1AVP | pdb_00001avp

STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AMINO ACID COFACTOR

• PDB DOI: https://doi.org/10.2210/pdb1AVP/pdb

• Classification: HYDROLASE
• Organism(s): Human adenovirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1996-04-04 Released: 1997-11-19 
• Deposition Author(s): Ding, J., Mcgrath, W.J., Sweet, R.M., Mangel, W.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of the human adenovirus proteinase with its 11 amino acid cofactor.

Ding, J., McGrath, W.J., Sweet, R.M., Mangel, W.F.

(1996) EMBO J 15: 1778-1783

• PubMed: 8617222 
• Primary Citation Related Structures: 
  1AVP


• PubMed Abstract: 
  

  The three-dimensional structure of the human adenovirus-2 proteinase complexed with its 11 amino acid cofactor, pVIc, was determined at 2.6 A resolution by X-ray crystallographic analysis. The fold of this protein has not been seen before. However, it represents an example of either subtly divergent or powerfully convergent evolution, because the active site contains a Cys-His-Glu triplet and oxyanion hole in an arrangement similar to that in papain. Thus, the adenovirus proteinase represents a new, fifth group of enzymes that contain catalytic triads. pVIc, which extends a beta-sheet in the main chain, is distant from the active site, yet its binding increases the catalytic rate constant 300-fold for substrate hydrolysis. The structure reveals several potential targets for antiviral therapy.

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Organizational Affiliation: 
• Physics Department, State University of New York at Stony Brook, 11794-3800, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 24.47 kDa 
• Atom Count: 1,760 
• Modeled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENOVIRAL PROTEINASE	A	204	Human adenovirus 2	Mutation(s): 0  EC: 3.4.22.39
UniProt
Find proteins for P03252 (Human adenovirus C serotype 2) Explore P03252  Go to UniProtKB:  P03252

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENOVIRAL PROTEINASE	B	11	Human adenovirus 2	Mutation(s): 0
UniProt
Find proteins for P03274 (Human adenovirus C serotype 2) Explore P03274  Go to UniProtKB:  P03274

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.3	α = 90
b = 114.3	β = 90
c = 50	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-11-19 
Deposition Author(s): Ding, J., Mcgrath, W.J., Sweet, R.M., Mangel, W.F.

Revision History  

• Version 1.0: 1997-11-19
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2016-05-25
  Changes: Structure summary
• Version 1.4: 2018-04-18
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Structure summary