data_3PPD # _entry.id 3PPD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 3PPD pdb_00003ppd 10.2210/pdb3ppd/pdb RCSB RCSB062655 ? ? WWPDB D_1000062655 ? ? # 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 2011-06-29 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_conn_angle 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 13 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 14 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 15 3 'Structure model' '_pdbx_struct_conn_angle.value' 16 3 'Structure model' '_struct_conn.pdbx_dist_value' 17 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 18 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 19 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 20 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 21 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 22 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 23 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 24 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 25 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 26 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 27 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 28 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 29 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 30 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3PPD _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 2010-11-24 _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zhao, A.' 1 'Sawaya, M.R.' 2 'Eisenberg, D.' 3 # _citation.id primary _citation.title 'Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation.' _citation.journal_abbrev Nature _citation.journal_volume 475 _citation.page_first 96 _citation.page_last 100 _citation.year 2011 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21677644 _citation.pdbx_database_id_DOI 10.1038/nature10154 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sievers, S.A.' 1 ? primary 'Karanicolas, J.' 2 ? primary 'Chang, H.W.' 3 ? primary 'Zhao, A.' 4 ? primary 'Jiang, L.' 5 ? primary 'Zirafi, O.' 6 ? primary 'Stevens, J.T.' 7 ? primary 'Munch, J.' 8 ? primary 'Baker, D.' 9 ? primary 'Eisenberg, D.' 10 ? # 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 syn 'GGVLVN peptide, amyloid forming segment' 557.641 1 ? ? 'Residue 260-265' ? 2 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ? 3 non-polymer syn 'ACETIC ACID' 60.052 1 ? ? ? ? 4 water nat water 18.015 1 ? ? ? ? # _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 GGVLVN _entity_poly.pdbx_seq_one_letter_code_can GGVLVN _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'ZINC ION' ZN 3 'ACETIC ACID' ACY 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 GLY n 1 3 VAL n 1 4 LEU n 1 5 VAL n 1 6 ASN n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name Human _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details 'GGVLVN from human Prostatic Acid Phosphatase Residue 260-265, Amyloid forming segment, synthesized' # 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 ACY non-polymer . 'ACETIC ACID' ? 'C2 H4 O2' 60.052 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # 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 1 1 GLY GLY A . n A 1 2 GLY 2 2 2 GLY GLY A . n A 1 3 VAL 3 3 3 VAL VAL A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 VAL 5 5 5 VAL VAL A . n A 1 6 ASN 6 6 6 ASN ASN 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 ZN 1 7 1 ZN ZN A . C 3 ACY 1 8 1 ACY ACY A . D 4 HOH 1 9 1 HOH HOH A . # 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 . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 PHASER . ? program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 4 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 5 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 ADSC Quantum ? ? ? ? 'data collection' ? ? ? # _cell.length_a 4.834 _cell.length_b 17.682 _cell.length_c 40.322 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3PPD _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _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.space_group_name_H-M 'P 21 21 21' _symmetry.entry_id 3PPD _symmetry.Int_Tables_number 19 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 2 _exptl.entry_id 3PPD _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.55 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 20.39 _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 6 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details '0.1M MES pH6.0, 0.2M Zn(OAc)2, 10%(w/v)PEG-8000, 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 CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2009-08-15 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _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 0.9791 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 24-ID-E' _diffrn_source.pdbx_wavelength_list 0.9791 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 24-ID-E # _reflns.entry_id 3PPD _reflns.d_resolution_high 1.500 _reflns.d_resolution_low 80.000 _reflns.number_obs 621 _reflns.pdbx_Rmerge_I_obs 0.149 _reflns.pdbx_netI_over_sigmaI 8.900 _reflns.pdbx_chi_squared 0.999 _reflns.pdbx_redundancy 4.900 _reflns.percent_possible_obs 86.400 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3.0 _reflns.number_all 621 _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 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 1.500 1.550 ? ? ? 0.256 ? ? 1.010 2.600 ? 54 74.000 1 1 1.550 1.620 ? ? ? 0.334 ? ? 1.002 3.400 ? 48 64.900 2 1 1.620 1.690 ? ? ? 0.295 ? ? 0.999 4.400 ? 48 82.800 3 1 1.690 1.780 ? ? ? 0.186 ? ? 0.982 4.200 ? 53 85.500 4 1 1.780 1.890 ? ? ? 0.206 ? ? 1.002 4.400 ? 54 90.000 5 1 1.890 2.040 ? ? ? 0.231 ? ? 1.010 6.600 ? 67 89.300 6 1 2.040 2.240 ? ? ? 0.177 ? ? 0.994 6.100 ? 77 97.500 7 1 2.240 2.560 ? ? ? 0.192 ? ? 1.012 5.900 ? 67 90.500 8 1 2.560 3.230 ? ? ? 0.118 ? ? 0.995 5.800 ? 62 96.900 9 1 3.230 80.000 ? ? ? 0.090 ? ? 0.985 4.700 ? 91 91.000 10 1 # _refine.entry_id 3PPD _refine.ls_d_res_high 1.5000 _refine.ls_d_res_low 20.1600 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 87.5000 _refine.ls_number_reflns_obs 609 _refine.ls_number_reflns_all 609 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY' _refine.ls_R_factor_all 0.1818 _refine.ls_R_factor_obs 0.1818 _refine.ls_R_factor_R_work 0.1779 _refine.ls_wR_factor_R_work 0.1874 _refine.ls_R_factor_R_free 0.2189 _refine.ls_wR_factor_R_free 0.2026 _refine.ls_percent_reflns_R_free 10.0000 _refine.ls_number_reflns_R_free 61 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 9.4571 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.2100 _refine.aniso_B[2][2] -0.4000 _refine.aniso_B[3][3] 0.6000 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9540 _refine.correlation_coeff_Fo_to_Fc_free 0.9450 _refine.overall_SU_R_Cruickshank_DPI 0.1011 _refine.overall_SU_R_free 0.1020 _refine.pdbx_overall_ESU_R_Free 0.1020 _refine.overall_SU_ML 0.0660 _refine.overall_SU_B 1.9460 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.8347 _refine.B_iso_max 17.520 _refine.B_iso_min 5.180 _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_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 39 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 45 _refine_hist.d_res_high 1.5000 _refine_hist.d_res_low 20.1600 # 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 r_bond_refined_d 41 0.003 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 20 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 54 1.291 2.109 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 51 0.755 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5 7.617 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 1 57.108 30.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 5 13.476 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 7 0.060 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 47 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 5 0.000 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 31 0.725 1.500 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 13 0.168 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 45 1.266 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 10 1.593 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 9 2.739 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.5010 _refine_ls_shell.d_res_low 1.6770 _refine_ls_shell.pdbx_total_number_of_bins_used 5 _refine_ls_shell.percent_reflns_obs 73.4400 _refine_ls_shell.number_reflns_R_work 129 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2300 _refine_ls_shell.R_factor_R_free 0.1580 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 12 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 141 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3PPD _struct.title 'GGVLVN segment from Human Prostatic Acid Phosphatase Residues 260-265, involved in Semen-Derived Enhancer of Viral Infection' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3PPD _struct_keywords.text 'amyloid-like protofibril, amyloid fibrils, PROTEIN FIBRIL' _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' # 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_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PPAP_HUMAN _struct_ref.pdbx_db_accession P15309 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 260 _struct_ref.pdbx_seq_one_letter_code GGVLVN _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3PPD _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 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P15309 _struct_ref_seq.db_align_beg 260 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 265 _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 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # 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' 1_655 x+1,y,z 1.0000000000 0.0000000000 0.0000000000 4.8340000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 1_455 x-1,y,z 1.0000000000 0.0000000000 0.0000000000 -4.8340000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 4_545 x+1/2,-y-1/2,-z 1.0000000000 0.0000000000 0.0000000000 2.4170000000 0.0000000000 -1.0000000000 0.0000000000 -8.8410000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 5 'crystal symmetry operation' 4_445 x-1/2,-y-1/2,-z 1.0000000000 0.0000000000 0.0000000000 -2.4170000000 0.0000000000 -1.0000000000 0.0000000000 -8.8410000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 6 'crystal symmetry operation' 4_645 x+3/2,-y-1/2,-z 1.0000000000 0.0000000000 0.0000000000 7.2510000000 0.0000000000 -1.0000000000 0.0000000000 -8.8410000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A GLY 1 O ? ? ? 1_555 B ZN . ZN ? ? A GLY 1 A ZN 7 1_555 ? ? ? ? ? ? ? 2.123 ? ? metalc2 metalc ? ? A GLY 1 N ? ? ? 1_555 B ZN . ZN ? ? A GLY 1 A ZN 7 1_555 ? ? ? ? ? ? ? 2.175 ? ? metalc3 metalc ? ? B ZN . ZN ? ? ? 1_555 C ACY . O ? ? A ZN 7 A ACY 8 1_555 ? ? ? ? ? ? ? 2.030 ? ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? A GLY 1 ? A GLY 1 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 N ? A GLY 1 ? A GLY 1 ? 1_555 78.3 ? 2 O ? A GLY 1 ? A GLY 1 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 8 ? 1_555 93.4 ? 3 N ? A GLY 1 ? A GLY 1 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 8 ? 1_555 118.1 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A ZN 7 ? 4 'BINDING SITE FOR RESIDUE ZN A 7' AC2 Software A ACY 8 ? 7 'BINDING SITE FOR RESIDUE ACY A 8' # 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 4 GLY A 1 ? GLY A 1 . ? 1_555 ? 2 AC1 4 ASN A 6 ? ASN A 6 . ? 2_554 ? 3 AC1 4 ACY C . ? ACY A 8 . ? 1_455 ? 4 AC1 4 ACY C . ? ACY A 8 . ? 1_555 ? 5 AC2 7 GLY A 1 ? GLY A 1 . ? 1_555 ? 6 AC2 7 GLY A 1 ? GLY A 1 . ? 1_655 ? 7 AC2 7 VAL A 3 ? VAL A 3 . ? 1_655 ? 8 AC2 7 ASN A 6 ? ASN A 6 . ? 2_554 ? 9 AC2 7 ASN A 6 ? ASN A 6 . ? 2_654 ? 10 AC2 7 ZN B . ? ZN A 7 . ? 1_655 ? 11 AC2 7 ZN B . ? ZN A 7 . ? 1_555 ? # _phasing.method MR # 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 ACY C C N N 1 ACY O O N N 2 ACY OXT O N N 3 ACY CH3 C N N 4 ACY HXT H N N 5 ACY H1 H N N 6 ACY H2 H N N 7 ACY H3 H N N 8 ASN N N N N 9 ASN CA C N S 10 ASN C C N N 11 ASN O O N N 12 ASN CB C N N 13 ASN CG C N N 14 ASN OD1 O N N 15 ASN ND2 N N N 16 ASN OXT O N N 17 ASN H H N N 18 ASN H2 H N N 19 ASN HA H N N 20 ASN HB2 H N N 21 ASN HB3 H N N 22 ASN HD21 H N N 23 ASN HD22 H N N 24 ASN HXT H N N 25 GLY N N N N 26 GLY CA C N N 27 GLY C C N N 28 GLY O O N N 29 GLY OXT O N N 30 GLY H H N N 31 GLY H2 H N N 32 GLY HA2 H N N 33 GLY HA3 H N N 34 GLY HXT H N N 35 HOH O O N N 36 HOH H1 H N N 37 HOH H2 H N N 38 LEU N N N N 39 LEU CA C N S 40 LEU C C N N 41 LEU O O N N 42 LEU CB C N N 43 LEU CG C N N 44 LEU CD1 C N N 45 LEU CD2 C N N 46 LEU OXT O N N 47 LEU H H N N 48 LEU H2 H N N 49 LEU HA H N N 50 LEU HB2 H N N 51 LEU HB3 H N N 52 LEU HG H N N 53 LEU HD11 H N N 54 LEU HD12 H N N 55 LEU HD13 H N N 56 LEU HD21 H N N 57 LEU HD22 H N N 58 LEU HD23 H N N 59 LEU HXT H N N 60 VAL N N N N 61 VAL CA C N S 62 VAL C C N N 63 VAL O O N N 64 VAL CB C N N 65 VAL CG1 C N N 66 VAL CG2 C N N 67 VAL OXT O N N 68 VAL H H N N 69 VAL H2 H N N 70 VAL HA H N N 71 VAL HB H N N 72 VAL HG11 H N N 73 VAL HG12 H N N 74 VAL HG13 H N N 75 VAL HG21 H N N 76 VAL HG22 H N N 77 VAL HG23 H N N 78 VAL HXT H N N 79 ZN ZN ZN N N 80 # 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 ACY C O doub N N 1 ACY C OXT sing N N 2 ACY C CH3 sing N N 3 ACY OXT HXT sing N N 4 ACY CH3 H1 sing N N 5 ACY CH3 H2 sing N N 6 ACY CH3 H3 sing N N 7 ASN N CA sing N N 8 ASN N H sing N N 9 ASN N H2 sing N N 10 ASN CA C sing N N 11 ASN CA CB sing N N 12 ASN CA HA sing N N 13 ASN C O doub N N 14 ASN C OXT sing N N 15 ASN CB CG sing N N 16 ASN CB HB2 sing N N 17 ASN CB HB3 sing N N 18 ASN CG OD1 doub N N 19 ASN CG ND2 sing N N 20 ASN ND2 HD21 sing N N 21 ASN ND2 HD22 sing N N 22 ASN OXT HXT sing N N 23 GLY N CA sing N N 24 GLY N H sing N N 25 GLY N H2 sing N N 26 GLY CA C sing N N 27 GLY CA HA2 sing N N 28 GLY CA HA3 sing N N 29 GLY C O doub N N 30 GLY C OXT sing N N 31 GLY OXT HXT sing N N 32 HOH O H1 sing N N 33 HOH O H2 sing N N 34 LEU N CA sing N N 35 LEU N H sing N N 36 LEU N H2 sing N N 37 LEU CA C sing N N 38 LEU CA CB sing N N 39 LEU CA HA sing N N 40 LEU C O doub N N 41 LEU C OXT sing N N 42 LEU CB CG sing N N 43 LEU CB HB2 sing N N 44 LEU CB HB3 sing N N 45 LEU CG CD1 sing N N 46 LEU CG CD2 sing N N 47 LEU CG HG sing N N 48 LEU CD1 HD11 sing N N 49 LEU CD1 HD12 sing N N 50 LEU CD1 HD13 sing N N 51 LEU CD2 HD21 sing N N 52 LEU CD2 HD22 sing N N 53 LEU CD2 HD23 sing N N 54 LEU OXT HXT sing N N 55 VAL N CA sing N N 56 VAL N H sing N N 57 VAL N H2 sing N N 58 VAL CA C sing N N 59 VAL CA CB sing N N 60 VAL CA HA sing N N 61 VAL C O doub N N 62 VAL C OXT sing N N 63 VAL CB CG1 sing N N 64 VAL CB CG2 sing N N 65 VAL CB HB sing N N 66 VAL CG1 HG11 sing N N 67 VAL CG1 HG12 sing N N 68 VAL CG1 HG13 sing N N 69 VAL CG2 HG21 sing N N 70 VAL CG2 HG22 sing N N 71 VAL CG2 HG23 sing N N 72 VAL OXT HXT sing N N 73 # _atom_sites.entry_id 3PPD _atom_sites.fract_transf_matrix[1][1] 0.206868 _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] 0.056555 _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] 0.024800 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O ZN # loop_