1APU | pdb_00001apu

Crystallographic analysis of a pepstatin analogue binding to the aspartyl proteinase penicillopepsin at 1.8 angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb1APU/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Penicillium janthinellum
• Mutation(s): No 


• Deposited: 1991-12-16 Released: 1994-01-31 
• Deposition Author(s): Sielecki, A.R., James, M.N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 
  0.131 (Depositor) 

Literature

Crystallographic Analysis of Transition State Mimics Bound to Penicillopepsin: Difluorostatine-and Difluorostatone-Containing Peptides

James, M.N.G., Sielecki, A.R., Moult, J.

(1992) Biochemistry 31: 3872

Biological Assembly 1  

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

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

Biological Assembly 2  

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 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.13 kDa 
• Atom Count: 2,726 
• Modeled Residue Count: 327 
• Deposited Residue Count: 327 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PENICILLOPEPSIN)	A [auth E]	323	Penicillium janthinellum	Mutation(s): 0  EC: 3.4.23.20
UniProt
Find proteins for P00798 (Penicillium janthinellum) Explore P00798  Go to UniProtKB:  P00798
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPSTATIN ANALOGUE ISOVALERYL-VAL-VAL-STA-O-ET	B [auth I]	4	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	C [auth I]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001238	B [auth I]	PEPSTATIN ANALOGUE ISOVALERYL-VAL-VAL-STA-O-ET	Oligopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.131 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.24	α = 90
b = 46.5	β = 115.34
c = 65.65	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Sielecki, A.R., James, M.N.G.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2014-06-04
  Changes: Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.5: 2024-10-16
  Changes: Data collection, Database references, Structure summary