5XM7 | pdb_00005xm7

Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-((2S,3R)-3-amino-2-hydroxy-4-phenylbutanamido)-N-hydroxy-4-methylpentanamide

PDB DOI: https://doi.org/10.2210/pdb5XM7/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Plasmodium falciparum FcB1/Columbia
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-05-12 Released: 2018-06-20
Deposition Author(s): Marapaka, A.K., Zhang, Y., Addlagatta, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.219 (Depositor), 0.226 (DCC)
R-Value Work:
0.168 (Depositor), 0.178 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Development of peptidomimetic hydroxamates as PfA-M1 and PfA-M17 dual inhibitors: Biological evaluation and structural characterization by cocrystallization

Marapaka, A.K., Sankoju, P., Zhang, G., Ding, Y., Ma, C., Pillalamarri, V., Sudhakar, P., Reddi, B., Sijwali, P.S., Zhang, Y., Addlagatta, A.

(2022) Chin Chem Lett 33: 2550-2554

DOI: https://doi.org/10.1016/j.cclet.2021.09.102

Macromolecule Content

Total Structure Weight: 107.86 kDa
Atom Count: 7,825
Modeled Residue Count: 890
Deposited Residue Count: 914
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M1 family aminopeptidase	A	914	Plasmodium falciparum FcB1/Columbia	Mutation(s): 0 EC: 3.4.11
UniProt
Find proteins for O96935 (Plasmodium falciparum (isolate 3D7)) Explore O96935 Go to UniProtKB: O96935
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O96935
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
89X Query on 89X Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	(2S)-4-methyl-N-[(1R)-2-(oxidanylamino)-2-oxidanylidene-1-phenyl-ethyl]-2-[(phenylmethyl)carbamoylamino]pentanamide C₂₂ H₂₈ N₄ O₄ HNVHIABPJCVMFJ-RBUKOAKNSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.219 (Depositor), 0.226 (DCC)
R-Value Work: 0.168 (Depositor), 0.178 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.462	α = 90
b = 109.103	β = 90
c = 112.372	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
MOLREP	model building
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-06-20

Deposition Author(s):

Marapaka, A.K.

Zhang, Y.

Addlagatta, A.

Revision History (Full details and data files)

Version 1.0: 2018-06-20
Type: Initial release
Version 1.1: 2022-07-27
Changes: Database references, Derived calculations, Refinement description
Version 1.2: 2023-11-22
Changes: Data collection, Refinement description