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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.196 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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 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

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), 0.210 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.180 (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

Entry History 

Deposition Data

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

Revision History  

• 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