data_1YP5 # _entry.id 1YP5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 1YP5 pdb_00001yp5 10.2210/pdb1yp5/pdb RCSB RCSB031773 ? ? WWPDB D_1000031773 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2006-01-17 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-09-26 5 'Structure model' 1 4 2024-03-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _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' Advisory 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Structure summary' 7 5 'Structure model' 'Data collection' 8 5 'Structure model' 'Database references' # 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' audit_author 2 4 'Structure model' citation_author 3 4 'Structure model' diffrn_radiation_wavelength 4 4 'Structure model' diffrn_source 5 5 'Structure model' chem_comp_atom 6 5 'Structure model' chem_comp_bond 7 5 'Structure model' database_2 # 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' '_audit_author.name' 2 4 'Structure model' '_citation_author.name' 3 4 'Structure model' '_diffrn_radiation_wavelength.wavelength' 4 4 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 5 4 'Structure model' '_diffrn_source.pdbx_wavelength_list' 6 5 'Structure model' '_database_2.pdbx_DOI' 7 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YP5 _pdbx_database_status.recvd_initial_deposition_date 2005-01-29 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1R6S _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Gonfloni, S.' 1 ? 'Kursula, P.' 2 ? 'Sacco, R.' 3 ? 'Cesareni, G.' 4 ? 'Wilmanns, M.' 5 ? # _citation.id primary _citation.title 'Yeast Myo5 SH3 domain, tetragonal crystal form' _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 'Gonfloni, S.' 1 ? primary 'Kursula, P.' 2 ? primary 'Sacco, R.' 3 ? primary 'Cesareni, G.' 4 ? primary 'Wilmanns, M.' 5 ? # 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 'Myosin-5 isoform' 6376.206 1 ? ? 'SH3 domain' ? 2 water nat water 18.015 60 ? ? ? ? # _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 PMFEAAYDFPGSGSPSELPLKKGDVIYITREEPSGWSLGKLLDGSKEGWVPTAYMKPH _entity_poly.pdbx_seq_one_letter_code_can PMFEAAYDFPGSGSPSELPLKKGDVIYITREEPSGWSLGKLLDGSKEGWVPTAYMKPH _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 PRO n 1 2 MET n 1 3 PHE n 1 4 GLU n 1 5 ALA n 1 6 ALA n 1 7 TYR n 1 8 ASP n 1 9 PHE n 1 10 PRO n 1 11 GLY n 1 12 SER n 1 13 GLY n 1 14 SER n 1 15 PRO n 1 16 SER n 1 17 GLU n 1 18 LEU n 1 19 PRO n 1 20 LEU n 1 21 LYS n 1 22 LYS n 1 23 GLY n 1 24 ASP n 1 25 VAL n 1 26 ILE n 1 27 TYR n 1 28 ILE n 1 29 THR n 1 30 ARG n 1 31 GLU n 1 32 GLU n 1 33 PRO n 1 34 SER n 1 35 GLY n 1 36 TRP n 1 37 SER n 1 38 LEU n 1 39 GLY n 1 40 LYS n 1 41 LEU n 1 42 LEU n 1 43 ASP n 1 44 GLY n 1 45 SER n 1 46 LYS n 1 47 GLU n 1 48 GLY n 1 49 TRP n 1 50 VAL n 1 51 PRO n 1 52 THR n 1 53 ALA n 1 54 TYR n 1 55 MET n 1 56 LYS n 1 57 PRO n 1 58 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 ;baker's yeast ; _entity_src_gen.gene_src_genus Saccharomyces _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Saccharomyces cerevisiae' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 4932 _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 ? _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 ? # 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 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 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 # 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 PRO 1 1 1 PRO PRO A . n A 1 2 MET 2 2 2 MET MET A . n A 1 3 PHE 3 3 3 PHE PHE A . n A 1 4 GLU 4 4 4 GLU GLU A . n A 1 5 ALA 5 5 5 ALA ALA A . n A 1 6 ALA 6 6 6 ALA ALA A . n A 1 7 TYR 7 7 7 TYR TYR A . n A 1 8 ASP 8 8 8 ASP ASP A . n A 1 9 PHE 9 9 9 PHE PHE A . n A 1 10 PRO 10 10 10 PRO PRO A . n A 1 11 GLY 11 11 11 GLY GLY A . n A 1 12 SER 12 12 12 SER SER A . n A 1 13 GLY 13 13 13 GLY GLY A . n A 1 14 SER 14 14 14 SER SER A . n A 1 15 PRO 15 15 15 PRO PRO A . n A 1 16 SER 16 16 16 SER SER A . n A 1 17 GLU 17 17 17 GLU GLU A . n A 1 18 LEU 18 18 18 LEU LEU A . n A 1 19 PRO 19 19 19 PRO PRO A . n A 1 20 LEU 20 20 20 LEU LEU A . n A 1 21 LYS 21 21 21 LYS LYS A . n A 1 22 LYS 22 22 22 LYS LYS A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 ASP 24 24 24 ASP ASP A . n A 1 25 VAL 25 25 25 VAL VAL A . n A 1 26 ILE 26 26 26 ILE ILE A . n A 1 27 TYR 27 27 27 TYR TYR A . n A 1 28 ILE 28 28 28 ILE ILE A . n A 1 29 THR 29 29 29 THR THR A . n A 1 30 ARG 30 30 30 ARG ARG A . n A 1 31 GLU 31 31 31 GLU GLU A . n A 1 32 GLU 32 32 32 GLU GLU A . n A 1 33 PRO 33 33 33 PRO PRO A . n A 1 34 SER 34 34 34 SER SER A . n A 1 35 GLY 35 35 35 GLY GLY A . n A 1 36 TRP 36 36 36 TRP TRP A . n A 1 37 SER 37 37 37 SER SER A . n A 1 38 LEU 38 38 38 LEU LEU A . n A 1 39 GLY 39 39 39 GLY GLY A . n A 1 40 LYS 40 40 40 LYS LYS A . n A 1 41 LEU 41 41 41 LEU LEU A . n A 1 42 LEU 42 42 42 LEU LEU A . n A 1 43 ASP 43 43 43 ASP ASP A . n A 1 44 GLY 44 44 44 GLY GLY A . n A 1 45 SER 45 45 45 SER SER A . n A 1 46 LYS 46 46 46 LYS LYS A . n A 1 47 GLU 47 47 47 GLU GLU A . n A 1 48 GLY 48 48 48 GLY GLY A . n A 1 49 TRP 49 49 49 TRP TRP A . n A 1 50 VAL 50 50 50 VAL VAL A . n A 1 51 PRO 51 51 51 PRO PRO A . n A 1 52 THR 52 52 52 THR THR A . n A 1 53 ALA 53 53 53 ALA ALA A . n A 1 54 TYR 54 54 54 TYR TYR A . n A 1 55 MET 55 55 55 MET MET A . n A 1 56 LYS 56 56 56 LYS LYS A . n A 1 57 PRO 57 57 57 PRO PRO A . n A 1 58 HIS 58 58 58 HIS HIS 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 HOH 1 59 57 HOH HOH A . B 2 HOH 2 60 58 HOH HOH A . B 2 HOH 3 61 59 HOH HOH A . B 2 HOH 4 62 60 HOH HOH A . B 2 HOH 5 63 61 HOH HOH A . B 2 HOH 6 64 62 HOH HOH A . B 2 HOH 7 65 63 HOH HOH A . B 2 HOH 8 66 64 HOH HOH A . B 2 HOH 9 67 65 HOH HOH A . B 2 HOH 10 68 66 HOH HOH A . B 2 HOH 11 69 67 HOH HOH A . B 2 HOH 12 70 68 HOH HOH A . B 2 HOH 13 71 69 HOH HOH A . B 2 HOH 14 72 70 HOH HOH A . B 2 HOH 15 73 71 HOH HOH A . B 2 HOH 16 74 72 HOH HOH A . B 2 HOH 17 75 73 HOH HOH A . B 2 HOH 18 76 74 HOH HOH A . B 2 HOH 19 77 75 HOH HOH A . B 2 HOH 20 78 76 HOH HOH A . B 2 HOH 21 79 77 HOH HOH A . B 2 HOH 22 80 78 HOH HOH A . B 2 HOH 23 81 79 HOH HOH A . B 2 HOH 24 82 80 HOH HOH A . B 2 HOH 25 83 81 HOH HOH A . B 2 HOH 26 84 82 HOH HOH A . B 2 HOH 27 85 83 HOH HOH A . B 2 HOH 28 86 84 HOH HOH A . B 2 HOH 29 87 85 HOH HOH A . B 2 HOH 30 88 86 HOH HOH A . B 2 HOH 31 89 87 HOH HOH A . B 2 HOH 32 90 88 HOH HOH A . B 2 HOH 33 91 89 HOH HOH A . B 2 HOH 34 92 90 HOH HOH A . B 2 HOH 35 93 91 HOH HOH A . B 2 HOH 36 94 92 HOH HOH A . B 2 HOH 37 95 93 HOH HOH A . B 2 HOH 38 96 94 HOH HOH A . B 2 HOH 39 97 95 HOH HOH A . B 2 HOH 40 98 96 HOH HOH A . B 2 HOH 41 99 97 HOH HOH A . B 2 HOH 42 100 98 HOH HOH A . B 2 HOH 43 101 99 HOH HOH A . B 2 HOH 44 102 100 HOH HOH A . B 2 HOH 45 103 101 HOH HOH A . B 2 HOH 46 104 102 HOH HOH A . B 2 HOH 47 105 103 HOH HOH A . B 2 HOH 48 106 104 HOH HOH A . B 2 HOH 49 107 105 HOH HOH A . B 2 HOH 50 108 106 HOH HOH A . B 2 HOH 51 109 107 HOH HOH A . B 2 HOH 52 110 108 HOH HOH A . B 2 HOH 53 111 109 HOH HOH A . B 2 HOH 54 112 110 HOH HOH A . B 2 HOH 55 113 111 HOH HOH A . B 2 HOH 56 114 112 HOH HOH A . B 2 HOH 57 115 113 HOH HOH A . B 2 HOH 58 116 114 HOH HOH A . B 2 HOH 59 117 115 HOH HOH A . B 2 HOH 60 118 116 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language REFMAC refinement 5.2.0000 ? 1 ? ? ? ? XDS 'data reduction' . ? 2 ? ? ? ? XDS 'data scaling' . ? 3 ? ? ? ? MOLREP phasing . ? 4 ? ? ? ? # _cell.entry_id 1YP5 _cell.length_a 34.620 _cell.length_b 34.620 _cell.length_c 99.480 _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 1YP5 _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1YP5 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.3 _exptl_crystal.density_percent_sol 46 _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.temp 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 295K' _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 MARRESEARCH _diffrn_detector.pdbx_collection_date ? _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.81 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE X11' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline X11 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.81 # _reflns.entry_id 1YP5 _reflns.observed_criterion_sigma_F -3 _reflns.observed_criterion_sigma_I -3 _reflns.d_resolution_high 1.68 _reflns.d_resolution_low 20 _reflns.number_all 7261 _reflns.number_obs 7261 _reflns.percent_possible_obs 96.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.053 _reflns.pdbx_netI_over_sigmaI 17.6 _reflns.B_iso_Wilson_estimate 26 _reflns.pdbx_redundancy 5 _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 # _reflns_shell.d_res_high 1.68 _reflns_shell.d_res_low 1.75 _reflns_shell.percent_possible_all 99.6 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.422 _reflns_shell.meanI_over_sigI_obs 3.7 _reflns_shell.pdbx_redundancy 4.9 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 824 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1YP5 _refine.ls_number_reflns_obs 7259 _refine.ls_number_reflns_all 7259 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F -3 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.00 _refine.ls_d_res_high 1.68 _refine.ls_percent_reflns_obs 96.89 _refine.ls_R_factor_obs 0.19156 _refine.ls_R_factor_all 0.19156 _refine.ls_R_factor_R_work 0.18997 _refine.ls_R_factor_R_free 0.22235 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 363 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.960 _refine.correlation_coeff_Fo_to_Fc_free 0.945 _refine.B_iso_mean 22.210 _refine.aniso_B[1][1] 1.01 _refine.aniso_B[2][2] 1.01 _refine.aniso_B[3][3] -2.02 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model 'TLS REFINEMENT' _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.109 _refine.pdbx_overall_ESU_R_Free 0.106 _refine.overall_SU_ML 0.083 _refine.overall_SU_B 5.089 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _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 450 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 60 _refine_hist.number_atoms_total 510 _refine_hist.d_res_high 1.68 _refine_hist.d_res_low 20.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.008 0.022 ? 484 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 427 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.162 1.993 ? 658 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.731 3.000 ? 1011 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.376 5.000 ? 61 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 20.227 24.118 ? 17 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 9.870 15.000 ? 79 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 27.177 15.000 ? 1 'X-RAY DIFFRACTION' ? r_chiral_restr 0.078 0.200 ? 65 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.004 0.020 ? 538 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 93 'X-RAY DIFFRACTION' ? r_nbd_refined 0.189 0.200 ? 64 'X-RAY DIFFRACTION' ? r_nbd_other 0.241 0.200 ? 413 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other 0.083 0.200 ? 219 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.170 0.200 ? 37 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.243 0.200 ? 5 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.209 0.200 ? 25 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.132 0.200 ? 9 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.987 2.000 ? 388 'X-RAY DIFFRACTION' ? r_mcbond_other 0.176 2.000 ? 120 'X-RAY DIFFRACTION' ? r_mcangle_it 1.163 3.000 ? 486 'X-RAY DIFFRACTION' ? r_scbond_it 1.573 4.000 ? 229 'X-RAY DIFFRACTION' ? r_scangle_it 2.022 5.000 ? 172 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.680 _refine_ls_shell.d_res_low 1.723 _refine_ls_shell.number_reflns_R_work 503 _refine_ls_shell.R_factor_R_work 0.28 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.359 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 26 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 1YP5 _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 # _struct.entry_id 1YP5 _struct.title 'Yeast Myo5 SH3 domain, tetragonal crystal form' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YP5 _struct_keywords.pdbx_keywords 'CONTRACTILE PROTEIN' _struct_keywords.text 'SH3 domain, CONTRACTILE 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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code MYS5_YEAST _struct_ref.pdbx_db_accession Q04439 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code PMFEAAYDFPGSGSPSELPLKKGDVIYITREEPSGWSLGKLLDGSKEGWVPTAYMKPH _struct_ref.pdbx_align_begin 1088 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1YP5 _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 58 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q04439 _struct_ref_seq.db_align_beg 1088 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 1145 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 58 # _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 # _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 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _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 A 3 4 ? anti-parallel A 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 47 ? PRO A 51 ? GLU A 47 PRO A 51 A 2 TRP A 36 ? LEU A 41 ? TRP A 36 LEU A 41 A 3 VAL A 25 ? GLU A 31 ? VAL A 25 GLU A 31 A 4 MET A 2 ? ALA A 5 ? MET A 2 ALA A 5 A 5 MET A 55 ? PRO A 57 ? MET A 55 PRO A 57 # 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 VAL A 50 ? O VAL A 50 N SER A 37 ? N SER A 37 A 2 3 O LYS A 40 ? O LYS A 40 N TYR A 27 ? N TYR A 27 A 3 4 O ILE A 26 ? O ILE A 26 N PHE A 3 ? N PHE A 3 A 4 5 N GLU A 4 ? N GLU A 4 O LYS A 56 ? O LYS A 56 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 75 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 113 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.19 # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 2.1890 _pdbx_refine_tls.origin_y 8.8090 _pdbx_refine_tls.origin_z 9.2660 _pdbx_refine_tls.T[1][1] -0.1004 _pdbx_refine_tls.T[2][2] -0.1153 _pdbx_refine_tls.T[3][3] -0.0508 _pdbx_refine_tls.T[1][2] -0.0134 _pdbx_refine_tls.T[1][3] -0.0121 _pdbx_refine_tls.T[2][3] -0.0017 _pdbx_refine_tls.L[1][1] 1.7072 _pdbx_refine_tls.L[2][2] 1.9520 _pdbx_refine_tls.L[3][3] 5.1987 _pdbx_refine_tls.L[1][2] -0.4604 _pdbx_refine_tls.L[1][3] 0.3479 _pdbx_refine_tls.L[2][3] 0.5994 _pdbx_refine_tls.S[1][1] 0.0201 _pdbx_refine_tls.S[1][2] -0.1929 _pdbx_refine_tls.S[1][3] 0.0153 _pdbx_refine_tls.S[2][1] -0.0388 _pdbx_refine_tls.S[2][2] -0.0213 _pdbx_refine_tls.S[2][3] 0.1676 _pdbx_refine_tls.S[3][1] -0.1039 _pdbx_refine_tls.S[3][2] -0.3064 _pdbx_refine_tls.S[3][3] 0.0012 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 1 _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 58 _pdbx_refine_tls_group.end_auth_seq_id 58 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASP N N N N 41 ASP CA C N S 42 ASP C C N N 43 ASP O O N N 44 ASP CB C N N 45 ASP CG C N N 46 ASP OD1 O N N 47 ASP OD2 O N N 48 ASP OXT O N N 49 ASP H H N N 50 ASP H2 H N N 51 ASP HA H N N 52 ASP HB2 H N N 53 ASP HB3 H N N 54 ASP HD2 H N N 55 ASP HXT H N N 56 GLU N N N N 57 GLU CA C N S 58 GLU C C N N 59 GLU O O N N 60 GLU CB C N N 61 GLU CG C N N 62 GLU CD C N N 63 GLU OE1 O N N 64 GLU OE2 O N N 65 GLU OXT O N N 66 GLU H H N N 67 GLU H2 H N N 68 GLU HA H N N 69 GLU HB2 H N N 70 GLU HB3 H N N 71 GLU HG2 H N N 72 GLU HG3 H N N 73 GLU HE2 H N N 74 GLU HXT H N N 75 GLY N N N N 76 GLY CA C N N 77 GLY C C N N 78 GLY O O N N 79 GLY OXT O N N 80 GLY H H N N 81 GLY H2 H N N 82 GLY HA2 H N N 83 GLY HA3 H N N 84 GLY HXT H N N 85 HIS N N N N 86 HIS CA C N S 87 HIS C C N N 88 HIS O O N N 89 HIS CB C N N 90 HIS CG C Y N 91 HIS ND1 N Y N 92 HIS CD2 C Y N 93 HIS CE1 C Y N 94 HIS NE2 N Y N 95 HIS OXT O N N 96 HIS H H N N 97 HIS H2 H N N 98 HIS HA H N N 99 HIS HB2 H N N 100 HIS HB3 H N N 101 HIS HD1 H N N 102 HIS HD2 H N N 103 HIS HE1 H N N 104 HIS HE2 H N N 105 HIS HXT H N N 106 HOH O O N N 107 HOH H1 H N N 108 HOH H2 H N N 109 ILE N N N N 110 ILE CA C N S 111 ILE C C N N 112 ILE O O N N 113 ILE CB C N S 114 ILE CG1 C N N 115 ILE CG2 C N N 116 ILE CD1 C N N 117 ILE OXT O N N 118 ILE H H N N 119 ILE H2 H N N 120 ILE HA H N N 121 ILE HB H N N 122 ILE HG12 H N N 123 ILE HG13 H N N 124 ILE HG21 H N N 125 ILE HG22 H N N 126 ILE HG23 H N N 127 ILE HD11 H N N 128 ILE HD12 H N N 129 ILE HD13 H N N 130 ILE HXT H N N 131 LEU N N N N 132 LEU CA C N S 133 LEU C C N N 134 LEU O O N N 135 LEU CB C N N 136 LEU CG C N N 137 LEU CD1 C N N 138 LEU CD2 C N N 139 LEU OXT O N N 140 LEU H H N N 141 LEU H2 H N N 142 LEU HA H N N 143 LEU HB2 H N N 144 LEU HB3 H N N 145 LEU HG H N N 146 LEU HD11 H N N 147 LEU HD12 H N N 148 LEU HD13 H N N 149 LEU HD21 H N N 150 LEU HD22 H N N 151 LEU HD23 H N N 152 LEU HXT H N N 153 LYS N N N N 154 LYS CA C N S 155 LYS C C N N 156 LYS O O N N 157 LYS CB C N N 158 LYS CG C N N 159 LYS CD C N N 160 LYS CE C N N 161 LYS NZ N N N 162 LYS OXT O N N 163 LYS H H N N 164 LYS H2 H N N 165 LYS HA H N N 166 LYS HB2 H N N 167 LYS HB3 H N N 168 LYS HG2 H N N 169 LYS HG3 H N N 170 LYS HD2 H N N 171 LYS HD3 H N N 172 LYS HE2 H N N 173 LYS HE3 H N N 174 LYS HZ1 H N N 175 LYS HZ2 H N N 176 LYS HZ3 H N N 177 LYS HXT H N N 178 MET N N N N 179 MET CA C N S 180 MET C C N N 181 MET O O N N 182 MET CB C N N 183 MET CG C N N 184 MET SD S N N 185 MET CE C N N 186 MET OXT O N N 187 MET H H N N 188 MET H2 H N N 189 MET HA H N N 190 MET HB2 H N N 191 MET HB3 H N N 192 MET HG2 H N N 193 MET HG3 H N N 194 MET HE1 H N N 195 MET HE2 H N N 196 MET HE3 H N N 197 MET HXT H N N 198 PHE N N N N 199 PHE CA C N S 200 PHE C C N N 201 PHE O O N N 202 PHE CB C N N 203 PHE CG C Y N 204 PHE CD1 C Y N 205 PHE CD2 C Y N 206 PHE CE1 C Y N 207 PHE CE2 C Y N 208 PHE CZ C Y N 209 PHE OXT O N N 210 PHE H H N N 211 PHE H2 H N N 212 PHE HA H N N 213 PHE HB2 H N N 214 PHE HB3 H N N 215 PHE HD1 H N N 216 PHE HD2 H N N 217 PHE HE1 H N N 218 PHE HE2 H N N 219 PHE HZ H N N 220 PHE HXT H N N 221 PRO N N N N 222 PRO CA C N S 223 PRO C C N N 224 PRO O O N N 225 PRO CB C N N 226 PRO CG C N N 227 PRO CD C N N 228 PRO OXT O N N 229 PRO H H N N 230 PRO HA H N N 231 PRO HB2 H N N 232 PRO HB3 H N N 233 PRO HG2 H N N 234 PRO HG3 H N N 235 PRO HD2 H N N 236 PRO HD3 H N N 237 PRO HXT H N N 238 SER N N N N 239 SER CA C N S 240 SER C C N N 241 SER O O N N 242 SER CB C N N 243 SER OG O N N 244 SER OXT O N N 245 SER H H N N 246 SER H2 H N N 247 SER HA H N N 248 SER HB2 H N N 249 SER HB3 H N N 250 SER HG H N N 251 SER HXT H N N 252 THR N N N N 253 THR CA C N S 254 THR C C N N 255 THR O O N N 256 THR CB C N R 257 THR OG1 O N N 258 THR CG2 C N N 259 THR OXT O N N 260 THR H H N N 261 THR H2 H N N 262 THR HA H N N 263 THR HB H N N 264 THR HG1 H N N 265 THR HG21 H N N 266 THR HG22 H N N 267 THR HG23 H N N 268 THR HXT H N N 269 TRP N N N N 270 TRP CA C N S 271 TRP C C N N 272 TRP O O N N 273 TRP CB C N N 274 TRP CG C Y N 275 TRP CD1 C Y N 276 TRP CD2 C Y N 277 TRP NE1 N Y N 278 TRP CE2 C Y N 279 TRP CE3 C Y N 280 TRP CZ2 C Y N 281 TRP CZ3 C Y N 282 TRP CH2 C Y N 283 TRP OXT O N N 284 TRP H H N N 285 TRP H2 H N N 286 TRP HA H N N 287 TRP HB2 H N N 288 TRP HB3 H N N 289 TRP HD1 H N N 290 TRP HE1 H N N 291 TRP HE3 H N N 292 TRP HZ2 H N N 293 TRP HZ3 H N N 294 TRP HH2 H N N 295 TRP HXT H N N 296 TYR N N N N 297 TYR CA C N S 298 TYR C C N N 299 TYR O O N N 300 TYR CB C N N 301 TYR CG C Y N 302 TYR CD1 C Y N 303 TYR CD2 C Y N 304 TYR CE1 C Y N 305 TYR CE2 C Y N 306 TYR CZ C Y N 307 TYR OH O N N 308 TYR OXT O N N 309 TYR H H N N 310 TYR H2 H N N 311 TYR HA H N N 312 TYR HB2 H N N 313 TYR HB3 H N N 314 TYR HD1 H N N 315 TYR HD2 H N N 316 TYR HE1 H N N 317 TYR HE2 H N N 318 TYR HH H N N 319 TYR HXT H N N 320 VAL N N N N 321 VAL CA C N S 322 VAL C C N N 323 VAL O O N N 324 VAL CB C N N 325 VAL CG1 C N N 326 VAL CG2 C N N 327 VAL OXT O N N 328 VAL H H N N 329 VAL H2 H N N 330 VAL HA H N N 331 VAL HB H N N 332 VAL HG11 H N N 333 VAL HG12 H N N 334 VAL HG13 H N N 335 VAL HG21 H N N 336 VAL HG22 H N N 337 VAL HG23 H N N 338 VAL HXT H N N 339 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASP N CA sing N N 39 ASP N H sing N N 40 ASP N H2 sing N N 41 ASP CA C sing N N 42 ASP CA CB sing N N 43 ASP CA HA sing N N 44 ASP C O doub N N 45 ASP C OXT sing N N 46 ASP CB CG sing N N 47 ASP CB HB2 sing N N 48 ASP CB HB3 sing N N 49 ASP CG OD1 doub N N 50 ASP CG OD2 sing N N 51 ASP OD2 HD2 sing N N 52 ASP OXT HXT sing N N 53 GLU N CA sing N N 54 GLU N H sing N N 55 GLU N H2 sing N N 56 GLU CA C sing N N 57 GLU CA CB sing N N 58 GLU CA HA sing N N 59 GLU C O doub N N 60 GLU C OXT sing N N 61 GLU CB CG sing N N 62 GLU CB HB2 sing N N 63 GLU CB HB3 sing N N 64 GLU CG CD sing N N 65 GLU CG HG2 sing N N 66 GLU CG HG3 sing N N 67 GLU CD OE1 doub N N 68 GLU CD OE2 sing N N 69 GLU OE2 HE2 sing N N 70 GLU OXT HXT sing N N 71 GLY N CA sing N N 72 GLY N H sing N N 73 GLY N H2 sing N N 74 GLY CA C sing N N 75 GLY CA HA2 sing N N 76 GLY CA HA3 sing N N 77 GLY C O doub N N 78 GLY C OXT sing N N 79 GLY OXT HXT sing N N 80 HIS N CA sing N N 81 HIS N H sing N N 82 HIS N H2 sing N N 83 HIS CA C sing N N 84 HIS CA CB sing N N 85 HIS CA HA sing N N 86 HIS C O doub N N 87 HIS C OXT sing N N 88 HIS CB CG sing N N 89 HIS CB HB2 sing N N 90 HIS CB HB3 sing N N 91 HIS CG ND1 sing Y N 92 HIS CG CD2 doub Y N 93 HIS ND1 CE1 doub Y N 94 HIS ND1 HD1 sing N N 95 HIS CD2 NE2 sing Y N 96 HIS CD2 HD2 sing N N 97 HIS CE1 NE2 sing Y N 98 HIS CE1 HE1 sing N N 99 HIS NE2 HE2 sing N N 100 HIS OXT HXT sing N N 101 HOH O H1 sing N N 102 HOH O H2 sing N N 103 ILE N CA sing N N 104 ILE N H sing N N 105 ILE N H2 sing N N 106 ILE CA C sing N N 107 ILE CA CB sing N N 108 ILE CA HA sing N N 109 ILE C O doub N N 110 ILE C OXT sing N N 111 ILE CB CG1 sing N N 112 ILE CB CG2 sing N N 113 ILE CB HB sing N N 114 ILE CG1 CD1 sing N N 115 ILE CG1 HG12 sing N N 116 ILE CG1 HG13 sing N N 117 ILE CG2 HG21 sing N N 118 ILE CG2 HG22 sing N N 119 ILE CG2 HG23 sing N N 120 ILE CD1 HD11 sing N N 121 ILE CD1 HD12 sing N N 122 ILE CD1 HD13 sing N N 123 ILE OXT HXT sing N N 124 LEU N CA sing N N 125 LEU N H sing N N 126 LEU N H2 sing N N 127 LEU CA C sing N N 128 LEU CA CB sing N N 129 LEU CA HA sing N N 130 LEU C O doub N N 131 LEU C OXT sing N N 132 LEU CB CG sing N N 133 LEU CB HB2 sing N N 134 LEU CB HB3 sing N N 135 LEU CG CD1 sing N N 136 LEU CG CD2 sing N N 137 LEU CG HG sing N N 138 LEU CD1 HD11 sing N N 139 LEU CD1 HD12 sing N N 140 LEU CD1 HD13 sing N N 141 LEU CD2 HD21 sing N N 142 LEU CD2 HD22 sing N N 143 LEU CD2 HD23 sing N N 144 LEU OXT HXT sing N N 145 LYS N CA sing N N 146 LYS N H sing N N 147 LYS N H2 sing N N 148 LYS CA C sing N N 149 LYS CA CB sing N N 150 LYS CA HA sing N N 151 LYS C O doub N N 152 LYS C OXT sing N N 153 LYS CB CG sing N N 154 LYS CB HB2 sing N N 155 LYS CB HB3 sing N N 156 LYS CG CD sing N N 157 LYS CG HG2 sing N N 158 LYS CG HG3 sing N N 159 LYS CD CE sing N N 160 LYS CD HD2 sing N N 161 LYS CD HD3 sing N N 162 LYS CE NZ sing N N 163 LYS CE HE2 sing N N 164 LYS CE HE3 sing N N 165 LYS NZ HZ1 sing N N 166 LYS NZ HZ2 sing N N 167 LYS NZ HZ3 sing N N 168 LYS OXT HXT sing N N 169 MET N CA sing N N 170 MET N H sing N N 171 MET N H2 sing N N 172 MET CA C sing N N 173 MET CA CB sing N N 174 MET CA HA sing N N 175 MET C O doub N N 176 MET C OXT sing N N 177 MET CB CG sing N N 178 MET CB HB2 sing N N 179 MET CB HB3 sing N N 180 MET CG SD sing N N 181 MET CG HG2 sing N N 182 MET CG HG3 sing N N 183 MET SD CE sing N N 184 MET CE HE1 sing N N 185 MET CE HE2 sing N N 186 MET CE HE3 sing N N 187 MET OXT HXT sing N N 188 PHE N CA sing N N 189 PHE N H sing N N 190 PHE N H2 sing N N 191 PHE CA C sing N N 192 PHE CA CB sing N N 193 PHE CA HA sing N N 194 PHE C O doub N N 195 PHE C OXT sing N N 196 PHE CB CG sing N N 197 PHE CB HB2 sing N N 198 PHE CB HB3 sing N N 199 PHE CG CD1 doub Y N 200 PHE CG CD2 sing Y N 201 PHE CD1 CE1 sing Y N 202 PHE CD1 HD1 sing N N 203 PHE CD2 CE2 doub Y N 204 PHE CD2 HD2 sing N N 205 PHE CE1 CZ doub Y N 206 PHE CE1 HE1 sing N N 207 PHE CE2 CZ sing Y N 208 PHE CE2 HE2 sing N N 209 PHE CZ HZ sing N N 210 PHE OXT HXT sing N N 211 PRO N CA sing N N 212 PRO N CD sing N N 213 PRO N H sing N N 214 PRO CA C sing N N 215 PRO CA CB sing N N 216 PRO CA HA sing N N 217 PRO C O doub N N 218 PRO C OXT sing N N 219 PRO CB CG sing N N 220 PRO CB HB2 sing N N 221 PRO CB HB3 sing N N 222 PRO CG CD sing N N 223 PRO CG HG2 sing N N 224 PRO CG HG3 sing N N 225 PRO CD HD2 sing N N 226 PRO CD HD3 sing N N 227 PRO OXT HXT sing N N 228 SER N CA sing N N 229 SER N H sing N N 230 SER N H2 sing N N 231 SER CA C sing N N 232 SER CA CB sing N N 233 SER CA HA sing N N 234 SER C O doub N N 235 SER C OXT sing N N 236 SER CB OG sing N N 237 SER CB HB2 sing N N 238 SER CB HB3 sing N N 239 SER OG HG sing N N 240 SER OXT HXT sing N N 241 THR N CA sing N N 242 THR N H sing N N 243 THR N H2 sing N N 244 THR CA C sing N N 245 THR CA CB sing N N 246 THR CA HA sing N N 247 THR C O doub N N 248 THR C OXT sing N N 249 THR CB OG1 sing N N 250 THR CB CG2 sing N N 251 THR CB HB sing N N 252 THR OG1 HG1 sing N N 253 THR CG2 HG21 sing N N 254 THR CG2 HG22 sing N N 255 THR CG2 HG23 sing N N 256 THR OXT HXT sing N N 257 TRP N CA sing N N 258 TRP N H sing N N 259 TRP N H2 sing N N 260 TRP CA C sing N N 261 TRP CA CB sing N N 262 TRP CA HA sing N N 263 TRP C O doub N N 264 TRP C OXT sing N N 265 TRP CB CG sing N N 266 TRP CB HB2 sing N N 267 TRP CB HB3 sing N N 268 TRP CG CD1 doub Y N 269 TRP CG CD2 sing Y N 270 TRP CD1 NE1 sing Y N 271 TRP CD1 HD1 sing N N 272 TRP CD2 CE2 doub Y N 273 TRP CD2 CE3 sing Y N 274 TRP NE1 CE2 sing Y N 275 TRP NE1 HE1 sing N N 276 TRP CE2 CZ2 sing Y N 277 TRP CE3 CZ3 doub Y N 278 TRP CE3 HE3 sing N N 279 TRP CZ2 CH2 doub Y N 280 TRP CZ2 HZ2 sing N N 281 TRP CZ3 CH2 sing Y N 282 TRP CZ3 HZ3 sing N N 283 TRP CH2 HH2 sing N N 284 TRP OXT HXT sing N N 285 TYR N CA sing N N 286 TYR N H sing N N 287 TYR N H2 sing N N 288 TYR CA C sing N N 289 TYR CA CB sing N N 290 TYR CA HA sing N N 291 TYR C O doub N N 292 TYR C OXT sing N N 293 TYR CB CG sing N N 294 TYR CB HB2 sing N N 295 TYR CB HB3 sing N N 296 TYR CG CD1 doub Y N 297 TYR CG CD2 sing Y N 298 TYR CD1 CE1 sing Y N 299 TYR CD1 HD1 sing N N 300 TYR CD2 CE2 doub Y N 301 TYR CD2 HD2 sing N N 302 TYR CE1 CZ doub Y N 303 TYR CE1 HE1 sing N N 304 TYR CE2 CZ sing Y N 305 TYR CE2 HE2 sing N N 306 TYR CZ OH sing N N 307 TYR OH HH sing N N 308 TYR OXT HXT sing N N 309 VAL N CA sing N N 310 VAL N H sing N N 311 VAL N H2 sing N N 312 VAL CA C sing N N 313 VAL CA CB sing N N 314 VAL CA HA sing N N 315 VAL C O doub N N 316 VAL C OXT sing N N 317 VAL CB CG1 sing N N 318 VAL CB CG2 sing N N 319 VAL CB HB sing N N 320 VAL CG1 HG11 sing N N 321 VAL CG1 HG12 sing N N 322 VAL CG1 HG13 sing N N 323 VAL CG2 HG21 sing N N 324 VAL CG2 HG22 sing N N 325 VAL CG2 HG23 sing N N 326 VAL OXT HXT sing N N 327 # _atom_sites.entry_id 1YP5 _atom_sites.fract_transf_matrix[1][1] 0.028885 _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] 0.028885 _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] 0.010052 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S # loop_