data_1BKM # _entry.id 1BKM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.375 _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 1BKM pdb_00001bkm 10.2210/pdb1bkm/pdb WWPDB D_1000171864 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1BKM _pdbx_database_status.recvd_initial_deposition_date 1997-05-02 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Holland, D.R.' 1 'Rubin, J.R.' 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 'Structure-Based Design of a Novel Series of Nonpeptide Ligands that Bind to the Pp60Src Sh2 Domain' J.Am.Chem.Soc. 119 12471 ? 1997 JACSAT US 0002-7863 0004 ? -1 ? 1 'Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms' 'Cell(Cambridge,Mass.)' 72 779 ? 1993 CELLB5 US 0092-8674 0998 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Holland, D.R.' 1 ? primary 'Lunney, E.A.' 2 ? primary 'Plummer, M.S.' 3 ? primary 'Mueller, W.T.' 4 ? primary 'Mcconnell, P.' 5 ? primary 'Pavlovsky, A.' 6 ? primary 'Para, K.S.' 7 ? primary 'Shahripour, A.' 8 ? primary 'Humblet, C.' 9 ? primary 'Sawyer, T.K.' 10 ? primary 'Rubin, J.R.' 11 ? 1 'Waksman, G.' 12 ? 1 'Shoelson, S.E.' 13 ? 1 'Pant, N.' 14 ? 1 'Cowburn, D.' 15 ? 1 'Kuriyan, J.' 16 ? # _cell.entry_id 1BKM _cell.length_a 30.200 _cell.length_b 46.900 _cell.length_c 74.520 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BKM _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # 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 'PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN' 12821.392 1 2.7.1.112 'INS(G0,S1), INS(EFIVTD) AT C-TERMINUS' DOMAIN ? 2 non-polymer syn '[[O-PHOSPHONO-N-ACETYL-TYROSINYL]-GLUTAMYL-3[CYCLOHEXYLMETHYL]ALANINYL]-AMINE' 598.582 1 ? ? ? ? 3 water nat water 18.015 61 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'SRC SH2' # _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 ;GSAEEWYFGKITRRESEALLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSS LQQLVAYYSKHADGLCHRLTNVCPTSKEFIVTD ; _entity_poly.pdbx_seq_one_letter_code_can ;GSAEEWYFGKITRRESEALLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSS LQQLVAYYSKHADGLCHRLTNVCPTSKEFIVTD ; _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 GLY n 1 2 SER n 1 3 ALA n 1 4 GLU n 1 5 GLU n 1 6 TRP n 1 7 TYR n 1 8 PHE n 1 9 GLY n 1 10 LYS n 1 11 ILE n 1 12 THR n 1 13 ARG n 1 14 ARG n 1 15 GLU n 1 16 SER n 1 17 GLU n 1 18 ALA n 1 19 LEU n 1 20 LEU n 1 21 LEU n 1 22 ASN n 1 23 PRO n 1 24 GLU n 1 25 ASN n 1 26 PRO n 1 27 ARG n 1 28 GLY n 1 29 THR n 1 30 PHE n 1 31 LEU n 1 32 VAL n 1 33 ARG n 1 34 GLU n 1 35 SER n 1 36 GLU n 1 37 THR n 1 38 THR n 1 39 LYS n 1 40 GLY n 1 41 ALA n 1 42 TYR n 1 43 CYS n 1 44 LEU n 1 45 SER n 1 46 VAL n 1 47 SER n 1 48 ASP n 1 49 PHE n 1 50 ASP n 1 51 ASN n 1 52 ALA n 1 53 LYS n 1 54 GLY n 1 55 LEU n 1 56 ASN n 1 57 VAL n 1 58 LYS n 1 59 HIS n 1 60 TYR n 1 61 LYS n 1 62 ILE n 1 63 ARG n 1 64 LYS n 1 65 LEU n 1 66 ASP n 1 67 SER n 1 68 GLY n 1 69 GLY n 1 70 PHE n 1 71 TYR n 1 72 ILE n 1 73 THR n 1 74 SER n 1 75 ARG n 1 76 THR n 1 77 GLN n 1 78 PHE n 1 79 SER n 1 80 SER n 1 81 LEU n 1 82 GLN n 1 83 GLN n 1 84 LEU n 1 85 VAL n 1 86 ALA n 1 87 TYR n 1 88 TYR n 1 89 SER n 1 90 LYS n 1 91 HIS n 1 92 ALA n 1 93 ASP n 1 94 GLY n 1 95 LEU n 1 96 CYS n 1 97 HIS n 1 98 ARG n 1 99 LEU n 1 100 THR n 1 101 ASN n 1 102 VAL n 1 103 CYS n 1 104 PRO n 1 105 THR n 1 106 SER n 1 107 LYS n 1 108 GLU n 1 109 PHE n 1 110 ILE n 1 111 VAL n 1 112 THR n 1 113 ASP 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 ? _entity_src_gen.gene_src_genus Alpharetrovirus _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'SCHMIDT-RUPPIN STRAIN A' _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 'Rous sarcoma virus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 11886 _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 Escherichia _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 JM83 _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code SRC_RSVSA _struct_ref.entity_id 1 _struct_ref.pdbx_db_accession P00524 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code ;MGSSKSKPKDPSQRRRSLEPPDSTHHGGFPASQTPNKTAAPDTHRTPSRSFGTVATEPKLFGGFNTSDTVTSPQRAGALA GGVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLTTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESER LLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHR LTNVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHE KLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVC KVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYR MPCPPECPESLHDLMCQCWRKDPEERPTFEYLQAFLEDYFTSTEPPVPAWREPIGLELLLAPEASLWGTGAWLRAEGPRF GEQPQSRMWHGEVSGAPSLIKTVLGHP ; _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1BKM _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 3 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 107 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P00524 _struct_ref_seq.db_align_beg 145 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 249 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 106 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 1BKM _struct_ref_seq_dif.mon_id ALA _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 18 _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 P00524 _struct_ref_seq_dif.db_mon_id ARG _struct_ref_seq_dif.pdbx_seq_db_seq_num 160 _struct_ref_seq_dif.details conflict _struct_ref_seq_dif.pdbx_auth_seq_num 17 _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 1C5 non-polymer . '[[O-PHOSPHONO-N-ACETYL-TYROSINYL]-GLUTAMYL-3[CYCLOHEXYLMETHYL]ALANINYL]-AMINE' ? 'C26 H39 N4 O10 P' 598.582 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 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 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 1BKM _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.0 _exptl_crystal.density_percent_sol 40.22 _exptl_crystal.description 'WAKSMAN AND KURIYAN SRC SH2 STRUCTURE' # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;5% PEG 6K, 0.1M TRIS, PH 8, SITTING DROP EXPERIMENT, PROTEIN 50 MG/ML, INHIBITOR 4 MG/ML, 4:4:2 RATIO (WELL:PROT:INHIB), pH 8.0, vapor diffusion - sitting drop ; # _diffrn.id 1 _diffrn.ambient_temp 293 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 1994-07 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'CU FILTER' _diffrn_radiation.pdbx_diffrn_protocol ? _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 _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1BKM _reflns.observed_criterion_sigma_I 2. _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 25. _reflns.d_resolution_high 2.0 _reflns.number_obs 6768 _reflns.number_all ? _reflns.percent_possible_obs 88.7 _reflns.pdbx_Rmerge_I_obs 0.0760000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 14.4 _reflns.B_iso_Wilson_estimate 21.5 _reflns.pdbx_redundancy 3. _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.0 _reflns_shell.d_res_low 2.12 _reflns_shell.percent_possible_all 71.9 _reflns_shell.Rmerge_I_obs 0.3170000 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5. _reflns_shell.pdbx_redundancy 2. _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1BKM _refine.ls_number_reflns_obs 5528 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2. _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8. _refine.ls_d_res_high 2.0 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.2000000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2000000 _refine.ls_R_factor_R_free 0.2750000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10. _refine.ls_number_reflns_R_free 546 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 20.6 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method R-FREE _refine.details ? _refine.pdbx_starting_model 'PROTEIN MODEL FROM 1SPS' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _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 813 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 61 _refine_hist.number_atoms_total 874 _refine_hist.d_res_high 2.0 _refine_hist.d_res_low 8. # 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 x_bond_d 0.015 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 3.1 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d 29.2 ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d 2.7 ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 8 _refine_ls_shell.d_res_high 2.00 _refine_ls_shell.d_res_low 2.1 _refine_ls_shell.number_reflns_R_work 387 _refine_ls_shell.R_factor_R_work 0.2400000 _refine_ls_shell.percent_reflns_obs 50. _refine_ls_shell.R_factor_R_free 0.3300000 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free 10. _refine_ls_shell.number_reflns_R_free 37 _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 1BKM _struct.title 'COCRYSTAL STRUCTURE OF D-AMINO ACID SUBSTITUTED PHOSPHOPEPTIDE COMPLEX' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1BKM _struct_keywords.pdbx_keywords 'TRANSFORMING PROTEIN' _struct_keywords.text 'V-SRC SH2 DOMAIN, PHOSPHOTYROSINE RECOGNITION DOMAIN, PP60 SRC SH2 DOMAIN, TRIPEPTIDE, D-AMINO ACID, TRANSFORMING PROTEIN' # 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 ? # _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 ARG A 13 ? LEU A 20 ? ARG A 12 LEU A 19 1 ? 8 HELX_P HELX_P2 2 LEU A 81 ? LYS A 90 ? LEU A 80 LYS A 89 1 ? 10 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id GLU _struct_mon_prot_cis.label_seq_id 5 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id GLU _struct_mon_prot_cis.auth_seq_id 4 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 TRP _struct_mon_prot_cis.pdbx_label_seq_id_2 6 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 TRP _struct_mon_prot_cis.pdbx_auth_seq_id_2 5 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 4.90 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 3 _struct_sheet.details ? # 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 # 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 30 ? GLU A 34 ? PHE A 29 GLU A 33 A 2 TYR A 42 ? ASP A 50 ? TYR A 41 ASP A 49 A 3 GLY A 54 ? ILE A 62 ? GLY A 53 ILE A 61 # 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 LEU A 31 ? O LEU A 30 N SER A 45 ? N SER A 44 A 2 3 O TYR A 42 ? O TYR A 41 N ILE A 62 ? N ILE A 61 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id 1C5 _struct_site.pdbx_auth_seq_id 113 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 16 _struct_site.details 'BINDING SITE FOR RESIDUE 1C5 A 113' # 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 16 ARG A 13 ? ARG A 12 . ? 1_555 ? 2 AC1 16 ARG A 33 ? ARG A 32 . ? 1_555 ? 3 AC1 16 SER A 35 ? SER A 34 . ? 1_555 ? 4 AC1 16 GLU A 36 ? GLU A 35 . ? 1_555 ? 5 AC1 16 THR A 37 ? THR A 36 . ? 1_555 ? 6 AC1 16 CYS A 43 ? CYS A 42 . ? 1_555 ? 7 AC1 16 HIS A 59 ? HIS A 58 . ? 1_555 ? 8 AC1 16 TYR A 60 ? TYR A 59 . ? 1_555 ? 9 AC1 16 LYS A 61 ? LYS A 60 . ? 1_555 ? 10 AC1 16 THR A 73 ? THR A 72 . ? 1_555 ? 11 AC1 16 LYS A 90 ? LYS A 89 . ? 1_655 ? 12 AC1 16 GLY A 94 ? GLY A 93 . ? 1_555 ? 13 AC1 16 HOH C . ? HOH A 117 . ? 1_555 ? 14 AC1 16 HOH C . ? HOH A 118 . ? 1_555 ? 15 AC1 16 HOH C . ? HOH A 119 . ? 1_555 ? 16 AC1 16 HOH C . ? HOH A 127 . ? 1_555 ? # _database_PDB_matrix.entry_id 1BKM _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 1BKM _atom_sites.fract_transf_matrix[1][1] 0.033113 _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] 0.021322 _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] 0.013419 _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 H 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 GLY 1 0 ? ? ? A . n A 1 2 SER 2 1 ? ? ? A . n A 1 3 ALA 3 2 ? ? ? A . n A 1 4 GLU 4 3 3 GLU GLU A . n A 1 5 GLU 5 4 4 GLU GLU A . n A 1 6 TRP 6 5 5 TRP TRP A . n A 1 7 TYR 7 6 6 TYR TYR A . n A 1 8 PHE 8 7 7 PHE PHE A . n A 1 9 GLY 9 8 8 GLY GLY A . n A 1 10 LYS 10 9 9 LYS LYS A . n A 1 11 ILE 11 10 10 ILE ILE A . n A 1 12 THR 12 11 11 THR THR A . n A 1 13 ARG 13 12 12 ARG ARG A . n A 1 14 ARG 14 13 13 ARG ARG A . n A 1 15 GLU 15 14 14 GLU GLU A . n A 1 16 SER 16 15 15 SER SER A . n A 1 17 GLU 17 16 16 GLU GLU A . n A 1 18 ALA 18 17 17 ALA ALA A . n A 1 19 LEU 19 18 18 LEU LEU A . n A 1 20 LEU 20 19 19 LEU LEU A . n A 1 21 LEU 21 20 20 LEU LEU A . n A 1 22 ASN 22 21 21 ASN ASN A . n A 1 23 PRO 23 22 22 PRO PRO A . n A 1 24 GLU 24 23 23 GLU GLU A . n A 1 25 ASN 25 24 24 ASN ASN A . n A 1 26 PRO 26 25 25 PRO PRO A . n A 1 27 ARG 27 26 26 ARG ARG A . n A 1 28 GLY 28 27 27 GLY GLY A . n A 1 29 THR 29 28 28 THR THR A . n A 1 30 PHE 30 29 29 PHE PHE A . n A 1 31 LEU 31 30 30 LEU LEU A . n A 1 32 VAL 32 31 31 VAL VAL A . n A 1 33 ARG 33 32 32 ARG ARG A . n A 1 34 GLU 34 33 33 GLU GLU A . n A 1 35 SER 35 34 34 SER SER A . n A 1 36 GLU 36 35 35 GLU GLU A . n A 1 37 THR 37 36 36 THR THR A . n A 1 38 THR 38 37 37 THR THR A . n A 1 39 LYS 39 38 38 LYS LYS A . n A 1 40 GLY 40 39 39 GLY GLY A . n A 1 41 ALA 41 40 40 ALA ALA A . n A 1 42 TYR 42 41 41 TYR TYR A . n A 1 43 CYS 43 42 42 CYS CYS A . n A 1 44 LEU 44 43 43 LEU LEU A . n A 1 45 SER 45 44 44 SER SER A . n A 1 46 VAL 46 45 45 VAL VAL A . n A 1 47 SER 47 46 46 SER SER A . n A 1 48 ASP 48 47 47 ASP ASP A . n A 1 49 PHE 49 48 48 PHE PHE A . n A 1 50 ASP 50 49 49 ASP ASP A . n A 1 51 ASN 51 50 50 ASN ASN A . n A 1 52 ALA 52 51 51 ALA ALA A . n A 1 53 LYS 53 52 52 LYS LYS A . n A 1 54 GLY 54 53 53 GLY GLY A . n A 1 55 LEU 55 54 54 LEU LEU A . n A 1 56 ASN 56 55 55 ASN ASN A . n A 1 57 VAL 57 56 56 VAL VAL A . n A 1 58 LYS 58 57 57 LYS LYS A . n A 1 59 HIS 59 58 58 HIS HIS A . n A 1 60 TYR 60 59 59 TYR TYR A . n A 1 61 LYS 61 60 60 LYS LYS A . n A 1 62 ILE 62 61 61 ILE ILE A . n A 1 63 ARG 63 62 62 ARG ARG A . n A 1 64 LYS 64 63 63 LYS LYS A . n A 1 65 LEU 65 64 64 LEU LEU A . n A 1 66 ASP 66 65 65 ASP ASP A . n A 1 67 SER 67 66 66 SER SER A . n A 1 68 GLY 68 67 67 GLY GLY A . n A 1 69 GLY 69 68 68 GLY GLY A . n A 1 70 PHE 70 69 69 PHE PHE A . n A 1 71 TYR 71 70 70 TYR TYR A . n A 1 72 ILE 72 71 71 ILE ILE A . n A 1 73 THR 73 72 72 THR THR A . n A 1 74 SER 74 73 73 SER SER A . n A 1 75 ARG 75 74 74 ARG ARG A . n A 1 76 THR 76 75 75 THR THR A . n A 1 77 GLN 77 76 76 GLN GLN A . n A 1 78 PHE 78 77 77 PHE PHE A . n A 1 79 SER 79 78 78 SER SER A . n A 1 80 SER 80 79 79 SER SER A . n A 1 81 LEU 81 80 80 LEU LEU A . n A 1 82 GLN 82 81 81 GLN GLN A . n A 1 83 GLN 83 82 82 GLN GLN A . n A 1 84 LEU 84 83 83 LEU LEU A . n A 1 85 VAL 85 84 84 VAL VAL A . n A 1 86 ALA 86 85 85 ALA ALA A . n A 1 87 TYR 87 86 86 TYR TYR A . n A 1 88 TYR 88 87 87 TYR TYR A . n A 1 89 SER 89 88 88 SER SER A . n A 1 90 LYS 90 89 89 LYS LYS A . n A 1 91 HIS 91 90 90 HIS HIS A . n A 1 92 ALA 92 91 91 ALA ALA A . n A 1 93 ASP 93 92 92 ASP ASP A . n A 1 94 GLY 94 93 93 GLY GLY A . n A 1 95 LEU 95 94 94 LEU LEU A . n A 1 96 CYS 96 95 95 CYS CYS A . n A 1 97 HIS 97 96 96 HIS HIS A . n A 1 98 ARG 98 97 97 ARG ARG A . n A 1 99 LEU 99 98 98 LEU LEU A . n A 1 100 THR 100 99 99 THR THR A . n A 1 101 ASN 101 100 100 ASN ASN A . n A 1 102 VAL 102 101 101 VAL VAL A . n A 1 103 CYS 103 102 102 CYS CYS A . n A 1 104 PRO 104 103 103 PRO PRO A . n A 1 105 THR 105 104 104 THR THR A . n A 1 106 SER 106 105 ? ? ? A . n A 1 107 LYS 107 106 ? ? ? A . n A 1 108 GLU 108 107 ? ? ? A . n A 1 109 PHE 109 108 ? ? ? A . n A 1 110 ILE 110 109 ? ? ? A . n A 1 111 VAL 111 110 ? ? ? A . n A 1 112 THR 112 111 ? ? ? A . n A 1 113 ASP 113 112 ? ? ? 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 1C5 1 113 1 1C5 1C5 A . C 3 HOH 1 114 106 HOH HOH A . C 3 HOH 2 115 107 HOH HOH A . C 3 HOH 3 116 108 HOH HOH A . C 3 HOH 4 117 202 HOH HOH A . C 3 HOH 5 118 204 HOH HOH A . C 3 HOH 6 119 205 HOH HOH A . C 3 HOH 7 120 206 HOH HOH A . C 3 HOH 8 121 207 HOH HOH A . C 3 HOH 9 122 209 HOH HOH A . C 3 HOH 10 123 210 HOH HOH A . C 3 HOH 11 124 211 HOH HOH A . C 3 HOH 12 125 212 HOH HOH A . C 3 HOH 13 126 213 HOH HOH A . C 3 HOH 14 127 214 HOH HOH A . C 3 HOH 15 128 215 HOH HOH A . C 3 HOH 16 129 216 HOH HOH A . C 3 HOH 17 130 217 HOH HOH A . C 3 HOH 18 131 218 HOH HOH A . C 3 HOH 19 132 219 HOH HOH A . C 3 HOH 20 133 220 HOH HOH A . C 3 HOH 21 134 221 HOH HOH A . C 3 HOH 22 135 222 HOH HOH A . C 3 HOH 23 136 224 HOH HOH A . C 3 HOH 24 137 302 HOH HOH A . C 3 HOH 25 138 310 HOH HOH A . C 3 HOH 26 139 316 HOH HOH A . C 3 HOH 27 140 317 HOH HOH A . C 3 HOH 28 141 318 HOH HOH A . C 3 HOH 29 142 319 HOH HOH A . C 3 HOH 30 143 320 HOH HOH A . C 3 HOH 31 144 321 HOH HOH A . C 3 HOH 32 145 322 HOH HOH A . C 3 HOH 33 146 323 HOH HOH A . C 3 HOH 34 147 324 HOH HOH A . C 3 HOH 35 148 325 HOH HOH A . C 3 HOH 36 149 326 HOH HOH A . C 3 HOH 37 150 327 HOH HOH A . C 3 HOH 38 151 328 HOH HOH A . C 3 HOH 39 152 330 HOH HOH A . C 3 HOH 40 153 331 HOH HOH A . C 3 HOH 41 154 332 HOH HOH A . C 3 HOH 42 155 333 HOH HOH A . C 3 HOH 43 156 334 HOH HOH A . C 3 HOH 44 157 335 HOH HOH A . C 3 HOH 45 158 337 HOH HOH A . C 3 HOH 46 159 338 HOH HOH A . C 3 HOH 47 160 341 HOH HOH A . C 3 HOH 48 161 343 HOH HOH A . C 3 HOH 49 162 344 HOH HOH A . C 3 HOH 50 163 346 HOH HOH A . C 3 HOH 51 164 348 HOH HOH A . C 3 HOH 52 165 349 HOH HOH A . C 3 HOH 53 166 350 HOH HOH A . C 3 HOH 54 167 351 HOH HOH A . C 3 HOH 55 168 352 HOH HOH A . C 3 HOH 56 169 353 HOH HOH A . C 3 HOH 57 170 354 HOH HOH A . C 3 HOH 58 171 356 HOH HOH A . C 3 HOH 59 172 357 HOH HOH A . C 3 HOH 60 173 358 HOH HOH A . C 3 HOH 61 174 359 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _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 1997-07-07 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-02 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' Other 6 4 'Structure model' 'Refinement description' # 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 4 'Structure model' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_initial_refinement_model 4 4 'Structure model' struct_ref_seq_dif 5 4 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.process_site' 4 4 'Structure model' '_struct_ref_seq_dif.details' 5 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.1 ? 1 X-PLOR refinement 3.1 ? 2 XDS 'data reduction' . ? 3 XDS 'data scaling' . ? 4 X-PLOR phasing 3.1 ? 5 # _pdbx_entry_details.entry_id 1BKM _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;G-S ARE NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING E-F-I-V-T-D NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING ; _pdbx_entry_details.has_ligand_of_interest ? # 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 CZ A ARG 13 ? ? H1 A HOH 140 ? ? 0.80 2 1 HG1 A THR 11 ? ? H A GLU 14 ? ? 1.03 3 1 OG1 A THR 11 ? ? H A GLU 14 ? ? 1.16 4 1 NH2 A ARG 13 ? ? H1 A HOH 140 ? ? 1.18 5 1 HE A ARG 13 ? ? H2 A HOH 140 ? ? 1.27 6 1 HH21 A ARG 13 ? ? O A HOH 140 ? ? 1.34 7 1 NE A ARG 13 ? ? H1 A HOH 140 ? ? 1.39 8 1 O A ARG 12 ? ? HG A SER 15 ? ? 1.41 9 1 HH21 A ARG 13 ? ? OE1 A GLU 14 ? ? 1.46 10 1 NH2 A ARG 13 ? ? OE1 A GLU 14 ? ? 1.49 11 1 HE A ARG 13 ? ? O A HOH 140 ? ? 1.55 12 1 NH2 A ARG 13 ? ? O A HOH 140 ? ? 1.63 13 1 CZ A ARG 13 ? ? O A HOH 140 ? ? 1.69 14 1 NE A ARG 13 ? ? O A HOH 140 ? ? 1.75 15 1 OG1 A THR 11 ? ? N A GLU 14 ? ? 2.04 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CB A THR 11 ? ? CA A THR 11 ? ? C A THR 11 ? ? 92.60 111.60 -19.00 2.70 N 2 1 CA A THR 11 ? ? CB A THR 11 ? ? OG1 A THR 11 ? ? 124.80 109.00 15.80 2.10 N 3 1 CA A THR 11 ? ? CB A THR 11 ? ? CG2 A THR 11 ? ? 92.65 112.40 -19.75 1.40 N 4 1 NE A ARG 12 ? ? CZ A ARG 12 ? ? NH2 A ARG 12 ? ? 116.59 120.30 -3.71 0.50 N 5 1 NE A ARG 13 ? ? CZ A ARG 13 ? ? NH1 A ARG 13 ? ? 104.74 120.30 -15.56 0.50 N 6 1 NE A ARG 13 ? ? CZ A ARG 13 ? ? NH2 A ARG 13 ? ? 133.77 120.30 13.47 0.50 N 7 1 CA A GLU 14 ? ? CB A GLU 14 ? ? CG A GLU 14 ? ? 129.45 113.40 16.05 2.20 N 8 1 CG A GLU 14 ? ? CD A GLU 14 ? ? OE1 A GLU 14 ? ? 131.56 118.30 13.26 2.00 N 9 1 CG A GLU 14 ? ? CD A GLU 14 ? ? OE2 A GLU 14 ? ? 103.52 118.30 -14.78 2.00 N 10 1 CA A LEU 30 ? ? CB A LEU 30 ? ? CG A LEU 30 ? ? 129.64 115.30 14.34 2.30 N 11 1 NE A ARG 32 ? ? CZ A ARG 32 ? ? NH1 A ARG 32 ? ? 123.64 120.30 3.34 0.50 N 12 1 CB A TYR 87 ? ? CG A TYR 87 ? ? CD1 A TYR 87 ? ? 117.37 121.00 -3.63 0.60 N # 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 LYS A 9 ? ? -90.49 39.12 2 1 THR A 99 ? ? -120.80 -103.88 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 TYR A 41 ? ? 0.079 'SIDE CHAIN' 2 1 TYR A 70 ? ? 0.073 'SIDE CHAIN' 3 1 ARG A 97 ? ? 0.088 'SIDE CHAIN' # 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 GLU 3 ? CB ? A GLU 4 CB 2 1 Y 1 A GLU 3 ? CG ? A GLU 4 CG 3 1 Y 1 A GLU 3 ? CD ? A GLU 4 CD 4 1 Y 1 A GLU 3 ? OE1 ? A GLU 4 OE1 5 1 Y 1 A GLU 3 ? OE2 ? A GLU 4 OE2 6 1 Y 1 A GLU 4 ? CG ? A GLU 5 CG 7 1 Y 1 A GLU 4 ? CD ? A GLU 5 CD 8 1 Y 1 A GLU 4 ? OE1 ? A GLU 5 OE1 9 1 Y 1 A GLU 4 ? OE2 ? A GLU 5 OE2 10 1 Y 1 A TYR 6 ? OH ? A TYR 7 OH # 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 0 ? A GLY 1 2 1 Y 1 A SER 1 ? A SER 2 3 1 Y 1 A ALA 2 ? A ALA 3 4 1 Y 1 A SER 105 ? A SER 106 5 1 Y 1 A LYS 106 ? A LYS 107 6 1 Y 1 A GLU 107 ? A GLU 108 7 1 Y 1 A PHE 108 ? A PHE 109 8 1 Y 1 A ILE 109 ? A ILE 110 9 1 Y 1 A VAL 110 ? A VAL 111 10 1 Y 1 A THR 111 ? A THR 112 11 1 Y 1 A ASP 112 ? A ASP 113 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '[[O-PHOSPHONO-N-ACETYL-TYROSINYL]-GLUTAMYL-3[CYCLOHEXYLMETHYL]ALANINYL]-AMINE' 1C5 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1SPS _pdbx_initial_refinement_model.details 'PROTEIN MODEL FROM 1SPS' #