1NLN

CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AMINO ACID COFACTOR AT 1.6 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic structure at 1.6-A resolution of the human adenovirus proteinase in a covalent complex with its 11-amino-acid peptide cofactor: insights on a new fold

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

(2003) Biochim.Biophys.Acta 1648: 1-11

  • Also Cited By: 4EKF

  • PubMed Abstract: 
  • The crystal structure of the human adenovirus proteinase (AVP), a cysteine proteinase covalently bound to its 11-amino-acid peptide cofactor pVIc, has been solved to 1.6-A resolution with a crystallographic R-factor of 0.136, R(free)=0.179. The fold ...

    The crystal structure of the human adenovirus proteinase (AVP), a cysteine proteinase covalently bound to its 11-amino-acid peptide cofactor pVIc, has been solved to 1.6-A resolution with a crystallographic R-factor of 0.136, R(free)=0.179. The fold of AVP-pVIc is new and the structural basis for it is described in detail. The polypeptide chain of AVP folds into two domains. One domain contains a five-strand beta-sheet with two peripheral alpha-helices; this region represents the hydrophobic core of the protein. A second domain contains the N terminus, several C-terminal alpha-helices, and a small peripheral anti-parallel beta-sheet. The domains interact through an extended polar interface. pVIc spans the two domains like a strap, its C-terminal portion forming a sixth strand on the beta-sheet. The active site is in a long, deep groove located between the two domains. Portions are structurally similar to the active site of the prototypical cysteine proteinase papain, especially some of the Calpha backbone atoms (r.m.s. deviation of 0.354 A for 12 Calpha atoms). The active-site nucleophile of AVP, the conserved Cys(122), was shown to have a pK(a) of 4.5, close to the pK(a) of 3.0 for the nucleophile of papain, suggesting that a similar ion pair arrangement with His(54) may be present in AVP-pVIc. The interactions between AVP and pVIc include 24 non-beta-strand hydrogen bonds, six beta-strand hydrogen bonds and one covalent bond. Of the 204 amino acid residues in AVP, 33 are conserved among the many serotypes of adenovirus, and these aid in forming the active site groove, are involved in substrate specificity or interact between secondary structure elements.


    Related Citations: 
    • 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


    Organizational Affiliation

    Biology Department, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973-5000, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenain
A
204Human adenovirus C serotype 2EC: 3.4.22.39
Find proteins for P03252 (Human adenovirus C serotype 2)
Go to UniProtKB:  P03252
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PVIC
B
11Human adenovirus C serotype 2N/A
Find proteins for P03274 (Human adenovirus C serotype 2)
Go to UniProtKB:  P03274
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.136 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 111.500α = 90.00
b = 111.500β = 90.00
c = 50.900γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance