12 1 Y 1 A HIS 165 ? A HIS 113 13 1 Y 1 A HIS 166 ? A HIS 114 14 1 Y 1 A HIS 167 ? A HIS 115 15 1 Y 1 A HIS 168 ? A HIS 116 16 1 Y 1 A HIS 169 ? A HIS 117 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-isoleucyl-L-aspartamide' FYI 3 'FORMIC ACID' FMT 4 water HOH #