9UF9 | pdb_00009uf9

CRYSTAL STRUCTURE OF PEPSTATIN A BOUND TO RHODOTORULA MUCILAGINOSA ASPARTIC PROTEASE RmuAP1

PDB DOI: https://doi.org/10.2210/pdb9UF9/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Streptomyces argenteolus subsp. toyonakensis, Rhodotorula mucilaginosa
Expression System: Yarrowia lipolytica
Mutation(s): No

Deposited: 2025-04-10 Released: 2026-04-15
Deposition Author(s): Zhang, Y.-H., Lin, C.-L., Meng, M.H.
Funding Organization(s): National Science Council (NSC, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.205 (Depositor), 0.199 (DCC)
R-Value Work:
0.175 (Depositor), 0.173 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Molecular and crystal structure of RmuAP1-pepstatin A complex refined at 1.8 A resolution.

Zhang, Y.-H., Lin, C.-L., Meng, M.H.

To be published.

Macromolecule Content

Total Structure Weight: 35.3 kDa
Atom Count: 2,782
Modeled Residue Count: 338
Deposited Residue Count: 342
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pepstatin A	A [auth I]	6	Streptomyces argenteolus subsp. toyonakensis	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Type I transmembrane sorting receptor	B [auth A]	336	Rhodotorula mucilaginosa	Mutation(s): 0 Gene Names: PEP1_2, C6P46_002930
UniProt
Find proteins for A0A9P6W3R0 (Rhodotorula mucilaginosa) Explore A0A9P6W3R0 Go to UniProtKB: A0A9P6W3R0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9P6W3R0
Sequence Annotations Expand
Reference Sequence

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000557 Query on PRD_000557	A [auth I]	Pepstatin	Oligopeptide / Enzyme inhibitor		Interactions Focus chain A [auth I] Interactions & Density Focus chain A [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.205 (Depositor), 0.199 (DCC)
R-Value Work: 0.175 (Depositor), 0.173 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.519	α = 90
b = 52.833	β = 90
c = 157.808	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Council (NSC, Taiwan)	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2026-04-15
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.