1HVC

CRYSTAL STRUCTURE OF A TETHERED DIMER OF HIV-1 PROTEASE COMPLEXED WITH AN INHIBITOR

PDB DOI: https://doi.org/10.2210/pdb1HVC/pdb

Classification: HYDROLASE(ACID PROTEASE)
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1994-06-22 Released: 1994-10-15
Deposition Author(s): Bhat, T.N., Baldwin, E.T., Erickson, J.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a tethered dimer of HIV-1 proteinase complexed with an inhibitor.

Bhat, T.N., Baldwin, E.T., Liu, B., Cheng, Y.S., Erickson, J.W.

(1994) Nat Struct Biol 1: 552-556

PubMed: 7664084 Search on PubMed
DOI: https://doi.org/10.1038/nsb0894-552
Primary Citation of Related Structures:
1HVC

PubMed Abstract:
HIV-1 proteinase (HIV PR) is a dimeric enzyme composed of two identical polypeptide chains that associate with twofold symmetry. We have determined to 1.8 A the crystal structure of a covalently tethered dimer of HIV PR. The tethered dimer:inhibitor complex is identical in nearly every respect to the complex of the same inhibitor with the wild type dimeric molecule, except for the linker region. Our results suggest that the tethered dimer may be a useful surrogate enzyme for studying the effects of single site mutations on substrate and inhibitor binding as well as on enzyme asymmetry, and for simulating independent mutational drift of the two domains which has been proposed to have led to the evolution of modern day, single-chain aspartic proteinases.

Organizational Affiliation

Structural Biochemistry Program, Frederick Biomedical Supercomputing Center, PRI/DynCorp, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702-1201, USA.

Macromolecule Content

Total Structure Weight: 22.76 kDa
Atom Count: 1,667
Modelled Residue Count: 203
Deposited Residue Count: 203
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	A	203	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: SYNTHETIC GENE
UniProt
Find proteins for Q4VE97 (Human immunodeficiency virus 1) Explore Q4VE97 Go to UniProtKB: Q4VE97
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4VE97
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A79 Query on A79 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-{1-BENZYL-(2S,3S)-2,3-DIHYDROXY-4-[3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRYLAMINO]-5-PHENYL-PENTYL}-3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRAMIDE C₄₄ H₅₈ N₈ O₆ QPVWMQXBTCSLCB-UNHORJANSA-N		Interactions Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
A79	BindingDB: 1HVC	Ki: min: 0.01, max: 9 (nM) from 3 assay(s)
A79	BindingDB: 1HVC	Kd: 0.08 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.1	α = 90
b = 59.8	β = 90
c = 62.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1994-10-15

Deposition Author(s):

Bhat, T.N.

Baldwin, E.T.

Erickson, J.W.

Revision History (Full details and data files)

Version 1.0: 1994-10-15
Type: Initial release
Version 1.1: 2008-03-10
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations, Other