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)

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
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

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

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

To be published.

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

Find similar proteins by:

| 3D Structure

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 (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VS02 Go to UniProtKB: J9VS02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J9VS02
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IY5 (Subject of Investigation/LOI) Query on A1IY5 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	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		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-07

Deposition Author(s):

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

Revision History (Full details and data files)

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