1FQ4

CRYSTAL STRUCTURE OF A COMPLEX BETWEEN HYDROXYETHYLENE INHIBITOR CP-108,420 AND YEAST ASPARTIC PROTEINASE A

• PDB DOI: https://doi.org/10.2210/pdb1FQ4/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2000-09-03 Released: 2000-09-20 
• Deposition Author(s): Cronin, N.B., Badasso, M.O., Tickle, I.J., Dreyer, T., Hoover, D.J., Rosati, R.L., Humblet, C.C., Lunney, E.A., Cooper, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Observed: 0.170 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.55 kDa 
• Atom Count: 2,749 
• Modelled Residue Count: 329 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SACCHAROPEPSIN	A	329	Saccharomyces cerevisiae	Mutation(s): 0  EC: 3.4.23.25
UniProt
Find proteins for P07267 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07267  Go to UniProtKB:  P07267

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G57658LA GlyCosmos:  G57658LA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2Y2	C [auth A]	N-[(2R)-1-{[(2S,3R,5R)-1-cyclohexyl-3-hydroxy-5-{[2-(morpholin-4-yl)ethyl]carbamoyl}oct-7-yn-2-yl]amino}-3-(methylsulfa nyl)-1-oxopropan-2-yl]-1H-benzimidazole-2-carboxamide C33 H48 N6 O5 S MDCNERSXJOKFTF-ZLPBPMGLSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000563 (2Y2)	C [auth A]	CP-108,420	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Observed: 0.170 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.91	α = 90
b = 86.91	β = 90
c = 110.22	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
ROTAVATA	data reduction
AMoRE	phasing
RESTRAIN	refinement
CCP4	data scaling
ROTAVATA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-09-20 
Deposition Author(s): Cronin, N.B., Badasso, M.O., Tickle, I.J., Dreyer, T., Hoover, D.J., Rosati, R.L., Humblet, C.C., Lunney, E.A., Cooper, J.B.

Revision History  

• Version 1.0: 2000-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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: 2012-12-12
  Changes: Other
• Version 1.4: 2017-10-04
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary