1ME6 | pdb_00001me6

CRYSTAL STRUCTURE OF PLASMEPSIN II, AN ASPARTYL PROTEASE FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH A STATINE-BASED INHIBITOR

PDB DOI: https://doi.org/10.2210/pdb1ME6/pdb

Classification: HYDROLASE
Organism(s): Plasmodium falciparum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2002-08-08 Released: 2004-01-20
Deposition Author(s): Freire, E., Nezami, A.G., Amzel, L.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.271 (Depositor)
R-Value Work:
0.214 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF PLASMEPSIN II, AN ASPARTYL PROTEASE FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH A STATINE-BASED INHIBITOR

Freire, E., Nezami, A.G., Amzel, L.M.

To be published.

Macromolecule Content

Total Structure Weight: 74.88 kDa
Atom Count: 5,402
Modeled Residue Count: 658
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin II	A, B	329	Plasmodium falciparum	Mutation(s): 0 Gene Names: PF00026 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IVS Query on IVS Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	3-HYDROXY-6-METHYL-4-(3-METHYL-2-(3-METHYL-2-(3-METHYL-BUTYRYLAMINO)-BUTYRYLAMINO)-BUTYRYLAMINO)-HEPTANOIC ACID ETHYL ESTER C₂₅ H₄₇ N₃ O₆ SMVMSLPPAGGLDL-ZZTDLJEGSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.271 (Depositor)
R-Value Work: 0.214 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.93	α = 90
b = 141.93	β = 90
c = 97.82	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-01-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-01-20
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, 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.