PDBsum entry 2f3k

Hydrolase

PDB id

2f3k

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Contents

			Protein chains

					99 a.a. *

			Ligands

					PO4 ×5


					RO1

			Waters ×211

* Residue conservation analysis

PDB id:

2f3k

Links
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Name:

Hydrolase

Title:

Substrate envelope and drug resistance: crystal structure of r01 in complex with wild-type HIV-1 protease

Structure:

Protease. Chain: a, b. Synonym: retropepsin, pr. Mutation: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: sf2

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å

R-factor:

0.165

R-free:

0.197

Authors:

M.Prabu-Jeyabalan,N.M.King,E.A.Nalivaika,G.Heilek-Snyder,N.Cammack, C.A.Schiffer

Key ref:

M.Prabu-Jeyabalan et al. (2006). Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease. Antimicrob Agents Chemother, 50, 1518-1521. PubMed id: 16569872

Date:

21-Nov-05

Release date:

21-Nov-06

PROCHECK

	Headers

	References

Protein chains

O38708 (O38708_9HIV1) - Protease (Fragment) from Human immunodeficiency virus 1

Seq: Struc:					99 a.a. 99 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)



		Enzyme reactions

Enzyme class:

E.C.3.4.23.16 - HIV-1 retropepsin.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

	Antimicrob Agents Chemother 50:1518-1521 (2006)
PubMed id: 16569872

Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease.
M.Prabu-Jeyabalan, N.M.King, E.A.Nalivaika, G.Heilek-Snyder, N.Cammack, C.A.Schiffer.

ABSTRACT

In our previous crystallographic studies of human immunodeficiency virus type 1 (HIV-1) protease-substrate complexes, we described a conserved "envelope" that appears to be important for substrate recognition and the selection of drug-resistant mutations. In this study, the complex of HIV-1 protease with the inhibitor RO1 was determined and comparison with the substrate envelope provides a rationale for mutational patterns.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20480379

H.Ode, M.Yokoyama, T.Kanda, and H.Sato (2011).
Identification of folding preferences of cleavage junctions of HIV-1 precursor proteins for regulation of cleavability.

J Mol Model, 17, 391-399.

21394574

Z.Liu, Y.Wang, J.Brunzelle, I.A.Kovari, and L.C.Kovari (2011).
Nine crystal structures determine the substrate envelope of the MDR HIV-1 protease.

Protein J, 30, 173-183.

PDB codes:

3ots 3oty 3ou1 3ou3 3ou4 3oua 3oub 3ouc 3oud

21084633

K.P.Romano, A.Ali, W.E.Royer, and C.A.Schiffer (2010).
Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding.

Proc Natl Acad Sci U S A, 107, 20986-20991.

PDB codes:

3m5l 3m5m 3m5n 3m5o

19193159

R.N.Jorissen, G.S.Reddy, A.Ali, M.D.Altman, S.Chellappan, S.G.Anjum, B.Tidor, C.A.Schiffer, T.M.Rana, and M.K.Gilson (2009).
Additivity in the analysis and design of HIV protease inhibitors.

J Med Chem, 52, 737-754.

19373036

M.N.Nalam, and C.A.Schiffer (2008).
New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors.

Curr Opin HIV AIDS, 3, 642-646.

17596316

M.N.Nalam, A.Peeters, T.H.Jonckers, I.Dierynck, and C.A.Schiffer (2007).
Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease.

J Virol, 81, 9512-9518.

PDB code:

2q3k

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.