6R61 | pdb_00006r61

Major aspartyl peptidase 1 from C. neoformans in complex with Inhibitor LP258

• PDB DOI: https://doi.org/10.2210/pdb6R61/pdb

• Classification: HYDROLASE
• Organism(s): Cryptococcus neoformans
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2019-03-26 Released: 2021-04-07 
• Deposition Author(s): Krystufek, R., Sacha, P., Brynda, J., Konvalinka, J.
• Funding Organization(s): Ministry of Education (MoE, Czech Republic)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.204 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Major aspartyl peptidase 1 from C. neoformans in complex with Inhibitor LP258

Krystufek, R., Sacha, P., Brynda, J., Konvalinka, J.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 48.96 kDa 
• Atom Count: 2,964 
• Modeled Residue Count: 350 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major aspartyl peptidase 1	A	436	Cryptococcus neoformans	Mutation(s): 0  Gene Names: cnap1, MAY1, CNAG_05872 EC: 3.4.23
UniProt
Find proteins for J9VS02 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VS02  Go to UniProtKB:  J9VS02
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IY5 (Subject of Investigation/LOI)	M [auth A]	(3~{S},7~{S},8~{S})-7-oxidanyl-8-(phenylmethyl)-3-(pyridin-3-ylmethyl)-1,4,9-triazacyclotricosane-2,5,10-trione C33 H48 N4 O4 RYGGELGJKGMCRW-DTXPUJKBSA-N
1PE	I [auth A], J [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	C [auth A], D [auth A], E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.204 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.17	α = 90
b = 113.39	β = 90
c = 91.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Krystufek, R., Sacha, P., Brynda, J., Konvalinka, J.

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Funding Organization	Location	Grant Number
Ministry of Education (MoE, Czech Republic)	Czech Republic	InterBioMed LO1302

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary
• Version 2.0: 2025-03-26
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary