1IBQ

ASPERGILLOPEPSIN FROM ASPERGILLUS PHOENICIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of aspergillopepsin I from Aspergillus phoenicis: variations of the S1'-S2 subsite in aspartic proteinases.

Cho, S.W.Kim, N.Choi, M.U.Shin, W.

(2001) Acta Crystallogr.,Sect.D 57: 948-956


  • PubMed Abstract: 
  • The crystal structure of aspergillopepsin I (AP) from Aspergillus phoenicis has been determined at 2.18 A resolution and refined to R and R(free) factors of 21.5 and 26.0%, respectively. AP has the typical two beta-barrel domain structure of aspartic ...

    The crystal structure of aspergillopepsin I (AP) from Aspergillus phoenicis has been determined at 2.18 A resolution and refined to R and R(free) factors of 21.5 and 26.0%, respectively. AP has the typical two beta-barrel domain structure of aspartic proteinases. The structures of the two independent molecules are partly different, exemplifying the flexible nature of the aspartic proteinase structure. Notably, the 'flap' in one molecule is closer, with a largest separation of 4.0 A, to the active site than in the other molecule. AP is most structurally homologous to penicillopepsin (PP) and then to endothiapepsin (EP), which share sequence identities of 68 and 56%, respectively. However, AP is similar to EP but differs from PP in the combined S1'-S2 subsite that is delineated by a flexible psi-loop in the C-terminal domain. The S1' and S2 subsites are well defined and small in AP, while there is no definite border between S1' and S2 and the open space for the S2 subsite is larger in PP. Comparison of the structures indicates that the two amino-acid residues equivalent to Leu295 and Leu297 of AP are the major determining factors in shaping the S1'-S2 subsite in the fungal aspartic proteinases.


    Organizational Affiliation

    School of Chemistry and Molecular Engineering, Seoul National University, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ASPERGILLOPEPSIN
A, B
325Aspergillus phoenicisGene Names: pep1 (pepA)
EC: 3.4.23.18
Find proteins for Q12567 (Aspergillus phoenicis)
Go to UniProtKB:  Q12567
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.190α = 90.00
b = 36.620β = 113.49
c = 104.940γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALAdata scaling
MADNESSdata reduction
CCP4data scaling
SHELXphasing
SHELXmodel building
MADNESSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-03-28 
  • Released Date: 2001-07-04 
  • Deposition Author(s): Cho, S.W., Shin, W.

Revision History 

  • Version 1.0: 2001-07-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description