Document:

Exhibit 4.3

Exhibit 4.3

FIRST SUPPLEMENTAL INDENTURE

First Supplemental Indenture (this “First Supplemental Indenture”), dated as of April
14, 2010, among Holly Energy Storage-Tulsa LLC, a Delaware limited liability company (“HES Tulsa”)
and Holly Energy Storage-Lovington LLC (“HES Lovington” and collectively with HES Tulsa, the
“Guaranteeing Subsidiaries”), Holly Energy Partners, L.P., a Delaware limited partnership (“Holly
Energy Partners”), and Holly Energy Finance Corp. (“Finance Corp.” and, together with Holly Energy
Partners, the “Issuers”), the other Guarantors (as defined in the Indenture referred to herein) and
U.S. Bank National Association, as trustee under the Indenture referred to below (the “Trustee”).

W I T N E S S E T H

WHEREAS, the Issuers have heretofore executed and delivered to the Trustee an indenture (the
“Indenture”), dated as of March 10, 2010 providing for the issuance of 8.25% Senior Notes due 2018
(the “Notes”);

WHEREAS, the Indenture provides that under certain circumstances the Guaranteeing Subsidiaries
shall execute and deliver to the Trustee a supplemental indenture pursuant to which the
Guaranteeing Subsidiaries shall unconditionally guarantee all of the Issuers’ Obligations under the
Notes and the Indenture on the terms and conditions set forth herein (the “Note Guarantee”); and

WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is authorized to execute and
deliver this First Supplemental Indenture.

NOW, THEREFORE, in consideration of the foregoing and for other good and valuable
consideration, the receipt of which is hereby acknowledged, the Guaranteeing Subsidiaries and the
Trustee mutually covenant and agree for the equal and ratable benefit of the Holders of the Notes
as follows:

1. Capitalized Terms. Capitalized terms used herein without definition shall have
the meanings assigned to them in the Indenture.

2. Agreement to Guarantee. The Guaranteeing Subsidiaries hereby agree to provide an
unconditional Guarantee on the terms and subject to the conditions set forth in the Note Guarantee
and in the Indenture including but not limited to Article 10 thereof.

4. No Recourse Against Others. No past, present or future director, officer,
employee, incorporator, stockholder or agent of the Guaranteeing Subsidiaries, as such, shall have
any liability for any obligations of the Issuers or any Guaranteeing Subsidiaries under the Notes,
any Note Guarantee, the Indenture or this First Supplemental Indenture or for any claim based on,
in respect of, or by reason of, such obligations or their creation. Each Holder of the Notes by
accepting a Note waives and releases all such liability. The waiver and release are part of the
consideration for issuance of the Notes. Such waiver may not be effective to waive liabilities
under the federal securities laws and it is the view of the SEC that such a waiver is against
public policy.

First Supplemental Indenture

 

 

 

5. NEW YORK LAW TO GOVERN. THE LAW OF THE STATE OF NEW YORK SHALL GOVERN AND BE USED TO
CONSTRUE THIS SUPPLEMENTAL INDENTURE.

6. Counterparts. The parties may sign any number of copies of this First
Supplemental Indenture. Each signed copy shall be an original, but all of them together represent
the same agreement.

7. Effect of Headings. The Section headings herein are for convenience only and
shall not affect the construction hereof.

8. The Trustee. The Trustee shall not be responsible in any manner whatsoever for or
in respect of the validity or sufficiency of this First Supplemental Indenture or for or in respect
of the recitals contained herein, all of which recitals are made solely by the Guaranteeing
Subsidiaries and the Issuers.

First Supplemental Indenture

 

 

 

IN WITNESS WHEREOF, the parties hereto have caused this Supplemental Indenture to be duly
executed and attested, all as of the date first above written.

	 	 	 	 	 
	 	GUARANTEEING SUBSIDIARIES:

HOLLY ENERGY STORAGE-TULSA LLC, a Delaware limited
liability company

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Senior Vice President and Chief Financial
Officer 	 
	 
	 	HOLLY ENERGY STORAGE-LOVINGTON LLC, a Delaware limited
liability company

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Senior Vice President and Chief Financial
Officer 	 

Signature Page to First Supplemental Indenture

 

S-1

 

	 	 	 	 	 	 	 	 	 	 	 
	 	 	ISSUERS:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HOLLY ENERGY PARTNERS, L.P.	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	HEP Logistic Holdings, L.P.,

Its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Logistic Services, L.L.C.,

Its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	Name: Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	Title: Senior Vice President and Chief

Financial Officer	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HOLLY ENERGY FINANCE CORP.	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	/s/ Bruce R. Shaw	 	 
	 	 	 	 	 	 	 
	 	 	 	 	Name: Bruce R. Shaw	 	 
	 	 	 	 	Title: Vice President and Chief Financial Officer	 	 

Signature Page to First Supplemental Indenture

 

S-2

 

	 	 	 	 	 
	 	OTHER GUARANTORS:

HEP LOGISTICS GP, L.L.C., a Delaware limited liability
company

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Vice President and Chief Financial Officer 	 
	 
	 	HOLLY ENERGY PARTNERS-OPERATING, L.P., a Delaware limited
partnership

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Vice President and Chief Financial Officer 	 

Signature Page to First Supplemental Indenture

 

S-3

 

	 	 	 	 	 	 	 	 	 
	 	 	HEP PIPELINE GP, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP PIPELINE, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	HEP MOUNTAIN HOME, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	HEP REFINING, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP REFINING GP, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP WOODS CROSS, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP TULSA LLC, a Delaware limited liability company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP SLC, LLC, a Delaware limited liability company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	LOVINGTON-ARTESIA, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	ROADRUNNER PIPELINE, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	Each By:	 	Holly Energy Partners – Operating, L.P., a 
Delaware
limited liability company and Its Sole Member	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	 	 	By:
	 	/s/ Bruce R. Shaw
 

Name: Bruce R. Shaw
	 	 
	 

	 	 	 	 	 	Title: Vice President and Chief Financial Officer	 	 

Signature Page to First Supplemental Indenture

 

S-4

 

	 	 	 	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HEP FIN-TEX/TRUST-RIVER, L.P., a Texas limited
partnership	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HEP NAVAJO SOUTHERN, L.P., a Delaware limited partnership	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HEP PIPELINE ASSETS, LIMITED PARTNERSHIP, a Delaware
limited partnership	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	Each by:	 	HEP Pipeline GP, L.L.C., a Delaware limited liability
company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	Name: Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	Title: Vice President and Chief Financial Officer	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HEP REFINING ASSETS, L.P., a Delaware limited partnership	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	HEP Refining GP, L.L.C., a Delaware limited liability
company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw
 

Name: Bruce R. Shaw
	 	 
	 

	 	 	 	 	 	 	 	Title: Vice President and Chief Financial Officer	 	 

Signature Page to First Supplemental Indenture

 

S-5

 

	 	 	 	 	 
	 	U.S. BANK NATIONAL ASSOCIATION,

as Trustee

 	 
	 	By:  	/s/ Steven A. Finklea
 	 
	 	 	Name:  	Steven A. Finklea 	 
	 	 	Title:  	Vice President 	 

Signature Page to First Supplemental Indenture

 

S-6Exhibit 4.4

Exhibit 4.4

SECOND SUPPLEMENTAL INDENTURE

Second Supplemental Indenture (this “Second Supplemental Indenture”), dated as of
June 4, 2010, among HEP Operations LLC, a Delaware limited liability company (the “Guaranteeing
Subsidiary”), Holly Energy Partners, L.P., a Delaware limited partnership (“Holly Energy
Partners”), and Holly Energy Finance Corp. (“Finance Corp.” and, together with Holly Energy
Partners, the “Issuers”), the other Guarantors (as defined in the Indenture referred to herein) and
U.S. Bank National Association, as trustee under the Indenture referred to below (the “Trustee”).

W I T N E S S E T H

WHEREAS, the Issuers have heretofore executed and delivered to the Trustee an Indenture (the
“Indenture”), dated as of March 10, 2010 providing for the issuance of 8.25% Senior Notes due 2018
(the “Notes”), and a First Supplemental Indenture, dated as of April 14, 2010, providing for the
addition of Holly Energy Storage-Tulsa LLC, a Delaware limited liability company and Holly Energy
Storage-Lovington LLC, a Delaware limited liability company, as Guarantors under the Indenture;

WHEREAS, the Indenture provides that under certain circumstances the Guaranteeing Subsidiary
shall execute and deliver to the Trustee a supplemental indenture pursuant to which the
Guaranteeing Subsidiary shall unconditionally guarantee all of the Issuers’ Obligations under the
Notes and the Indenture on the terms and conditions set forth herein (the “Note Guarantee”); and

WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is authorized to execute and
deliver this Second Supplemental Indenture.

NOW, THEREFORE, in consideration of the foregoing and for other good and valuable
consideration, the receipt of which is hereby acknowledged, the Guaranteeing Subsidiary and the
Trustee mutually covenant and agree for the equal and ratable benefit of the Holders of the Notes
as follows:

1. Capitalized Terms. Capitalized terms used herein without definition shall have
the meanings assigned to them in the Indenture.

2. Agreement to Guarantee. The Guaranteeing Subsidiary hereby agrees to provide an
unconditional Guarantee on the terms and subject to the conditions set forth in the Note Guarantee
and in the Indenture including but not limited to Article 10 thereof.

4. No Recourse Against Others. No past, present or future director, officer,
employee, incorporator, stockholder or agent of the Guaranteeing Subsidiary, as such, shall have
any liability for any obligations of the Issuers or any Guaranteeing Subsidiary under the Notes,
any Note Guarantee, the Indenture or this Second Supplemental Indenture or for any claim based on,
in respect of, or by reason of, such obligations or their creation. Each Holder of the Notes by
accepting a Note waives and releases all such liability. The waiver and release are part of the
consideration for issuance of the Notes. Such waiver may not be effective to waive liabilities
under the federal securities laws and it is the view of the SEC that such a waiver is against
public policy.

Second Supplemental Indenture

 

 

 

5. NEW YORK LAW TO GOVERN. THE LAW OF THE STATE OF NEW YORK SHALL GOVERN AND BE USED TO
CONSTRUE THIS SECOND SUPPLEMENTAL INDENTURE.

6. Counterparts. The parties may sign any number of copies of this Second
Supplemental Indenture. Each signed copy shall be an original, but all of them together represent
the same agreement.

7. Effect of Headings. The Section headings herein are for convenience only and
shall not affect the construction hereof.

8. The Trustee. The Trustee shall not be responsible in any manner whatsoever for or
in respect of the validity or sufficiency of this Second Supplemental Indenture or for or in
respect of the recitals contained herein, all of which recitals are made solely by the Guaranteeing
Subsidiary and the Issuers.

Second Supplemental Indenture

 

 

 

IN WITNESS WHEREOF, the parties hereto have caused this Second Supplemental Indenture to be
duly executed and attested, all as of the date first above written.

	 	 	 	 	 	 	 	 	 	 	 
	 	 	GUARANTEEING SUBSIDIARY:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HEP OPERATIONS LLC, a Delaware limited liability company	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	/s/ Bruce R. Shaw	 	 
	 	 	 	 	 	 	 
	 	 	 	 	Name: Bruce R. Shaw	 	 
	 	 	 	 	Title: Senior Vice President and Chief Financial Officer	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	ISSUERS:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HOLLY ENERGY PARTNERS, L.P.	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	HEP Logistic Holdings, L.P.,

Its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Logistic Services, L.L.C.,

Its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	Name: Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	Title: Senior Vice President and Chief

Financial Officer	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HOLLY ENERGY FINANCE CORP.	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	/s/ Bruce R. Shaw	 	 
	 	 	 	 	 	 	 
	 	 	 	 	Name: Bruce R. Shaw	 	 
	 	 	 	 	Title: Vice President and Chief Financial Officer	 	 

Signature Page to Second Supplemental Indenture

 

S-1

 

	 	 	 	 	 
	 	OTHER GUARANTORS:

HEP LOGISTICS GP, L.L.C., a Delaware limited liability
company

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Vice President and Chief Financial Officer 	 
	 
	 	HOLLY ENERGY PARTNERS-OPERATING, L.P., a Delaware limited
partnership

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Vice President and Chief Financial Officer 	 
	 
	 	HOLLY ENERGY STORAGE-TULSA LLC, a Delaware limited
liability company

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Senior Vice President and Chief Financial
Officer 	 
	 
	 	HOLLY ENERGY STORAGE-LOVINGTON LLC, a Delaware limited
liability company

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Senior Vice President and Chief Financial
Officer 	 

Signature Page to Second Supplemental Indenture

 

S-2

 

	 	 	 	 	 	 	 	 	 
	 	 	HEP PIPELINE GP, L.L.C., a Delaware limited liability company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP PIPELINE, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP MOUNTAIN HOME, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP REFINING, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP REFINING GP, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP WOODS CROSS, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP TULSA LLC, a Delaware limited liability company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP SLC, LLC, a Delaware limited liability company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	LOVINGTON-ARTESIA, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	ROADRUNNER PIPELINE, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	Each By:	 	Holly Energy Partners – Operating, L.P., a Delaware
limited liability company and Its Sole Member	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	 	 	By:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	Name: Bruce R. Shaw	 	 
	 

	 	 	 	 	 	Title: Vice President and Chief Financial
Officer	 	 

Signature Page to Second Supplemental Indenture

 

S-3

 

	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	HEP FIN-TEX/TRUST-RIVER, L.P., a Texas limited partnership	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	HEP NAVAJO SOUTHERN, L.P., a Delaware limited partnership	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	HEP PIPELINE ASSETS, LIMITED PARTNERSHIP, a Delaware

limited partnership	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Each by:	 	HEP Pipeline GP, L.L.C., a Delaware limited liability
company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	Name: Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	Title:   Vice President and Chief Financial Officer	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	HEP REFINING ASSETS, L.P., a Delaware limited partnership	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	HEP Refining GP, L.L.C., a Delaware limited liability
company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	Name: Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	Title:   Vice President and Chief Financial Officer	 	 

Signature Page to Second Supplemental Indenture

 

S-4

 

	 	 	 	 	 
	 	TRUSTEE:

U.S. BANK NATIONAL ASSOCIATION,

as Trustee

 	 
	 	By:  	/s/ Steven A. Finklea
 	 
	 	 	Name:  	Steven A. Finklea 	 
	 	 	Title:  	Vice President 	 

Signature Page to Second Supplemental Indenture

 

S-5

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