data_2Y2A
#
_entry.id 2Y2A
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.279
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
PDB 2Y2A
PDBE EBI-46719
WWPDB D_1290046719
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.db_id
_pdbx_database_related.content_type
_pdbx_database_related.details
PDB 1UOA unspecified 'AFTER 3NS'
PDB 1TAW unspecified 'BOVINE TRYPSIN COMPLEXED TO APPI'
PDB 2Y3J unspecified 'STRUCTURE OF SEGMENT AIIGLM FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 30-35)'
PDB 1TKN unspecified
'SOLUTION STRUCTURE OF CAPPD*, AN INDEPENDENTLY FOLDEDEXTRACELLULAR DOMAIN OF HUMAN AMYLOID-BETA PRECURSORPROTEIN'
PDB 1QCM unspecified 'AMYLOID BETA PEPTIDE (25-35), NMR, 20 STRUCTURES'
PDB 1BA6 unspecified
;SOLUTION STRUCTURE OF THE METHIONINE-OXIDIZED AMYLOID BETA-PEPTIDE (1-40). DOES OXIDATION AFFECT CONFORMATIONAL SWITCHING? NMR, 10 STRUCTURES
;
PDB 1QYT unspecified 'SOLUTION STRUCTURE OF FRAGMENT (25-35) OF BETA AMYLOIDPEPTIDE IN SDS MICELLAR SOLUTION'
PDB 1BJB unspecified 'SOLUTION NMR STRUCTURE OF AMYLOID BETA[E16], RESIDUES 1-28, 14 STRUCTURES'
PDB 2Y3L unspecified 'STRUCTURE OF SEGMENT MVGGVVIA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 35-42), ALTERNATE POLYMORPH 2'
PDB 2Y3K unspecified 'STRUCTURE OF SEGMENT MVGGVVIA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 35-42), ALTERNATE POLYMORPH 1'
PDB 1CA0 unspecified 'BOVINE CHYMOTRYPSIN COMPLEXED TO APPI'
PDB 1BRC unspecified .
PDB 1UO8 unspecified 'AFTER 2NS'
PDB 1BA4 unspecified
;THE SOLUTION STRUCTURE OF AMYLOID BETA-PEPTIDE (1-40 ) IN A WATER-MICELLE ENVIRONMENT. IS THE MEMBRANE- SPANNING DOMAIN WHERE WE THINK IT IS? NMR, 10 STRUCTURES
;
PDB 2WK3 unspecified 'CRYSTAL STRUCTURE OF HUMAN INSULIN-DEGRADING ENZYME IN COMPLEX WITH AMYLOID-BETA (1-42)'
PDB 1AAP unspecified .
PDB 1X11 unspecified 'X11 PTB DOMAIN'
PDB 1QWP unspecified 'NMR ANALYSIS OF 25-35 FRAGMENT OF BETA AMYLOID PEPTIDE'
PDB 1ZE9 unspecified
;ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE COMPLEXED WITH A ZINC (II) CATION
;
PDB 1QXC unspecified 'NMR STRUCTURE OF THE FRAGMENT 25-35 OF BETA AMYLOID PEPTIDEIN 20/80 V:V HEXAFLUOROISOPROPANOL/WATER MIXTURE'
PDB 1IYT unspecified
;SOLUTION STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (1-42)
;
PDB 1ZE7 unspecified
;ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE IN WATER SOLUTION AT PH 6.5
;
PDB 2BEG unspecified
;3D STRUCTURE OF ALZHEIMER'S ABETA(1-42) FIBRILS
;
PDB 1UOI unspecified 'AFTER 4NS'
PDB 1AMB unspecified
;ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (RESIDUES 1 - 28) (NMR, MINIMIZED AVERAGE STRUCTURE)
;
PDB 1RW6 unspecified 'HUMAN APP CORE DOMAIN'
PDB 1UO7 unspecified 'MOLECULAR DYNAMICS SIMULATION OF AMYLOID BETA 1-42 ( PDB: 1IYT) IN WATER'
PDB 1OWT unspecified
;STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID PRECURSORPROTEIN COPPER BINDING DOMAIN
;
PDB 1AML unspecified
;THE ALZHEIMER'S DISEASE AMYLOID A4 PEPTIDE (RESIDUES 1 -40)
;
PDB 1AMC unspecified
;ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (RESIDUES 1 - 28) (NMR, 5 STRUCTURES)
;
PDB 1ZJD unspecified
;CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH KUNITZ PROTEASE INHIBITOR DOMAINOF PROTEASE NEXIN II
;
PDB 2BP4 unspecified
;ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE IN TFE-WATER (80-20) SOLUTION
;
PDB 2BOM unspecified
;MODEL OF ALZHEIMER'S DISEASE AMYLOID-SS PEPTIDE BASED ON A RNA BINDING PROTEIN
;
PDB 1BJC unspecified 'SOLUTION NMR STRUCTURE OF AMYLOID BETA[F16], RESIDUES 1-28, 15 STRUCTURES'
PDB 2Y29 unspecified 'STRUCTURE OF SEGMENT KLVFFA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 16-21), ALTERNATE POLYMORPH III'
PDB 1MWP unspecified 'N-TERMINAL DOMAIN OF THE AMYLOID PRECURSOR PROTEIN'
PDB 1HZ3 unspecified
;ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE (RESIDUES 10- 35)
;
#
_pdbx_database_status.status_code REL
_pdbx_database_status.entry_id 2Y2A
_pdbx_database_status.deposit_site PDBE
_pdbx_database_status.process_site PDBE
_pdbx_database_status.SG_entry .
_pdbx_database_status.recvd_initial_deposition_date 2010-12-14
_pdbx_database_status.pdb_format_compatible Y
_pdbx_database_status.status_code_sf ?
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.methods_development_category ?
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Colletier, J.' 1
'Laganowsky, A.' 2
'Sawaya, M.R.' 3
'Eisenberg, D.' 4
#
_citation.id primary
_citation.title 'Molecular Basis for Amyloid-{Beta} Polymorphism.'
_citation.journal_abbrev Proc.Natl.Acad.Sci.USA
_citation.journal_volume 108
_citation.page_first 16938
_citation.page_last ?
_citation.year 2011
_citation.journal_id_ASTM PNASA6
_citation.country US
_citation.journal_id_ISSN 0027-8424
_citation.journal_id_CSD 0040
_citation.book_publisher ?
_citation.pdbx_database_id_PubMed 21949245
_citation.pdbx_database_id_DOI 10.1073/PNAS.1112600108
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
primary 'Colletier, J.' 1
primary 'Laganowsky, A.' 2
primary 'Landau, M.' 3
primary 'Zhao, M.' 4
primary 'Soriaga, A.B.' 5
primary 'Goldschmidt, L.' 6
primary 'Flot, D.' 7
primary 'Cascio, D.' 8
primary 'Sawaya, M.R.' 9
primary 'Eisenberg, D.' 10
#
_cell.entry_id 2Y2A
_cell.length_a 9.580
_cell.length_b 11.850
_cell.length_c 42.470
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
_cell.Z_PDB 4
_cell.pdbx_unique_axis ?
#
_symmetry.entry_id 2Y2A
_symmetry.space_group_name_H-M 'P 21 21 21'
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 19
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer syn 'AMYLOID BETA A4 PROTEIN' 724.909 1 ? ? 'SEGMENT KLVFFA, RESIDUES 687-692' ?
2 non-polymer syn 'ACETATE ION' 59.044 1 ? ? ? ?
3 water nat water 18.015 3 ? ? ? ?
#
_entity_name_com.entity_id 1
_entity_name_com.name
;AMYLOID BETA PEPTIDE, ABPP, APPI, APP, ALZHEIMER DISEASE AMYLOID PROTEIN, CEREBRAL VASCULAR AMYLOID PEPTIDE, CVAP, PREA4, PROTEASE NEXIN-II, PN-II
;
#
_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 KLVFFA
_entity_poly.pdbx_seq_one_letter_code_can KLVFFA
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_target_identifier ?
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 LYS n
1 2 LEU n
1 3 VAL n
1 4 PHE n
1 5 PHE n
1 6 ALA 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 ?
#
_struct_ref.id 1
_struct_ref.db_name UNP
_struct_ref.db_code A4_HUMAN
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code ?
_struct_ref.pdbx_align_begin ?
_struct_ref.pdbx_db_accession P05067
_struct_ref.pdbx_db_isoform ?
#
_struct_ref_seq.align_id 1
_struct_ref_seq.ref_id 1
_struct_ref_seq.pdbx_PDB_id_code 2Y2A
_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 P05067
_struct_ref_seq.db_align_beg 687
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 692
_struct_ref_seq.pdbx_db_align_end_ins_code ?
_struct_ref_seq.pdbx_auth_seq_align_beg 2
_struct_ref_seq.pdbx_auth_seq_align_end 7
#
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
ACT non-polymer . 'ACETATE ION' ? 'C2 H3 O2 -1' 59.044
ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093
HOH non-polymer . WATER ? 'H2 O' 18.015
LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173
LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189
VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146
#
_exptl.entry_id 2Y2A
_exptl.method 'X-RAY DIFFRACTION'
_exptl.crystals_number 1
#
_exptl_crystal.id 1
_exptl_crystal.density_meas ?
_exptl_crystal.density_Matthews 1.71
_exptl_crystal.density_percent_sol 28
_exptl_crystal.description NONE
#
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method ?
_exptl_crystal_grow.temp ?
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.pH 5.5
_exptl_crystal_grow.pdbx_pH_range ?
_exptl_crystal_grow.pdbx_details
;AB16-21 FORM I CRYSTALS WERE OBTAINED AFTER THE SEGMENT WAS DISSOLVED IN WATER AT 5 MG/ML AND MIXED WITH 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 5.5, 45 % V/V MPD
;
#
_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 'MARMOSAIC 225 mm CCD'
_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 0.87260
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.diffrn_id 1
_diffrn_source.source SYNCHROTRON
_diffrn_source.type 'ESRF BEAMLINE ID23-2'
_diffrn_source.pdbx_synchrotron_site ESRF
_diffrn_source.pdbx_synchrotron_beamline ID23-2
_diffrn_source.pdbx_wavelength 0.87260
_diffrn_source.pdbx_wavelength_list ?
#
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_ordinal 1
_reflns.entry_id 2Y2A
_reflns.observed_criterion_sigma_I 3.5
_reflns.observed_criterion_sigma_F ?
_reflns.d_resolution_low 21.20
_reflns.d_resolution_high 1.90
_reflns.number_obs 392
_reflns.number_all ?
_reflns.percent_possible_obs 85.0
_reflns.pdbx_Rmerge_I_obs 0.15
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_sigmaI 7.40
_reflns.B_iso_Wilson_estimate 19.348
_reflns.pdbx_redundancy 3.5
#
_reflns_shell.pdbx_diffrn_id 1
_reflns_shell.pdbx_ordinal 1
_reflns_shell.d_res_high 1.90
_reflns_shell.d_res_low 2.20
_reflns_shell.percent_possible_all 75.7
_reflns_shell.Rmerge_I_obs 0.36
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.meanI_over_sigI_obs 3.85
_reflns_shell.pdbx_redundancy 3.9
#
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine.entry_id 2Y2A
_refine.pdbx_diffrn_id 1
_refine.pdbx_TLS_residual_ADP_flag ?
_refine.ls_number_reflns_obs 372
_refine.ls_number_reflns_all ?
_refine.pdbx_ls_sigma_I ?
_refine.pdbx_ls_sigma_F .
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.ls_d_res_low 11.41
_refine.ls_d_res_high 1.91
_refine.ls_percent_reflns_obs 85.03
_refine.ls_R_factor_obs 0.20837
_refine.ls_R_factor_all ?
_refine.ls_R_factor_R_work 0.20640
_refine.ls_R_factor_R_free 0.24787
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_percent_reflns_R_free 5.1
_refine.ls_number_reflns_R_free 20
_refine.ls_number_parameters ?
_refine.ls_number_restraints ?
_refine.occupancy_min ?
_refine.occupancy_max ?
_refine.correlation_coeff_Fo_to_Fc 0.946
_refine.correlation_coeff_Fo_to_Fc_free 0.962
_refine.B_iso_mean 16.442
_refine.aniso_B[1][1] -4.28
_refine.aniso_B[2][2] 22.62
_refine.aniso_B[3][3] -18.34
_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 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 ?
_refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD'
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_R_Free_selection_details RANDOM
_refine.pdbx_overall_ESU_R 0.059
_refine.pdbx_overall_ESU_R_Free 0.043
_refine.overall_SU_ML 0.074
_refine.pdbx_overall_phase_error ?
_refine.overall_SU_B 2.823
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_Blow_DPI ?
_refine.pdbx_overall_SU_R_free_Blow_DPI ?
#
_refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine_hist.cycle_id LAST
_refine_hist.pdbx_number_atoms_protein 52
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 4
_refine_hist.number_atoms_solvent 3
_refine_hist.number_atoms_total 59
_refine_hist.d_res_high 1.91
_refine_hist.d_res_low 11.41
#
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 0.020 0.023 ? 56 'X-RAY DIFFRACTION' ?
r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ?
r_angle_refined_deg 1.703 2.029 ? 73 'X-RAY DIFFRACTION' ?
r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ?
r_dihedral_angle_1_deg 10.614 5.000 ? 5 'X-RAY DIFFRACTION' ?
r_dihedral_angle_2_deg 4.237 20.000 ? 2 'X-RAY DIFFRACTION' ?
r_dihedral_angle_3_deg 11.363 15.000 ? 9 'X-RAY DIFFRACTION' ?
r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ?
r_chiral_restr 0.121 0.200 ? 8 'X-RAY DIFFRACTION' ?
r_gen_planes_refined 0.009 0.020 ? 42 'X-RAY DIFFRACTION' ?
r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ?
r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ?
r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ?
r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ?
r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ?
r_xyhbond_nbd_refined ? ? ? ? '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 ? ? ? ? 'X-RAY DIFFRACTION' ?
r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ?
r_symmetry_hbond_refined ? ? ? ? '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 ? ? ? ? 'X-RAY DIFFRACTION' ?
r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ?
r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ?
r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ?
r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ?
r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ?
r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ?
r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ?
r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ?
r_long_range_B_other ? ? ? ? '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_refine_id 'X-RAY DIFFRACTION'
_refine_ls_shell.pdbx_total_number_of_bins_used 20
_refine_ls_shell.d_res_high 1.906
_refine_ls_shell.d_res_low 1.954
_refine_ls_shell.number_reflns_R_work 12
_refine_ls_shell.R_factor_R_work 0.226
_refine_ls_shell.percent_reflns_obs 40.63
_refine_ls_shell.R_factor_R_free ?
_refine_ls_shell.R_factor_R_free_error ?
_refine_ls_shell.percent_reflns_R_free ?
_refine_ls_shell.number_reflns_R_free ?
_refine_ls_shell.number_reflns_all ?
_refine_ls_shell.R_factor_all ?
#
_struct.entry_id 2Y2A
_struct.title
'Structure of segment KLVFFA from the amyloid-beta peptide (Ab, residues 16-21), alternate polymorph I'
_struct.pdbx_descriptor 'AMYLOID BETA A4 PROTEIN'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 2Y2A
_struct_keywords.pdbx_keywords 'PROTEIN FIBRIL'
_struct_keywords.text 'PROTEIN FIBRIL, ALZHEIMER DISEASE'
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 2 ?
C N N 3 ?
#
_struct_biol.id 1
#
_struct_site.id AC1
_struct_site.pdbx_evidence_code Software
_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 5
_struct_site.details 'BINDING SITE FOR RESIDUE ACT A 1008'
#
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 5 LYS A 1 ? LYS A 2 . ? 4_435 ?
2 AC1 5 LYS A 1 ? LYS A 2 . ? 2_445 ?
3 AC1 5 PHE A 5 ? PHE A 6 . ? 1_555 ?
4 AC1 5 ALA A 6 ? ALA A 7 . ? 1_555 ?
5 AC1 5 HOH C . ? HOH A 2003 . ? 1_555 ?
#
_database_PDB_matrix.entry_id 2Y2A
_database_PDB_matrix.origx[1][1] 1.000000
_database_PDB_matrix.origx[1][2] 0.000000
_database_PDB_matrix.origx[1][3] 0.000000
_database_PDB_matrix.origx[2][1] 0.000000
_database_PDB_matrix.origx[2][2] 1.000000
_database_PDB_matrix.origx[2][3] 0.000000
_database_PDB_matrix.origx[3][1] 0.000000
_database_PDB_matrix.origx[3][2] 0.000000
_database_PDB_matrix.origx[3][3] 1.000000
_database_PDB_matrix.origx_vector[1] 0.00000
_database_PDB_matrix.origx_vector[2] 0.00000
_database_PDB_matrix.origx_vector[3] 0.00000
#
_atom_sites.entry_id 2Y2A
_atom_sites.fract_transf_matrix[1][1] 0.104384
_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] 0.084388
_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] 0.023546
_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
#
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 . LYS A 1 1 ? -1.334 1.852 -7.753 1.00 12.07 ? 2 LYS A N 1
ATOM 2 C CA . LYS A 1 1 ? -1.943 0.655 -7.101 1.00 11.60 ? 2 LYS A CA 1
ATOM 3 C C . LYS A 1 1 ? -1.325 0.528 -5.746 1.00 11.69 ? 2 LYS A C 1
ATOM 4 O O . LYS A 1 1 ? -0.084 0.407 -5.672 1.00 11.66 ? 2 LYS A O 1
ATOM 5 C CB . LYS A 1 1 ? -1.631 -0.609 -7.915 1.00 12.71 ? 2 LYS A CB 1
ATOM 6 C CG . LYS A 1 1 ? -1.974 -1.892 -7.241 1.00 15.55 ? 2 LYS A CG 1
ATOM 7 C CD . LYS A 1 1 ? -2.102 -3.103 -8.198 1.00 16.66 ? 2 LYS A CD 1
ATOM 8 C CE . LYS A 1 1 ? -0.815 -3.611 -8.824 1.00 15.73 ? 2 LYS A CE 1
ATOM 9 N NZ . LYS A 1 1 ? -1.061 -4.900 -9.632 1.00 13.21 ? 2 LYS A NZ 1
ATOM 10 N N . LEU A 1 2 ? -2.165 0.536 -4.686 1.00 9.76 ? 3 LEU A N 1
ATOM 11 C CA . LEU A 1 2 ? -1.709 0.188 -3.332 1.00 8.84 ? 3 LEU A CA 1
ATOM 12 C C . LEU A 1 2 ? -2.242 -1.190 -2.970 1.00 8.55 ? 3 LEU A C 1
ATOM 13 O O . LEU A 1 2 ? -3.433 -1.466 -3.093 1.00 8.36 ? 3 LEU A O 1
ATOM 14 C CB . LEU A 1 2 ? -2.254 1.169 -2.282 1.00 8.38 ? 3 LEU A CB 1
ATOM 15 C CG . LEU A 1 2 ? -2.026 0.948 -0.760 1.00 7.99 ? 3 LEU A CG 1
ATOM 16 C CD1 . LEU A 1 2 ? -0.558 1.217 -0.331 1.00 7.38 ? 3 LEU A CD1 1
ATOM 17 C CD2 . LEU A 1 2 ? -2.946 1.828 0.075 1.00 7.69 ? 3 LEU A CD2 1
ATOM 18 N N . VAL A 1 3 ? -1.364 -2.007 -2.421 1.00 8.06 ? 4 VAL A N 1
ATOM 19 C CA . VAL A 1 3 ? -1.802 -3.187 -1.756 1.00 8.60 ? 4 VAL A CA 1
ATOM 20 C C . VAL A 1 3 ? -1.169 -3.244 -0.378 1.00 9.07 ? 4 VAL A C 1
ATOM 21 O O . VAL A 1 3 ? 0.040 -3.304 -0.239 1.00 10.22 ? 4 VAL A O 1
ATOM 22 C CB . VAL A 1 3 ? -1.428 -4.429 -2.531 1.00 7.98 ? 4 VAL A CB 1
ATOM 23 C CG1 . VAL A 1 3 ? -2.051 -5.716 -1.886 1.00 7.84 ? 4 VAL A CG1 1
ATOM 24 C CG2 . VAL A 1 3 ? -1.750 -4.301 -4.025 1.00 8.19 ? 4 VAL A CG2 1
ATOM 25 N N . PHE A 1 4 ? -2.014 -3.237 0.640 1.00 11.83 ? 5 PHE A N 1
ATOM 26 C CA . PHE A 1 4 ? -1.588 -3.380 2.032 1.00 12.27 ? 5 PHE A CA 1
ATOM 27 C C . PHE A 1 4 ? -2.275 -4.573 2.662 1.00 13.82 ? 5 PHE A C 1
ATOM 28 O O . PHE A 1 4 ? -3.521 -4.672 2.575 1.00 15.79 ? 5 PHE A O 1
ATOM 29 C CB . PHE A 1 4 ? -1.980 -2.139 2.822 1.00 11.97 ? 5 PHE A CB 1
ATOM 30 C CG . PHE A 1 4 ? -1.754 -2.267 4.292 1.00 11.24 ? 5 PHE A CG 1
ATOM 31 C CD1 . PHE A 1 4 ? -0.509 -2.005 4.837 1.00 13.30 ? 5 PHE A CD1 1
ATOM 32 C CD2 . PHE A 1 4 ? -2.784 -2.614 5.127 1.00 10.94 ? 5 PHE A CD2 1
ATOM 33 C CE1 . PHE A 1 4 ? -0.320 -2.088 6.234 1.00 13.41 ? 5 PHE A CE1 1
ATOM 34 C CE2 . PHE A 1 4 ? -2.591 -2.745 6.500 1.00 11.77 ? 5 PHE A CE2 1
ATOM 35 C CZ . PHE A 1 4 ? -1.365 -2.458 7.047 1.00 11.58 ? 5 PHE A CZ 1
ATOM 36 N N . PHE A 1 5 ? -1.476 -5.455 3.275 1.00 14.81 ? 6 PHE A N 1
ATOM 37 C CA . PHE A 1 5 ? -1.984 -6.541 4.123 1.00 15.73 ? 6 PHE A CA 1
ATOM 38 C C . PHE A 1 5 ? -1.218 -6.607 5.435 1.00 16.89 ? 6 PHE A C 1
ATOM 39 O O . PHE A 1 5 ? -0.016 -6.875 5.416 1.00 13.20 ? 6 PHE A O 1
ATOM 40 C CB . PHE A 1 5 ? -1.848 -7.895 3.449 1.00 14.69 ? 6 PHE A CB 1
ATOM 41 C CG . PHE A 1 5 ? -2.572 -8.988 4.176 1.00 17.56 ? 6 PHE A CG 1
ATOM 42 C CD1 . PHE A 1 5 ? -3.928 -9.217 3.932 1.00 16.39 ? 6 PHE A CD1 1
ATOM 43 C CD2 . PHE A 1 5 ? -1.910 -9.768 5.145 1.00 20.27 ? 6 PHE A CD2 1
ATOM 44 C CE1 . PHE A 1 5 ? -4.613 -10.201 4.614 1.00 18.91 ? 6 PHE A CE1 1
ATOM 45 C CE2 . PHE A 1 5 ? -2.602 -10.752 5.845 1.00 21.33 ? 6 PHE A CE2 1
ATOM 46 C CZ . PHE A 1 5 ? -3.959 -10.975 5.552 1.00 18.84 ? 6 PHE A CZ 1
ATOM 47 N N . ALA A 1 6 ? -1.907 -6.448 6.572 1.00 21.78 ? 7 ALA A N 1
ATOM 48 C CA . ALA A 1 6 ? -1.277 -6.712 7.898 1.00 23.97 ? 7 ALA A CA 1
ATOM 49 C C . ALA A 1 6 ? -2.066 -7.660 8.834 1.00 32.80 ? 7 ALA A C 1
ATOM 50 O O . ALA A 1 6 ? -3.245 -7.905 8.595 1.00 29.64 ? 7 ALA A O 1
ATOM 51 C CB . ALA A 1 6 ? -0.953 -5.441 8.593 1.00 26.09 ? 7 ALA A CB 1
ATOM 52 O OXT . ALA A 1 6 ? -1.550 -8.249 9.820 1.00 33.63 ? 7 ALA A OXT 1
HETATM 53 C C . ACT B 2 . ? -3.334 -11.524 9.718 1.00 35.51 ? 1008 ACT A C 1
HETATM 54 O O . ACT B 2 . ? -3.296 -12.741 10.153 1.00 36.47 ? 1008 ACT A O 1
HETATM 55 O OXT . ACT B 2 . ? -4.406 -10.873 9.502 1.00 26.04 ? 1008 ACT A OXT 1
HETATM 56 C CH3 . ACT B 2 . ? -2.025 -10.826 9.449 1.00 27.90 ? 1008 ACT A CH3 1
HETATM 57 O O . HOH C 3 . ? -2.149 4.522 -7.326 1.00 36.53 ? 2001 HOH A O 1
HETATM 58 O O . HOH C 3 . ? -3.671 -6.911 -8.668 1.00 39.72 ? 2002 HOH A O 1
HETATM 59 O O . HOH C 3 . ? -1.183 -14.039 10.669 1.00 25.69 ? 2003 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 LYS 1 2 2 LYS LYS A . n
A 1 2 LEU 2 3 3 LEU LEU A . n
A 1 3 VAL 3 4 4 VAL VAL A . n
A 1 4 PHE 4 5 5 PHE PHE A . n
A 1 5 PHE 5 6 6 PHE PHE A . n
A 1 6 ALA 6 7 7 ALA ALA 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 ACT 1 1008 1008 ACT ACT A .
C 3 HOH 1 2001 2001 HOH HOH A .
C 3 HOH 2 2002 2002 HOH HOH A .
C 3 HOH 3 2003 2003 HOH HOH A .
#
_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_and_software_defined_assembly
_pdbx_struct_assembly.method_details PISA
_pdbx_struct_assembly.oligomeric_details monomeric
_pdbx_struct_assembly.oligomeric_count 1
#
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1
_pdbx_struct_assembly_gen.asym_id_list A,B,C
#
_pdbx_struct_oper_list.id 1
_pdbx_struct_oper_list.type 'identity operation'
_pdbx_struct_oper_list.name 1_555
_pdbx_struct_oper_list.symmetry_operation x,y,z
_pdbx_struct_oper_list.matrix[1][1] 1.0000000000
_pdbx_struct_oper_list.matrix[1][2] 0.0000000000
_pdbx_struct_oper_list.matrix[1][3] 0.0000000000
_pdbx_struct_oper_list.vector[1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][2] 1.0000000000
_pdbx_struct_oper_list.matrix[2][3] 0.0000000000
_pdbx_struct_oper_list.vector[2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][1] 0.0000000000
_pdbx_struct_oper_list.matrix[3][2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][3] 1.0000000000
_pdbx_struct_oper_list.vector[3] 0.0000000000
#
_pdbx_audit_revision_history.ordinal 1
_pdbx_audit_revision_history.data_content_type 'Structure model'
_pdbx_audit_revision_history.major_revision 1
_pdbx_audit_revision_history.minor_revision 0
_pdbx_audit_revision_history.revision_date 2011-10-26
#
_pdbx_audit_revision_details.ordinal 1
_pdbx_audit_revision_details.revision_ordinal 1
_pdbx_audit_revision_details.data_content_type 'Structure model'
_pdbx_audit_revision_details.provider repository
_pdbx_audit_revision_details.type 'Initial release'
_pdbx_audit_revision_details.description ?
#
loop_
_software.name
_software.classification
_software.version
_software.citation_id
_software.pdbx_ordinal
REFMAC refinement 5.6.0081 ? 1
XDS 'data reduction' . ? 2
XSCALE 'data scaling' . ? 3
PHASER phasing . ? 4
#
_pdbx_entry_details.entry_id 2Y2A
_pdbx_entry_details.compound_details ?
_pdbx_entry_details.source_details ?
_pdbx_entry_details.nonpolymer_details ?
_pdbx_entry_details.sequence_details
;IN VIVO AMYLOID BETA PEPTIDE (AB) IS A PROTEOLYTIC PRODUCT OF
THE AMYLOID PRECURSOR PROTEIN (APP). AB SEGMENT 16-KLVFFA-21
CORRESPONDS TO RESIDUES 687-692 OF APP
;
#
_pdbx_validate_symm_contact.id 1
_pdbx_validate_symm_contact.PDB_model_num 1
_pdbx_validate_symm_contact.auth_atom_id_1 O
_pdbx_validate_symm_contact.auth_asym_id_1 A
_pdbx_validate_symm_contact.auth_comp_id_1 HOH
_pdbx_validate_symm_contact.auth_seq_id_1 2001
_pdbx_validate_symm_contact.PDB_ins_code_1 ?
_pdbx_validate_symm_contact.label_alt_id_1 ?
_pdbx_validate_symm_contact.site_symmetry_1 1_555
_pdbx_validate_symm_contact.auth_atom_id_2 O
_pdbx_validate_symm_contact.auth_asym_id_2 A
_pdbx_validate_symm_contact.auth_comp_id_2 HOH
_pdbx_validate_symm_contact.auth_seq_id_2 2002
_pdbx_validate_symm_contact.PDB_ins_code_2 ?
_pdbx_validate_symm_contact.label_alt_id_2 ?
_pdbx_validate_symm_contact.site_symmetry_2 1_565
_pdbx_validate_symm_contact.dist 2.07
#
loop_
_pdbx_entity_nonpoly.entity_id
_pdbx_entity_nonpoly.name
_pdbx_entity_nonpoly.comp_id
2 'ACETATE ION' ACT
3 water HOH
#