6R61

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 (Czech Republic)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.202
R-Value Work: 0.185
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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: 38.83 kDa
Atom Count: 2,965
Modelled Residue Count: 350
Deposited Residue Count: 350
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endopeptidase	A	350	Cryptococcus neoformans	Mutation(s): 0 Gene Names: CNAG_05872
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J9VS02
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JT8 Query on JT8 Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	(3~{S},7~{S},8~{S})-7-oxidanyl-8-(phenylmethyl)-3-(pyridin-2-ylmethyl)-1,4,9-triazacyclotricosane-2,5,10-trione C₃₃ H₄₈ N₄ O₄ XVVTWLRLITWYAF-DTXPUJKBSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain C [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	C [auth A], I [auth A], J [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth A] Focus chain I [auth A] Focus chain J [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 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]	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]	L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]