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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.271 (Depositor), 0.272 (DCC)
R-Value Work:
0.224 (Depositor), 0.229 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4IVH

This is version 2.0 of the entry. See complete history.

Literature

Structures of beta-Amyloid Peptide Oligomers

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

(2013) J Am Chem Soc

Macromolecule Content

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

Macromolecules

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
TBU Query on TBU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	TERTIARY-BUTYL ALCOHOL C₄ H₁₀ O DKGAVHZHDRPRBM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4BF Query on 4BF	A	L-PEPTIDE LINKING	C₉ H₁₀ Br N O₂		TYR
HAO Query on HAO	A	PEPTIDE-LIKE	C₁₀ H₁₁ N₃ O₅		--
ORN Query on 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), 0.272 (DCC)
R-Value Work: 0.224 (Depositor), 0.229 (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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-07-31

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.