4F76 | pdb_00004f76

Crystal Structure of the active HIV-1 Protease in Complex with the products of p1-p6 substrate

PDB DOI: https://doi.org/10.2210/pdb4F76/pdb

Classification: hydrolase/hydrolase product
Organism(s): HIV-1 M:B_ARV2/SF2, Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-05-15 Released: 2013-05-15
Deposition Author(s): Schiffer, C.A., Nalam, M.N.L., Mittal, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.196 (Depositor), 0.208 (DCC)
R-Value Work:
0.167 (Depositor), 0.177 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the active HIV-1 Protease in Complex with the products of p1-p6 substrate

Mittal, S., Nalam, M.N.L., Schiffer, C.A.

To be published.

Macromolecule Content

Total Structure Weight: 22.79 kDa
Atom Count: 1,671
Modeled Residue Count: 204
Deposited Residue Count: 208
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	HIV-1 M:B_ARV2/SF2	Mutation(s): 1 Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Explore P03369 Go to UniProtKB: P03369
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03369
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N terminal product of substrate p1-p6	C	5	Human immunodeficiency virus 1	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C terminal product of substrate p1-p6	D	5	Human immunodeficiency virus 1	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.196 (Depositor), 0.208 (DCC)
R-Value Work: 0.167 (Depositor), 0.177 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.906	α = 90
b = 58.367	β = 90
c = 61.928	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-05-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-15
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references

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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.