data_3NHD # _entry.id 3NHD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.362 _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 3NHD pdb_00003nhd 10.2210/pdb3nhd/pdb RCSB RCSB059830 ? ? WWPDB D_1000059830 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3NHC _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 3NHD _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 2010-06-14 _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 'Apostol, M.I.' 1 'Eisenberg, D.' 2 # _citation.id primary _citation.title ;Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease. ; _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 285 _citation.page_first 29671 _citation.page_last 29675 _citation.year 2010 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20685658 _citation.pdbx_database_id_DOI 10.1074/jbc.C110.158303 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Apostol, M.I.' 1 ? primary 'Sawaya, M.R.' 2 ? primary 'Cascio, D.' 3 ? primary 'Eisenberg, D.' 4 ? # _cell.length_a 41.173 _cell.length_b 18.959 _cell.length_c 9.585 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3NHD _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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 2' _symmetry.entry_id 3NHD _symmetry.Int_Tables_number 18 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'Major prion protein' 594.659 2 ? M129V 'residues 127-132' ? 2 non-polymer syn 'ACETIC ACID' 60.052 2 ? ? ? ? 3 water nat water 18.015 2 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'PrP, PrP27-30, PrP33-35C, ASCR' # _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 GYVLGS _entity_poly.pdbx_seq_one_letter_code_can GYVLGS _entity_poly.pdbx_strand_id A,B _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 TYR n 1 3 VAL n 1 4 LEU n 1 5 GLY n 1 6 SER 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 'GYVLGS (residues 127-132 with V129) from human prion protein, synthesized' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PRIO_HUMAN _struct_ref.pdbx_db_accession P04156 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GYMLGS _struct_ref.pdbx_align_begin 127 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3NHD A 1 ? 6 ? P04156 127 ? 132 ? 1 6 2 1 3NHD B 1 ? 6 ? P04156 127 ? 132 ? 1 6 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3NHD VAL A 3 ? UNP P04156 MET 129 variant 3 1 2 3NHD VAL B 3 ? UNP P04156 MET 129 variant 3 2 # 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 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 3NHD _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.57 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 21.79 _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 5.5 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details '0.1M Sodium Acetate pH 5.5, PEG 10,000, vapor diffusion, hanging drop, temperature 298K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2008-01-01 _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 0.97915 _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 0.97915 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 24-ID-E # _reflns.entry_id 3NHD _reflns.d_resolution_high 1.900 _reflns.d_resolution_low 90.000 _reflns.number_obs 637 _reflns.pdbx_Rmerge_I_obs 0.193 _reflns.pdbx_netI_over_sigmaI 7.900 _reflns.pdbx_chi_squared 1.034 _reflns.pdbx_redundancy 5.700 _reflns.percent_possible_obs 91.500 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _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_diffrn_id 1 _reflns.pdbx_ordinal 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_diffrn_id _reflns_shell.pdbx_ordinal 1.900 1.970 ? ? ? 0.223 ? ? 1.005 3.200 ? 31 56.400 ? 1 1.970 2.050 ? ? ? 0.374 ? ? 1.019 5.600 ? 53 79.100 ? 2 2.050 2.140 ? ? ? 0.380 ? ? 1.156 5.900 ? 60 90.900 ? 3 2.140 2.250 ? ? ? 0.389 ? ? 1.003 6.800 ? 67 100.000 ? 4 2.250 2.390 ? ? ? 0.305 ? ? 1.051 5.300 ? 65 87.800 ? 5 2.390 2.580 ? ? ? 0.303 ? ? 1.028 6.400 ? 58 100.000 ? 6 2.580 2.840 ? ? ? 0.266 ? ? 0.998 5.900 ? 70 100.000 ? 7 2.840 3.250 ? ? ? 0.184 ? ? 1.063 5.400 ? 77 97.500 ? 8 3.250 4.090 ? ? ? 0.160 ? ? 1.001 5.800 ? 68 98.600 ? 9 4.090 90.000 ? ? ? 0.104 ? ? 1.013 5.300 ? 88 96.700 ? 10 # _refine.entry_id 3NHD _refine.ls_d_res_high 1.9200 _refine.ls_d_res_low 20.5800 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 91.5900 _refine.ls_number_reflns_obs 621 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2097 _refine.ls_R_factor_R_work 0.2033 _refine.ls_wR_factor_R_work 0.2138 _refine.ls_R_factor_R_free 0.2613 _refine.ls_wR_factor_R_free 0.2942 _refine.ls_percent_reflns_R_free 10.1000 _refine.ls_number_reflns_R_free 63 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 10.8356 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.5600 _refine.aniso_B[2][2] 0.9700 _refine.aniso_B[3][3] -0.4200 _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 0.9360 _refine.correlation_coeff_Fo_to_Fc_free 0.9410 _refine.overall_SU_R_Cruickshank_DPI 0.2994 _refine.overall_SU_R_free 0.2197 _refine.pdbx_overall_ESU_R_Free 0.2200 _refine.overall_SU_ML 0.0770 _refine.overall_SU_B 2.4530 _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 0.8950 _refine.B_iso_max 40.690 _refine.B_iso_min 2.430 _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 84 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 94 _refine_hist.d_res_high 1.9200 _refine_hist.d_res_low 20.5800 # 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 90 0.015 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 50 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 118 1.480 2.125 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 122 0.801 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 10 6.083 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 2 5.255 20.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 10 15.528 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 12 0.093 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 102 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 18 0.000 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 62 1.131 1.500 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 26 0.237 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 88 1.836 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 28 1.997 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 30 2.388 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.9200 _refine_ls_shell.d_res_low 2.1440 _refine_ls_shell.pdbx_total_number_of_bins_used 5 _refine_ls_shell.percent_reflns_obs 75.4400 _refine_ls_shell.number_reflns_R_work 116 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.1480 _refine_ls_shell.R_factor_R_free 0.2680 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 13 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 129 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3NHD _struct.title 'GYVLGS segment 127-132 from human prion with V129' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3NHD _struct_keywords.text 'amyloid-like protofibril, 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 1 ? C N N 2 ? D N N 2 ? E N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id A _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense 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 TYR A 2 ? LEU A 4 ? TYR A 2 LEU A 4 A 2 VAL B 3 ? GLY B 5 ? VAL B 3 GLY B 5 # _pdbx_struct_sheet_hbond.sheet_id A _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id TYR _pdbx_struct_sheet_hbond.range_1_label_asym_id A _pdbx_struct_sheet_hbond.range_1_label_seq_id 2 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id TYR _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 2 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id GLY _pdbx_struct_sheet_hbond.range_2_label_asym_id B _pdbx_struct_sheet_hbond.range_2_label_seq_id 5 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id GLY _pdbx_struct_sheet_hbond.range_2_auth_asym_id B _pdbx_struct_sheet_hbond.range_2_auth_seq_id 5 # 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 ACY 7 ? 6 'BINDING SITE FOR RESIDUE ACY A 7' AC2 Software A ACY 8 ? 6 '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 6 ACY D . ? ACY A 8 . ? 1_554 ? 2 AC1 6 ACY D . ? ACY A 8 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH A 9 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH A 10 . ? 1_555 ? 5 AC1 6 TYR B 2 ? TYR B 2 . ? 2_565 ? 6 AC1 6 TYR B 2 ? TYR B 2 . ? 2_566 ? 7 AC2 6 GLY A 5 ? GLY A 5 . ? 1_555 ? 8 AC2 6 ACY C . ? ACY A 7 . ? 1_556 ? 9 AC2 6 ACY C . ? ACY A 7 . ? 1_555 ? 10 AC2 6 HOH E . ? HOH A 10 . ? 1_556 ? 11 AC2 6 GLY B 1 ? GLY B 1 . ? 1_556 ? 12 AC2 6 TYR B 2 ? TYR B 2 . ? 2_566 ? # _atom_sites.entry_id 3NHD _atom_sites.fract_transf_matrix[1][1] 0.024288 _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] 0.052745 _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] 0.104330 _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 # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . GLY A 1 1 ? -17.487 8.458 1.793 1.00 9.22 ? 1 GLY A N 1 ATOM 2 C CA . GLY A 1 1 ? -16.196 8.315 1.061 1.00 8.08 ? 1 GLY A CA 1 ATOM 3 C C . GLY A 1 1 ? -15.180 7.542 1.884 1.00 7.28 ? 1 GLY A C 1 ATOM 4 O O . GLY A 1 1 ? -15.344 7.405 3.105 1.00 6.83 ? 1 GLY A O 1 ATOM 5 N N . TYR A 1 2 ? -14.120 7.049 1.220 1.00 5.95 ? 2 TYR A N 1 ATOM 6 C CA . TYR A 1 2 ? -12.977 6.460 1.908 1.00 3.97 ? 2 TYR A CA 1 ATOM 7 C C . TYR A 1 2 ? -11.635 6.761 1.214 1.00 3.82 ? 2 TYR A C 1 ATOM 8 O O . TYR A 1 2 ? -11.592 7.119 0.063 1.00 4.39 ? 2 TYR A O 1 ATOM 9 C CB . TYR A 1 2 ? -13.152 4.947 2.038 1.00 4.94 ? 2 TYR A CB 1 ATOM 10 C CG . TYR A 1 2 ? -13.505 4.229 0.762 1.00 2.69 ? 2 TYR A CG 1 ATOM 11 C CD1 . TYR A 1 2 ? -14.839 3.978 0.410 1.00 7.02 ? 2 TYR A CD1 1 ATOM 12 C CD2 . TYR A 1 2 ? -12.517 3.823 -0.130 1.00 6.90 ? 2 TYR A CD2 1 ATOM 13 C CE1 . TYR A 1 2 ? -15.161 3.297 -0.784 1.00 6.10 ? 2 TYR A CE1 1 ATOM 14 C CE2 . TYR A 1 2 ? -12.837 3.178 -1.335 1.00 7.12 ? 2 TYR A CE2 1 ATOM 15 C CZ . TYR A 1 2 ? -14.148 2.896 -1.647 1.00 5.18 ? 2 TYR A CZ 1 ATOM 16 O OH . TYR A 1 2 ? -14.434 2.230 -2.840 1.00 6.91 ? 2 TYR A OH 1 ATOM 17 N N . VAL A 1 3 ? -10.554 6.578 1.944 1.00 3.33 ? 3 VAL A N 1 ATOM 18 C CA . VAL A 1 3 ? -9.178 6.745 1.448 1.00 3.41 ? 3 VAL A CA 1 ATOM 19 C C . VAL A 1 3 ? -8.271 5.686 2.052 1.00 3.98 ? 3 VAL A C 1 ATOM 20 O O . VAL A 1 3 ? -8.302 5.435 3.275 1.00 2.43 ? 3 VAL A O 1 ATOM 21 C CB . VAL A 1 3 ? -8.569 8.141 1.850 1.00 2.94 ? 3 VAL A CB 1 ATOM 22 C CG1 . VAL A 1 3 ? -7.243 8.341 1.137 1.00 3.64 ? 3 VAL A CG1 1 ATOM 23 C CG2 . VAL A 1 3 ? -9.506 9.248 1.551 1.00 2.51 ? 3 VAL A CG2 1 ATOM 24 N N . LEU A 1 4 ? -7.493 5.039 1.178 1.00 4.86 ? 4 LEU A N 1 ATOM 25 C CA . LEU A 1 4 ? -6.455 4.112 1.558 1.00 7.11 ? 4 LEU A CA 1 ATOM 26 C C . LEU A 1 4 ? -5.144 4.789 1.137 1.00 8.00 ? 4 LEU A C 1 ATOM 27 O O . LEU A 1 4 ? -4.991 5.186 -0.023 1.00 5.56 ? 4 LEU A O 1 ATOM 28 C CB . LEU A 1 4 ? -6.653 2.775 0.822 1.00 7.31 ? 4 LEU A CB 1 ATOM 29 C CG . LEU A 1 4 ? -7.772 1.803 1.262 1.00 9.56 ? 4 LEU A CG 1 ATOM 30 C CD1 . LEU A 1 4 ? -9.162 2.443 1.409 1.00 12.21 ? 4 LEU A CD1 1 ATOM 31 C CD2 . LEU A 1 4 ? -7.861 0.678 0.299 1.00 9.79 ? 4 LEU A CD2 1 ATOM 32 N N . GLY A 1 5 ? -4.238 4.996 2.080 1.00 9.24 ? 5 GLY A N 1 ATOM 33 C CA . GLY A 1 5 ? -3.006 5.750 1.782 1.00 10.72 ? 5 GLY A CA 1 ATOM 34 C C . GLY A 1 5 ? -2.098 4.966 0.844 1.00 12.25 ? 5 GLY A C 1 ATOM 35 O O . GLY A 1 5 ? -1.458 5.544 -0.034 1.00 13.84 ? 5 GLY A O 1 ATOM 36 N N . SER A 1 6 ? -2.075 3.643 1.016 1.00 13.04 ? 6 SER A N 1 ATOM 37 C CA . SER A 1 6 ? -1.226 2.750 0.233 1.00 14.80 ? 6 SER A CA 1 ATOM 38 C C . SER A 1 6 ? -1.987 1.565 -0.309 1.00 15.72 ? 6 SER A C 1 ATOM 39 O O . SER A 1 6 ? -3.052 1.183 0.195 1.00 16.50 ? 6 SER A O 1 ATOM 40 C CB . SER A 1 6 ? -0.065 2.221 1.081 1.00 14.87 ? 6 SER A CB 1 ATOM 41 O OG . SER A 1 6 ? 1.056 3.054 0.901 1.00 16.70 ? 6 SER A OG 1 ATOM 42 O OXT . SER A 1 6 ? -1.517 0.977 -1.272 1.00 15.87 ? 6 SER A OXT 1 ATOM 43 N N . GLY B 1 1 ? -0.618 1.490 -4.772 1.00 12.38 ? 1 GLY B N 1 ATOM 44 C CA . GLY B 1 1 ? -0.959 2.950 -4.817 1.00 11.45 ? 1 GLY B CA 1 ATOM 45 C C . GLY B 1 1 ? -2.108 3.273 -3.898 1.00 10.49 ? 1 GLY B C 1 ATOM 46 O O . GLY B 1 1 ? -2.845 2.382 -3.477 1.00 11.76 ? 1 GLY B O 1 ATOM 47 N N . TYR B 1 2 ? -2.271 4.545 -3.578 1.00 8.44 ? 2 TYR B N 1 ATOM 48 C CA . TYR B 1 2 ? -3.465 4.999 -2.846 1.00 8.33 ? 2 TYR B CA 1 ATOM 49 C C . TYR B 1 2 ? -4.755 4.698 -3.588 1.00 8.03 ? 2 TYR B C 1 ATOM 50 O O . TYR B 1 2 ? -4.729 4.533 -4.816 1.00 4.69 ? 2 TYR B O 1 ATOM 51 C CB . TYR B 1 2 ? -3.387 6.500 -2.551 1.00 8.54 ? 2 TYR B CB 1 ATOM 52 C CG . TYR B 1 2 ? -3.448 7.423 -3.745 1.00 10.37 ? 2 TYR B CG 1 ATOM 53 C CD1 . TYR B 1 2 ? -2.292 7.932 -4.326 1.00 12.18 ? 2 TYR B CD1 1 ATOM 54 C CD2 . TYR B 1 2 ? -4.663 7.828 -4.270 1.00 9.38 ? 2 TYR B CD2 1 ATOM 55 C CE1 . TYR B 1 2 ? -2.364 8.831 -5.427 1.00 9.31 ? 2 TYR B CE1 1 ATOM 56 C CE2 . TYR B 1 2 ? -4.740 8.705 -5.343 1.00 9.76 ? 2 TYR B CE2 1 ATOM 57 C CZ . TYR B 1 2 ? -3.586 9.206 -5.909 1.00 10.74 ? 2 TYR B CZ 1 ATOM 58 O OH . TYR B 1 2 ? -3.681 10.074 -6.959 1.00 12.65 ? 2 TYR B OH 1 ATOM 59 N N . VAL B 1 3 ? -5.864 4.658 -2.818 1.00 7.32 ? 3 VAL B N 1 ATOM 60 C CA . VAL B 1 3 ? -7.213 4.412 -3.340 1.00 8.27 ? 3 VAL B CA 1 ATOM 61 C C . VAL B 1 3 ? -8.198 5.435 -2.733 1.00 8.17 ? 3 VAL B C 1 ATOM 62 O O . VAL B 1 3 ? -8.357 5.499 -1.491 1.00 7.07 ? 3 VAL B O 1 ATOM 63 C CB . VAL B 1 3 ? -7.719 3.008 -2.968 1.00 8.09 ? 3 VAL B CB 1 ATOM 64 C CG1 . VAL B 1 3 ? -9.115 2.731 -3.622 1.00 7.67 ? 3 VAL B CG1 1 ATOM 65 C CG2 . VAL B 1 3 ? -6.680 1.924 -3.361 1.00 9.47 ? 3 VAL B CG2 1 ATOM 66 N N . LEU B 1 4 ? -8.835 6.225 -3.593 1.00 7.41 ? 4 LEU B N 1 ATOM 67 C CA . LEU B 1 4 ? -9.954 7.078 -3.168 1.00 7.43 ? 4 LEU B CA 1 ATOM 68 C C . LEU B 1 4 ? -11.309 6.628 -3.679 1.00 7.97 ? 4 LEU B C 1 ATOM 69 O O . LEU B 1 4 ? -11.477 6.342 -4.866 1.00 8.34 ? 4 LEU B O 1 ATOM 70 C CB . LEU B 1 4 ? -9.727 8.516 -3.596 1.00 7.05 ? 4 LEU B CB 1 ATOM 71 C CG . LEU B 1 4 ? -8.349 9.113 -3.358 1.00 5.21 ? 4 LEU B CG 1 ATOM 72 C CD1 . LEU B 1 4 ? -8.233 10.399 -4.155 1.00 2.54 ? 4 LEU B CD1 1 ATOM 73 C CD2 . LEU B 1 4 ? -8.053 9.346 -1.862 1.00 3.64 ? 4 LEU B CD2 1 ATOM 74 N N . GLY B 1 5 ? -12.306 6.642 -2.787 1.00 8.79 ? 5 GLY B N 1 ATOM 75 C CA . GLY B 1 5 ? -13.660 6.241 -3.137 1.00 8.78 ? 5 GLY B CA 1 ATOM 76 C C . GLY B 1 5 ? -14.713 7.188 -2.598 1.00 9.53 ? 5 GLY B C 1 ATOM 77 O O . GLY B 1 5 ? -14.675 7.606 -1.428 1.00 8.42 ? 5 GLY B O 1 ATOM 78 N N . SER B 1 6 ? -15.640 7.574 -3.463 1.00 11.38 ? 6 SER B N 1 ATOM 79 C CA . SER B 1 6 ? -16.702 8.507 -3.074 1.00 13.63 ? 6 SER B CA 1 ATOM 80 C C . SER B 1 6 ? -17.998 8.020 -3.684 1.00 14.74 ? 6 SER B C 1 ATOM 81 O O . SER B 1 6 ? -18.286 8.087 -4.887 1.00 16.24 ? 6 SER B O 1 ATOM 82 C CB . SER B 1 6 ? -16.380 9.936 -3.506 1.00 13.62 ? 6 SER B CB 1 ATOM 83 O OG . SER B 1 6 ? -17.167 10.849 -2.758 1.00 16.41 ? 6 SER B OG 1 ATOM 84 O OXT . SER B 1 6 ? -18.780 7.461 -2.940 1.00 16.10 ? 6 SER B OXT 1 HETATM 85 C C . ACY C 2 . ? 2.981 8.121 -1.507 1.00 23.42 ? 7 ACY A C 1 HETATM 86 O O . ACY C 2 . ? 2.793 7.229 -2.362 1.00 23.38 ? 7 ACY A O 1 HETATM 87 O OXT . ACY C 2 . ? 2.224 8.340 -0.522 1.00 24.25 ? 7 ACY A OXT 1 HETATM 88 C CH3 . ACY C 2 . ? 4.210 8.946 -1.683 1.00 22.51 ? 7 ACY A CH3 1 HETATM 89 C C . ACY D 2 . ? 1.611 6.056 3.167 1.00 31.39 ? 8 ACY A C 1 HETATM 90 O O . ACY D 2 . ? 2.452 5.652 3.993 1.00 31.45 ? 8 ACY A O 1 HETATM 91 O OXT . ACY D 2 . ? 1.902 6.666 2.124 1.00 31.52 ? 8 ACY A OXT 1 HETATM 92 C CH3 . ACY D 2 . ? 0.158 5.798 3.442 1.00 31.33 ? 8 ACY A CH3 1 HETATM 93 O O . HOH E 3 . ? 0.831 5.471 -2.227 1.00 20.23 ? 9 HOH A O 1 HETATM 94 O O . HOH E 3 . ? 0.890 7.271 -3.764 1.00 40.69 ? 10 HOH A O 1 # 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 TYR 2 2 2 TYR TYR 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 GLY 5 5 5 GLY GLY A . n A 1 6 SER 6 6 6 SER SER A . n B 1 1 GLY 1 1 1 GLY GLY B . n B 1 2 TYR 2 2 2 TYR TYR B . n B 1 3 VAL 3 3 3 VAL VAL B . n B 1 4 LEU 4 4 4 LEU LEU B . n B 1 5 GLY 5 5 5 GLY GLY B . n B 1 6 SER 6 6 6 SER SER B . 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 C 2 ACY 1 7 1 ACY ACY A . D 2 ACY 1 8 1 ACY ACY A . E 3 HOH 1 9 1 HOH HOH A . E 3 HOH 2 10 2 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 dodecameric _pdbx_struct_assembly.oligomeric_count 12 # _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,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 180 ? 1 MORE -1 ? 1 'SSA (A^2)' 1740 ? # 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_556 x,y,z+1 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 9.5850000000 3 'crystal symmetry operation' 1_554 x,y,z-1 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -9.5850000000 4 'crystal symmetry operation' 3_455 -x-1/2,y+1/2,-z -1.0000000000 0.0000000000 0.0000000000 -20.5865000000 0.0000000000 1.0000000000 0.0000000000 9.4795000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 5 'crystal symmetry operation' 3_454 -x-1/2,y+1/2,-z-1 -1.0000000000 0.0000000000 0.0000000000 -20.5865000000 0.0000000000 1.0000000000 0.0000000000 9.4795000000 0.0000000000 0.0000000000 -1.0000000000 -9.5850000000 6 'crystal symmetry operation' 3_456 -x-1/2,y+1/2,-z+1 -1.0000000000 0.0000000000 0.0000000000 -20.5865000000 0.0000000000 1.0000000000 0.0000000000 9.4795000000 0.0000000000 0.0000000000 -1.0000000000 9.5850000000 # 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 2010-08-04 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-12-21 # _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' 'Database references' 3 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' database_2 2 3 'Structure model' struct_ref_seq_dif 3 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' '_struct_ref_seq_dif.details' 4 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_phasing_MR.entry_id 3NHD _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO' _pdbx_phasing_MR.R_factor ? _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation 1.920 _pdbx_phasing_MR.d_res_low_rotation 20.590 _pdbx_phasing_MR.d_res_high_translation 1.920 _pdbx_phasing_MR.d_res_low_translation 20.590 _pdbx_phasing_MR.packing ? _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 2 PHASER 1.3.2 'Wed Feb 15 11:59:26 2006' program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 3 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 4 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'ACETIC ACID' ACY 3 water HOH #