4F73 | pdb_00004f73

Crystal Structure of active HIV-1 Protease in Complex with the N terminal product of CA-p2 cleavage site

• PDB DOI: https://doi.org/10.2210/pdb4F73/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., Mittal, S., Nalam, M.N.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal Structure of active HIV-1 Protease in Complex with the N terminal product of CA-p2 cleavage site

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 22.93 kDa 
• Atom Count: 1,698 
• Modeled Residue Count: 205 
• Deposited Residue Count: 208 
• Unique protein chains: 2

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 CA-p2	C, D	5	Human immunodeficiency virus 1	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.788	α = 90
b = 58.327	β = 90
c = 61.636	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., Mittal, S., Nalam, M.N.L.

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, Derived calculations