3F87

An alpha/beta-Peptide Helix Bundle with a Pure beta-Amino Acid Core and a Distinctive Quarternary Structure: GCN4pLI derivative with beta residues at a and d heptad positions - higher symmetry crystal

PDB DOI: https://doi.org/10.2210/pdb3F87/pdb

Classification: UNKNOWN FUNCTION
Mutation(s): No

Deposited: 2008-11-11 Released: 2009-07-21
Deposition Author(s): Giuliano, M.W., Horne, W.S., Gellman, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.296
R-Value Work: 0.230
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

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

Literature

An alpha/beta-peptide helix bundle with a pure beta3-amino acid core and a distinctive quaternary structure.

Giuliano, M.W., Horne, W.S., Gellman, S.H.

(2009) J Am Chem Soc 131: 9860-9861

PubMed: 19580264 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/ja8099294
Primary Citation of Related Structures:
3F86, 3F87

PubMed Abstract:
Helix bundles are among the most widely studied tertiary and quaternary structural motifs in proteins. Here we present the crystal structure of an alpha/beta-peptide foldamer that adopts a tetrameric helix-bundle quaternary structure with a hydrophobic core composed solely of beta-amino acids. The structure displays features that are unprecedented among all known helix bundles composed of either alpha-peptides or peptidic foldamers. The tetramer is characterized by an asymmetry of interaction between neighboring helices, and the side-chain packing within the hydrophobic core differs fundamentally from the knobs-into-holes arrangement typical of most helix bundles.

Organizational Affiliation

Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Macromolecule Content

Total Structure Weight: 17.99 kDa
Atom Count: 1,298
Modelled Residue Count: 136
Deposited Residue Count: 136
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN4pLI-betaAD	A, B, C, D	34	N/A	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth C], M [auth C]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HMR Query on HMR	A, B, C, D	L-PEPTIDE LINKING	C₇ H₁₆ N₄ O₂		ARG

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.296
R-Value Work: 0.230
R-Value Observed: 0.233
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.313	α = 90
b = 71.313	β = 90
c = 97.44	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-21

Deposition Author(s):

Giuliano, M.W.

Horne, W.S.

Gellman, S.H.

Revision History (Full details and data files)

Version 1.0: 2009-07-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations