3O42

Complex of an alpha/beta-peptide based on the gp41 CHR domain bound to gp41-5

PDB DOI: https://doi.org/10.2210/pdb3O42/pdb

Classification: VIRAL PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
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: 3.00 Å
R-Value Free: 0.290
R-Value Work: 0.202
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

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: 27 kDa
Atom Count: 1,882
Modelled Residue Count: 232
Deposited Residue Count: 238
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gp41-5	A	198	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha/beta-peptide based on HIV gp41 CHR domain sequence	B	40	N/A	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3A Query on B3A	B	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
B3E Query on B3E	B	L-PEPTIDE LINKING	C₆ H₁₁ N O₄		GLU
HMR Query on HMR	B	L-PEPTIDE LINKING	C₇ H₁₆ N₄ O₂		ARG

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.290
R-Value Work: 0.202
R-Value Observed: 0.206
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.407	α = 90
b = 57.162	β = 90
c = 102.178	γ = 90

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):

Horne, W.S.

Johnson, L.M.

Gellman, S.H.

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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Help and Resources

3O42

Complex of an alpha/beta-peptide based on the gp41 CHR domain bound to gp41-5

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

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2