4IVH | pdb_00004ivh

Crystal structure of QKLVFFAED nonapeptide segment from amyloid beta incorporated into a macrocyclic beta-sheet template

• PDB DOI: https://doi.org/10.2210/pdb4IVH/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2013-01-22 Released: 2013-07-31 
• Deposition Author(s): Pham, J.D., Chim, N., Goulding, C.W., Nowick, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.271 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Structures of beta-Amyloid Peptide Oligomers

Pham, J.D., Chim, N., Goulding, C.W., Nowick, J.S.

(2013) J Am Chem Soc 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.35 kDa 
• Atom Count: 171 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cyclo[Gln-Lys-Leu-Val-Phe-Phe-Ala-Glu-Asp-(delta-linked-Orn)-Hao-Lys-Hao-(p-bromoPhe)-Thr-(delta-linked-Orn)]	A	16	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TBU	B [auth A]	TERTIARY-BUTYL ALCOHOL C4 H10 O DKGAVHZHDRPRBM-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4BF	A	L-PEPTIDE LINKING	C9 H10 Br N O2		TYR
ORN	A	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.271 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.085	α = 90
b = 45.085	β = 90
c = 29.247	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AutoSol	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Pham, J.D., Chim, N., Goulding, C.W., Nowick, J.S.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations