1M43 | pdb_00001m43

Crystal structure of PMII in complex with pepstatin a to 2.4 A

PDB DOI: https://doi.org/10.2210/pdb1M43/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Plasmodium falciparum, Streptomyces argenteolus subsp. toyonakensis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2002-07-02 Released: 2002-07-24
Deposition Author(s): Asojo, O.A., Silva, A.M., Gulnik, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.245 (Depositor)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1M43

This is version 1.5 of the entry. See complete history.

Literature

Novel uncomplexed and complex structures of PM II, an aspartic protease from P. falciparum

Asojo, O.A., Silva, A.M., Gulnik, S.

To be published.

Macromolecule Content

Total Structure Weight: 75.53 kDa
Atom Count: 5,885
Modeled Residue Count: 674
Deposited Residue Count: 674
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
plasmepsin II	A, B	331	Plasmodium falciparum	Mutation(s): 1 EC: 3.4.23.39
UniProt
Find proteins for P46925 (Plasmodium falciparum (isolate HB3)) Explore P46925 Go to UniProtKB: P46925
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46925
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pepstatin	C, D	6	Streptomyces argenteolus subsp. toyonakensis	Mutation(s): 0

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000557 Query on PRD_000557	C, D	Pepstatin	Oligopeptide / Enzyme inhibitor		Interactions Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.245 (Depositor)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.197 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.235	α = 90
b = 142.235	β = 90
c = 97.892	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-07-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-07-24
Type: Initial release
Version 1.1: 2008-04-28
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: 2013-02-27
Changes: Other
Version 1.4: 2021-10-27
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary

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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.