3O3Y | pdb_00003o3y

A chimeric alpha+alpha/beta peptide based on the CHR domain sequence of gp41

PDB DOI: https://doi.org/10.2210/pdb3O3Y/pdb

Classification: VIRAL PROTEIN
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2010-07-26 Released: 2011-08-24
Deposition Author(s): Horne, W.S., Johnson, L.M., Gellman, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.171 (Depositor), 0.168 (DCC)
R-Value Work:
0.143 (Depositor), 0.143 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Chimeric and Non-Chimeric Foldamer Mimics of the CHR Segment of HIV Protein gp41: Evidence for the Importance of a Large Binding Interface in Six-Helix Bundle Formation

Horne, W.S., Johnson, L.M., Gellman, S.H.

To be published.

Macromolecule Content

Total Structure Weight: 4.51 kDa
Atom Count: 347
Modeled Residue Count: 37
Deposited Residue Count: 40
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chimeric alpha+alpha/beta peptide based on the CHR domain sequence of gp41	A	40	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3E Query on B3E	A	L-PEPTIDE LINKING	C₆ H₁₁ N O₄		GLU
XCP Query on XCP	A	PEPTIDE-LIKE	C₆ H₁₁ N O₂		--
XPC Query on XPC	A	PEPTIDE-LIKE	C₅ H₁₀ N₂ O₂		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.171 (Depositor), 0.168 (DCC)
R-Value Work: 0.143 (Depositor), 0.143 (DCC)
R-Value Observed: 0.144 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.036	α = 90
b = 33.036	β = 90
c = 48.9	γ = 120

Software Package:

Software Name	Purpose
MD2	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-08-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-24
Type: Initial release
Version 1.1: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection

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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.